tophat - amd64
Documentation
./doc/changelog.Debian.gz
./doc/copyright
./doc/README
Binaries
fix_map_ordering
compile units
fix_map_ordering.cpp
Gimple
./fix_map_ordering.cpp.004t.gimple
GKD
./fix_map_ordering.o.gkd
OBJ
obj: ./fix_map_ordering.o
unassigned
common.cpp
Gimple
./common.cpp.004t.gimple
GKD
./common.o.gkd
OBJ
obj: ./common.o
unassigned
tokenize.cpp
Gimple
./tokenize.cpp.004t.gimple
GKD
./tokenize.o.gkd
OBJ
obj: ./tokenize.o
bam_aux.c
Gimple
./bam_aux.c.004t.gimple
GKD
./bam_aux.o.gkd
OBJ
obj: ./bam_aux.o
unassigned
bam.c
Gimple
./bam.c.004t.gimple
GKD
./bam.o.gkd
OBJ
obj: ./bam.o
bam_import.c
Gimple
./bam_import.c.004t.gimple
GKD
./bam_import.o.gkd
OBJ
obj: ./bam_import.o
sam.c
Gimple
./sam.c.004t.gimple
GKD
./sam.o.gkd
OBJ
obj: ./sam.o
bam_pileup.c
Gimple
./bam_pileup.c.004t.gimple
GKD
./bam_pileup.o.gkd
OBJ
obj: ./bam_pileup.o
faidx.c
Gimple
./faidx.c.004t.gimple
GKD
./faidx.o.gkd
OBJ
obj: ./faidx.o
knetfile.c
Gimple
./knetfile.c.004t.gimple
GKD
./knetfile.o.gkd
OBJ
obj: ./knetfile.o
sam_header.c
Gimple
./sam_header.c.004t.gimple
GKD
./sam_header.o.gkd
OBJ
obj: ./sam_header.o
bgzf.c
Gimple
./bgzf.c.004t.gimple
GKD
./bgzf.o.gkd
OBJ
obj: ./bgzf.o
kstring.c
Gimple
./kstring.c.004t.gimple
GKD
./kstring.o.gkd
OBJ
obj: ./kstring.o
razf.c
Gimple
./razf.c.004t.gimple
GKD
./razf.o.gkd
OBJ
obj: ./razf.o
includes
fix_map_ordering.cpp
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/bits/stl_heap.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
./common.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.h
../headers//usr/include/stdlib.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/samtools/bam.h
../headers//usr/include/string.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/limits
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/stl_list.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/stl_pair.h
../headers//usr/include/c++/4.9/bits/stl_queue.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/new
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/stdint.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/wchar.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/seqan/basic/debug_test_system.h
../headers//usr/include/seqan/basic/profiling.h
../headers//usr/include/seqan/basic/alphabet_residue_tabs.h
../headers//usr/include/seqan/modifier/modifier_functors.h
../headers//usr/include/seqan/basic/alphabet_math.h
../headers//usr/include/seqan/basic/metaprogramming_control.h
../headers//usr/include/seqan/basic/alphabet_residue.h
../headers//usr/include/samtools/bgzf.h
../headers//usr/include/samtools/sam.h
./reads.h
./bwt_map.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/getopt.h
../headers//usr/include/c++/4.9/cxxabi.h
unassigned
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
common.cpp
../headers//usr/include/c++/4.9/ostream
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
./common.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.h
../headers//usr/include/samtools/bam.h
../headers//usr/include/stdlib.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/libio.h
../headers//usr/include/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/locale_facets.h
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/getopt.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/samtools/bgzf.h
../headers//usr/include/samtools/sam.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/new
./tokenize.h
../headers//usr/include/ctype.h
unassigned
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
tokenize.cpp
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/new
bam_aux.c
./khash.h
./bam.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdint.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/string.h
../headers//usr/include/ctype.h
unassigned
./kstring.h
bam.c
./bam_endian.h
./bam.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./knetfile.h
./bgzf.h
../headers//usr/include/stdlib.h
./sam_header.h
../headers//usr/include/ctype.h
../headers//usr/include/x86_64-linux-gnu/bits/errno.h
../headers//usr/include/string.h
bam_import.c
../headers//usr/include/stdlib.h
./khash.h
./bam.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/zlib.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./kstring.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
./sam_header.h
../headers//usr/include/ctype.h
sam.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdint.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
./knetfile.h
./bgzf.h
./bam.h
./sam.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/string.h
../headers//usr/include/unistd.h
./faidx.h
bam_pileup.c
./bam.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
./knetfile.h
./bgzf.h
../headers//usr/include/stdlib.h
../headers//usr/include/assert.h
faidx.c
./khash.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./faidx.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./razf.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/ctype.h
knetfile.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/x86_64-linux-gnu/bits/time.h
../headers//usr/include/x86_64-linux-gnu/sys/select.h
../headers//usr/include/unistd.h
../headers//usr/include/x86_64-linux-gnu/bits/sockaddr.h
../headers//usr/include/x86_64-linux-gnu/bits/socket.h
../headers//usr/include/netdb.h
./knetfile.h
../headers//usr/include/x86_64-linux-gnu/sys/socket.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/ctype.h
../headers//usr/include/x86_64-linux-gnu/bits/errno.h
../headers//usr/include/fcntl.h
../headers//usr/include/x86_64-linux-gnu/bits/socket_type.h
sam_header.c
./khash.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/string.h
bgzf.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./bgzf.h
./khash.h
../headers//usr/include/stdlib.h
../headers//usr/include/fcntl.h
../headers//usr/include/string.h
kstring.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./kstring.h
../headers//usr/include/stdio.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/ctype.h
razf.c
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/fcntl.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./razf.h
../headers//usr/include/unistd.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
libraries
../libs/lib/x86_64-linux-gnu/libz.so.1
../libs/usr/lib/x86_64-linux-gnu/libstdc++.so.6
../libs/lib/x86_64-linux-gnu/libm.so.6
../libs/lib/x86_64-linux-gnu/libgcc_s.so.1
../libs/lib/x86_64-linux-gnu/libpthread.so.0
../libs/lib/x86_64-linux-gnu/libc.so.6
manual
bam_merge
compile units
bam_merge.cpp
Gimple
./bam_merge.cpp.004t.gimple
GKD
./bam_merge.o.gkd
OBJ
obj: ./bam_merge.o
unassigned
common.cpp
Gimple
./common.cpp.004t.gimple
GKD
./common.o.gkd
OBJ
obj: ./common.o
unassigned
tokenize.cpp
Gimple
./tokenize.cpp.004t.gimple
GKD
./tokenize.o.gkd
OBJ
obj: ./tokenize.o
bam_merge_impl.cpp
Gimple
./bam_merge_impl.cpp.004t.gimple
GKD
./bam_merge_impl.o.gkd
OBJ
obj: ./bam_merge_impl.o
bgzf.c
Gimple
./bgzf.c.004t.gimple
GKD
./bgzf.o.gkd
OBJ
obj: ./bgzf.o
bam_aux.c
Gimple
./bam_aux.c.004t.gimple
GKD
./bam_aux.o.gkd
OBJ
obj: ./bam_aux.o
unassigned
bam.c
Gimple
./bam.c.004t.gimple
GKD
./bam.o.gkd
OBJ
obj: ./bam.o
bam_import.c
Gimple
./bam_import.c.004t.gimple
GKD
./bam_import.o.gkd
OBJ
obj: ./bam_import.o
sam.c
Gimple
./sam.c.004t.gimple
GKD
./sam.o.gkd
OBJ
obj: ./sam.o
bam_pileup.c
Gimple
./bam_pileup.c.004t.gimple
GKD
./bam_pileup.o.gkd
OBJ
obj: ./bam_pileup.o
faidx.c
Gimple
./faidx.c.004t.gimple
GKD
./faidx.o.gkd
OBJ
obj: ./faidx.o
knetfile.c
Gimple
./knetfile.c.004t.gimple
GKD
./knetfile.o.gkd
OBJ
obj: ./knetfile.o
sam_header.c
Gimple
./sam_header.c.004t.gimple
GKD
./sam_header.o.gkd
OBJ
obj: ./sam_header.o
kstring.c
Gimple
./kstring.c.004t.gimple
GKD
./kstring.o.gkd
OBJ
obj: ./kstring.o
razf.c
Gimple
./razf.c.004t.gimple
GKD
./razf.o.gkd
OBJ
obj: ./razf.o
includes
bam_merge.cpp
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
./common.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
./bam_merge.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/stl_queue.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/wchar.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/string.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/samtools/bgzf.h
../headers//usr/include/samtools/bam.h
../headers//usr/include/samtools/sam.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/new
../headers//usr/include/getopt.h
unassigned
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
common.cpp
../headers//usr/include/c++/4.9/ostream
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
./common.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.h
../headers//usr/include/samtools/bam.h
../headers//usr/include/stdlib.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/libio.h
../headers//usr/include/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/locale_facets.h
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/getopt.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/samtools/bgzf.h
../headers//usr/include/samtools/sam.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/new
./tokenize.h
../headers//usr/include/ctype.h
unassigned
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
tokenize.cpp
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/new
bam_merge_impl.cpp
../headers//usr/include/stdlib.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers//usr/include/c++/4.9/bits/stl_heap.h
./bam_merge.h
../headers//usr/include/c++/4.9/bits/stl_queue.h
../headers//usr/include/c++/4.9/bits/stl_algo.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/bits/stl_bvector.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/new
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/wchar.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/string.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/x86_64-linux-gnu/bits/confname.h
../headers//usr/include/samtools/bgzf.h
../headers//usr/include/samtools/bam.h
../headers//usr/include/samtools/sam.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
./common.h
bgzf.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./bgzf.h
./khash.h
../headers//usr/include/stdlib.h
../headers//usr/include/fcntl.h
../headers//usr/include/string.h
bam_aux.c
./khash.h
./bam.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdint.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/string.h
../headers//usr/include/ctype.h
unassigned
./kstring.h
bam.c
./bam_endian.h
./bam.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./knetfile.h
./bgzf.h
../headers//usr/include/stdlib.h
./sam_header.h
../headers//usr/include/ctype.h
../headers//usr/include/x86_64-linux-gnu/bits/errno.h
../headers//usr/include/string.h
bam_import.c
../headers//usr/include/stdlib.h
./khash.h
./bam.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/zlib.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./kstring.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
./sam_header.h
../headers//usr/include/ctype.h
sam.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdint.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
./knetfile.h
./bgzf.h
./bam.h
./sam.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/string.h
../headers//usr/include/unistd.h
./faidx.h
bam_pileup.c
./bam.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
./knetfile.h
./bgzf.h
../headers//usr/include/stdlib.h
../headers//usr/include/assert.h
faidx.c
./khash.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./faidx.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./razf.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/ctype.h
knetfile.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/x86_64-linux-gnu/bits/time.h
../headers//usr/include/x86_64-linux-gnu/sys/select.h
../headers//usr/include/unistd.h
../headers//usr/include/x86_64-linux-gnu/bits/sockaddr.h
../headers//usr/include/x86_64-linux-gnu/bits/socket.h
../headers//usr/include/netdb.h
./knetfile.h
../headers//usr/include/x86_64-linux-gnu/sys/socket.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/ctype.h
../headers//usr/include/x86_64-linux-gnu/bits/errno.h
../headers//usr/include/fcntl.h
../headers//usr/include/x86_64-linux-gnu/bits/socket_type.h
sam_header.c
./khash.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/string.h
kstring.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./kstring.h
../headers//usr/include/stdio.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/ctype.h
razf.c
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/fcntl.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./razf.h
../headers//usr/include/unistd.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
libraries
../libs/lib/x86_64-linux-gnu/libz.so.1
../libs/usr/lib/x86_64-linux-gnu/libstdc++.so.6
../libs/lib/x86_64-linux-gnu/libm.so.6
../libs/lib/x86_64-linux-gnu/libgcc_s.so.1
../libs/lib/x86_64-linux-gnu/libpthread.so.0
../libs/lib/x86_64-linux-gnu/libc.so.6
manual
gtf_to_fasta
compile units
unassigned
GTFToFasta.cpp
Gimple
./GTFToFasta.cpp.004t.gimple
GKD
./GTFToFasta.o.gkd
OBJ
obj: ./GTFToFasta.o
unassigned
FastaTools.cpp
Gimple
./FastaTools.cpp.004t.gimple
GKD
./FastaTools.o.gkd
OBJ
obj: ./FastaTools.o
unassigned
common.cpp
Gimple
./common.cpp.004t.gimple
GKD
./common.o.gkd
OBJ
obj: ./common.o
unassigned
tokenize.cpp
Gimple
./tokenize.cpp.004t.gimple
GKD
./tokenize.o.gkd
OBJ
obj: ./tokenize.o
GBase.cpp
Gimple
./GBase.cpp.004t.gimple
GKD
./GBase.o.gkd
OBJ
obj: ./GBase.o
GFaSeqGet.cpp
Gimple
./GFaSeqGet.cpp.004t.gimple
GKD
./GFaSeqGet.o.gkd
OBJ
obj: ./GFaSeqGet.o
unassigned
gff.cpp
Gimple
./gff.cpp.004t.gimple
GKD
./gff.o.gkd
OBJ
obj: ./gff.o
codons.cpp
Gimple
./codons.cpp.004t.gimple
GKD
./codons.o.gkd
OBJ
obj: ./codons.o
gdna.cpp
Gimple
./gdna.cpp.004t.gimple
GKD
./gdna.o.gkd
OBJ
obj: ./gdna.o
bam_aux.c
Gimple
./bam_aux.c.004t.gimple
GKD
./bam_aux.o.gkd
OBJ
obj: ./bam_aux.o
unassigned
bam.c
Gimple
./bam.c.004t.gimple
GKD
./bam.o.gkd
OBJ
obj: ./bam.o
bam_import.c
Gimple
./bam_import.c.004t.gimple
GKD
./bam_import.o.gkd
OBJ
obj: ./bam_import.o
sam.c
Gimple
./sam.c.004t.gimple
GKD
./sam.o.gkd
OBJ
obj: ./sam.o
bam_pileup.c
Gimple
./bam_pileup.c.004t.gimple
GKD
./bam_pileup.o.gkd
OBJ
obj: ./bam_pileup.o
faidx.c
Gimple
./faidx.c.004t.gimple
GKD
./faidx.o.gkd
OBJ
obj: ./faidx.o
knetfile.c
Gimple
./knetfile.c.004t.gimple
GKD
./knetfile.o.gkd
OBJ
obj: ./knetfile.o
sam_header.c
Gimple
./sam_header.c.004t.gimple
GKD
./sam_header.o.gkd
OBJ
obj: ./sam_header.o
bgzf.c
Gimple
./bgzf.c.004t.gimple
GKD
./bgzf.o.gkd
OBJ
obj: ./bgzf.o
kstring.c
Gimple
./kstring.c.004t.gimple
GKD
./kstring.o.gkd
OBJ
obj: ./kstring.o
razf.c
Gimple
./razf.c.004t.gimple
GKD
./razf.o.gkd
OBJ
obj: ./razf.o
includes
unassigned
../headers//usr/include/c++/4.9/bits/locale_facets.h
./GHash.hh
./GList.hh
./GVec.hh
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
GTFToFasta.cpp
../headers//usr/include/c++/4.9/ostream
../headers//usr/include/c++/4.9/bits/basic_ios.h
./gff.h
./FastaTools.h
../headers//usr/include/c++/4.9/fstream
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/streambuf
../headers//usr/include/c++/4.9/sstream
../headers//usr/include/c++/4.9/bits/stl_tree.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_map.h
./GFaSeqGet.h
../headers//usr/include/c++/4.9/bits/stl_pair.h
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stl_iterator_base_funcs.h
../headers//usr/include/c++/4.9/istream
../headers//usr/include/c++/4.9/iostream
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/ostream.tcc
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/stl_function.h
../headers//usr/include/c++/4.9/bits/basic_ios.tcc
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/bits/fstream.tcc
../headers//usr/include/c++/4.9/bits/ostream_insert.h
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/c++/4.9/ext/type_traits.h
../headers//usr/include/string.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/wchar.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/stdint.h
./GBase.h
./GTFToFasta.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/new
../headers//usr/include/getopt.h
./common.h
unassigned
../headers//usr/include/c++/4.9/bits/locale_facets.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
FastaTools.cpp
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/c++/4.9/istream
../headers//usr/include/c++/4.9/fstream
../headers//usr/include/c++/4.9/streambuf
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/ostream
./FastaTools.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdlib.h
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/ostream.tcc
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/basic_ios.tcc
../headers//usr/include/c++/4.9/bits/fstream.tcc
../headers//usr/include/c++/4.9/bits/ostream_insert.h
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/string.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/wchar.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
unassigned
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
common.cpp
../headers//usr/include/c++/4.9/ostream
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
./common.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.h
../headers//usr/include/samtools/bam.h
../headers//usr/include/stdlib.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/libio.h
../headers//usr/include/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/locale_facets.h
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/getopt.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/samtools/bgzf.h
../headers//usr/include/samtools/sam.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/new
./tokenize.h
../headers//usr/include/ctype.h
unassigned
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
tokenize.cpp
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/new
GBase.cpp
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.h
../headers//usr/include/ctype.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/sys/stat.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/time.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/x86_64-linux-gnu/bits/stat.h
../headers//usr/include/stdint.h
./GBase.h
../headers//usr/include/stdlib.h
GFaSeqGet.cpp
../headers//usr/include/x86_64-linux-gnu/bits/string3.h
./GFaSeqGet.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/ctype.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./GBase.h
./gdna.h
unassigned
./GList.hh
./GBase.h
./GVec.hh
./gff.h
./GHash.hh
gff.cpp
../headers//usr/include/x86_64-linux-gnu/bits/string3.h
./codons.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/ctype.h
../headers//usr/include/string.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/bits/confname.h
./GFaSeqGet.h
./gdna.h
../headers//usr/include/stdlib.h
codons.cpp
../headers//usr/include/x86_64-linux-gnu/bits/string3.h
../headers//usr/include/ctype.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/libio.h
./GBase.h
./codons.h
../headers//usr/include/stdio.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/confname.h
gdna.cpp
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/libio.h
./GBase.h
../headers//usr/include/stdio.h
../headers//usr/include/x86_64-linux-gnu/bits/confname.h
../headers//usr/include/string.h
bam_aux.c
./khash.h
./bam.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdint.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/string.h
../headers//usr/include/ctype.h
unassigned
./kstring.h
bam.c
./bam_endian.h
./bam.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./knetfile.h
./bgzf.h
../headers//usr/include/stdlib.h
./sam_header.h
../headers//usr/include/ctype.h
../headers//usr/include/x86_64-linux-gnu/bits/errno.h
../headers//usr/include/string.h
bam_import.c
../headers//usr/include/stdlib.h
./khash.h
./bam.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/zlib.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./kstring.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
./sam_header.h
../headers//usr/include/ctype.h
sam.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdint.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
./knetfile.h
./bgzf.h
./bam.h
./sam.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/string.h
../headers//usr/include/unistd.h
./faidx.h
bam_pileup.c
./bam.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
./knetfile.h
./bgzf.h
../headers//usr/include/stdlib.h
../headers//usr/include/assert.h
faidx.c
./khash.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./faidx.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./razf.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/ctype.h
knetfile.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/x86_64-linux-gnu/bits/time.h
../headers//usr/include/x86_64-linux-gnu/sys/select.h
../headers//usr/include/unistd.h
../headers//usr/include/x86_64-linux-gnu/bits/sockaddr.h
../headers//usr/include/x86_64-linux-gnu/bits/socket.h
../headers//usr/include/netdb.h
./knetfile.h
../headers//usr/include/x86_64-linux-gnu/sys/socket.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/ctype.h
../headers//usr/include/x86_64-linux-gnu/bits/errno.h
../headers//usr/include/fcntl.h
../headers//usr/include/x86_64-linux-gnu/bits/socket_type.h
sam_header.c
./khash.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/string.h
bgzf.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./bgzf.h
./khash.h
../headers//usr/include/stdlib.h
../headers//usr/include/fcntl.h
../headers//usr/include/string.h
kstring.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./kstring.h
../headers//usr/include/stdio.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/ctype.h
razf.c
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/fcntl.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./razf.h
../headers//usr/include/unistd.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
libraries
../libs/lib/x86_64-linux-gnu/libz.so.1
../libs/usr/lib/x86_64-linux-gnu/libstdc++.so.6
../libs/lib/x86_64-linux-gnu/libm.so.6
../libs/lib/x86_64-linux-gnu/libgcc_s.so.1
../libs/lib/x86_64-linux-gnu/libpthread.so.0
../libs/lib/x86_64-linux-gnu/libc.so.6
manual
samtools_0.1.18
compile units
bam_tview.c
Gimple
./bam_tview.c.004t.gimple
GKD
./bam_tview.o.gkd
OBJ
obj: ./bam_tview.o
bam_plcmd.c
Gimple
./bam_plcmd.c.004t.gimple
GKD
./bam_plcmd.o.gkd
OBJ
obj: ./bam_plcmd.o
sam_view.c
Gimple
./sam_view.c.004t.gimple
GKD
./sam_view.o.gkd
OBJ
obj: ./sam_view.o
bam_rmdup.c
Gimple
./bam_rmdup.c.004t.gimple
GKD
./bam_rmdup.o.gkd
OBJ
obj: ./bam_rmdup.o
bam_rmdupse.c
Gimple
./bam_rmdupse.c.004t.gimple
GKD
./bam_rmdupse.o.gkd
OBJ
obj: ./bam_rmdupse.o
bam_mate.c
Gimple
./bam_mate.c.004t.gimple
GKD
./bam_mate.o.gkd
OBJ
obj: ./bam_mate.o
bam_stat.c
Gimple
./bam_stat.c.004t.gimple
GKD
./bam_stat.o.gkd
OBJ
obj: ./bam_stat.o
bam_color.c
Gimple
./bam_color.c.004t.gimple
GKD
./bam_color.o.gkd
OBJ
obj: ./bam_color.o
bamtk.c
Gimple
./bamtk.c.004t.gimple
GKD
./bamtk.o.gkd
OBJ
obj: ./bamtk.o
kaln.c
Gimple
./kaln.c.004t.gimple
GKD
./kaln.o.gkd
OBJ
obj: ./kaln.o
bam2bcf.c
Gimple
./bam2bcf.c.004t.gimple
GKD
./bam2bcf.o.gkd
OBJ
obj: ./bam2bcf.o
bam2bcf_indel.c
Gimple
./bam2bcf_indel.c.004t.gimple
GKD
./bam2bcf_indel.o.gkd
OBJ
obj: ./bam2bcf_indel.o
errmod.c
Gimple
./errmod.c.004t.gimple
GKD
./errmod.o.gkd
OBJ
obj: ./errmod.o
sample.c
Gimple
./sample.c.004t.gimple
GKD
./sample.o.gkd
OBJ
obj: ./sample.o
cut_target.c
Gimple
./cut_target.c.004t.gimple
GKD
./cut_target.o.gkd
OBJ
obj: ./cut_target.o
phase.c
Gimple
./phase.c.004t.gimple
GKD
./phase.o.gkd
OBJ
obj: ./phase.o
bam2depth.c
Gimple
./bam2depth.c.004t.gimple
GKD
./bam2depth.o.gkd
OBJ
obj: ./bam2depth.o
bgzf.c
Gimple
./bgzf.c.004t.gimple
GKD
./bgzf.o.gkd
OBJ
obj: ./bgzf.o
kstring.c
Gimple
./kstring.c.004t.gimple
GKD
./kstring.o.gkd
OBJ
obj: ./kstring.o
bam_aux.c
Gimple
./bam_aux.c.004t.gimple
GKD
./bam_aux.o.gkd
OBJ
obj: ./bam_aux.o
unassigned
bam.c
Gimple
./bam.c.004t.gimple
GKD
./bam.o.gkd
OBJ
obj: ./bam.o
bam_import.c
Gimple
./bam_import.c.004t.gimple
GKD
./bam_import.o.gkd
OBJ
obj: ./bam_import.o
sam.c
Gimple
./sam.c.004t.gimple
GKD
./sam.o.gkd
OBJ
obj: ./sam.o
bam_index.c
Gimple
./bam_index.c.004t.gimple
GKD
./bam_index.o.gkd
OBJ
obj: ./bam_index.o
bam_pileup.c
Gimple
./bam_pileup.c.004t.gimple
GKD
./bam_pileup.o.gkd
OBJ
obj: ./bam_pileup.o
bam_md.c
Gimple
./bam_md.c.004t.gimple
GKD
./bam_md.o.gkd
OBJ
obj: ./bam_md.o
faidx.c
Gimple
./faidx.c.004t.gimple
GKD
./faidx.o.gkd
OBJ
obj: ./faidx.o
bedidx.c
Gimple
./bedidx.c.004t.gimple
GKD
./bedidx.o.gkd
OBJ
obj: ./bedidx.o
knetfile.c
Gimple
./knetfile.c.004t.gimple
GKD
./knetfile.o.gkd
OBJ
obj: ./knetfile.o
bam_sort.c
Gimple
./bam_sort.c.004t.gimple
GKD
./bam_sort.o.gkd
OBJ
obj: ./bam_sort.o
sam_header.c
Gimple
./sam_header.c.004t.gimple
GKD
./sam_header.o.gkd
OBJ
obj: ./sam_header.o
bam_reheader.c
Gimple
./bam_reheader.c.004t.gimple
GKD
./bam_reheader.o.gkd
OBJ
obj: ./bam_reheader.o
kprobaln.c
Gimple
./kprobaln.c.004t.gimple
GKD
./kprobaln.o.gkd
OBJ
obj: ./kprobaln.o
bam_cat.c
Gimple
./bam_cat.c.004t.gimple
GKD
./bam_cat.o.gkd
OBJ
obj: ./bam_cat.o
razf.c
Gimple
./razf.c.004t.gimple
GKD
./razf.o.gkd
OBJ
obj: ./razf.o
bcf.c
Gimple
./bcf.c.004t.gimple
GKD
./bcf.o.gkd
OBJ
obj: ./bcf.o
bcfutils.c
Gimple
./bcfutils.c.004t.gimple
GKD
./bcfutils.o.gkd
OBJ
obj: ./bcfutils.o
fet.c
Gimple
./fet.c.004t.gimple
GKD
./fet.o.gkd
OBJ
obj: ./fet.o
includes
bam_tview.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/libio.h
../headers//usr/include/stdio.h
bam_plcmd.c
../headers//usr/include/ctype.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
./kstring.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./knetfile.h
./bgzf.h
./bam.h
./faidx.h
./errmod.h
../headers/bcftools/bcf.h
./bam2bcf.h
./sample.h
../headers//usr/include/getopt.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/errno.h
sam_view.c
./khash.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/stdlib.h
./kstring.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./knetfile.h
./bgzf.h
./bam.h
./sam.h
../headers//usr/include/getopt.h
bam_rmdup.c
./khash.h
./bam.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./knetfile.h
./bgzf.h
./sam.h
../headers//usr/include/getopt.h
../headers//usr/include/string.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
bam_rmdupse.c
./khash.h
./bam.h
../headers//usr/include/stdint.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
./knetfile.h
./bgzf.h
./sam.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
bam_mate.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
./knetfile.h
./bgzf.h
./bam.h
../headers//usr/include/stdlib.h
bam_stat.c
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/stdint.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
./knetfile.h
./bgzf.h
./bam.h
../headers//usr/include/getopt.h
../headers//usr/include/stdlib.h
../headers//usr/include/assert.h
bam_color.c
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdint.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/libio.h
./bam.h
../headers//usr/include/stdio.h
../headers//usr/include/string.h
../headers//usr/include/ctype.h
bamtk.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
kaln.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./kaln.h
../headers//usr/include/stdio.h
../headers//usr/include/stdlib.h
bam2bcf.c
./kstring.h
../headers//usr/include/stdint.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/libio.h
./bam.h
./errmod.h
../headers/bcftools/bcf.h
./bam2bcf.h
../headers//usr/include/stdio.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h
bam2bcf_indel.c
./khash.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/stdint.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
./bam.h
./errmod.h
./bam2bcf.h
./kprobaln.h
./ksort.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/ctype.h
errmod.c
../headers//usr/include/stdint.h
./errmod.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
./ksort.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h
sample.c
./khash.h
./kstring.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
./sample.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
cut_target.c
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
./knetfile.h
./bgzf.h
./bam.h
./errmod.h
./faidx.h
../headers//usr/include/getopt.h
phase.c
./bam.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/stdlib.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./bgzf.h
./errmod.h
./kseq.h
./khash.h
./ksort.h
../headers//usr/include/getopt.h
../headers//usr/include/string.h
../headers//usr/include/ctype.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
bam2depth.c
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./knetfile.h
./bgzf.h
./bam.h
../headers//usr/include/getopt.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
bgzf.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./bgzf.h
./khash.h
../headers//usr/include/stdlib.h
../headers//usr/include/fcntl.h
../headers//usr/include/string.h
kstring.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./kstring.h
../headers//usr/include/stdio.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/ctype.h
bam_aux.c
./khash.h
./bam.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdint.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/string.h
../headers//usr/include/ctype.h
unassigned
./kstring.h
bam.c
./bam_endian.h
./bam.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./knetfile.h
./bgzf.h
../headers//usr/include/stdlib.h
./sam_header.h
../headers//usr/include/ctype.h
../headers//usr/include/x86_64-linux-gnu/bits/errno.h
../headers//usr/include/string.h
bam_import.c
../headers//usr/include/stdlib.h
./khash.h
./bam.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/zlib.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./kstring.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
./sam_header.h
../headers//usr/include/ctype.h
sam.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdint.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
./knetfile.h
./bgzf.h
./bam.h
./sam.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/string.h
../headers//usr/include/unistd.h
./faidx.h
bam_index.c
./bam_endian.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdint.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
./knetfile.h
./bgzf.h
./bam.h
./khash.h
./ksort.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/assert.h
bam_pileup.c
./bam.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
./knetfile.h
./bgzf.h
../headers//usr/include/stdlib.h
../headers//usr/include/assert.h
bam_md.c
./kstring.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
./faidx.h
../headers//usr/include/stdint.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
./knetfile.h
./bgzf.h
./bam.h
./sam.h
./kprobaln.h
../headers//usr/include/getopt.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h
../headers//usr/include/ctype.h
faidx.c
./khash.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./faidx.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./razf.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/ctype.h
bedidx.c
./khash.h
../headers//usr/include/stdlib.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./ksort.h
./kseq.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/ctype.h
knetfile.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/x86_64-linux-gnu/bits/time.h
../headers//usr/include/x86_64-linux-gnu/sys/select.h
../headers//usr/include/unistd.h
../headers//usr/include/x86_64-linux-gnu/bits/sockaddr.h
../headers//usr/include/x86_64-linux-gnu/bits/socket.h
../headers//usr/include/netdb.h
./knetfile.h
../headers//usr/include/x86_64-linux-gnu/sys/socket.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/ctype.h
../headers//usr/include/x86_64-linux-gnu/bits/errno.h
../headers//usr/include/fcntl.h
../headers//usr/include/x86_64-linux-gnu/bits/socket_type.h
bam_sort.c
../headers//usr/include/stdlib.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./knetfile.h
./bgzf.h
./bam.h
./ksort.h
../headers//usr/include/getopt.h
../headers//usr/include/ctype.h
../headers//usr/include/x86_64-linux-gnu/bits/errno.h
../headers//usr/include/string.h
sam_header.c
./khash.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/string.h
bam_reheader.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
./knetfile.h
./bgzf.h
./bam.h
kprobaln.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./kprobaln.h
../headers//usr/include/stdio.h
../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h
../headers//usr/include/stdlib.h
bam_cat.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
./knetfile.h
./bgzf.h
./bam.h
../headers//usr/include/getopt.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
razf.c
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/fcntl.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./razf.h
../headers//usr/include/unistd.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
bcf.c
./bcf.h
../headers/../kstring.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
../headers/../knetfile.h
../headers/../bgzf.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
bcfutils.c
./bcf.h
../headers/../khash.h
../headers/../kstring.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdint.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h
fet.c
../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h
libraries
../libs/lib/x86_64-linux-gnu/libm.so.6
../libs/lib/x86_64-linux-gnu/libz.so.1
../libs/lib/x86_64-linux-gnu/libc.so.6
manual
segment_juncs
compile units
unassigned
segment_juncs.cpp
Gimple
./segment_juncs.cpp.004t.gimple
GKD
./segment_juncs.o.gkd
OBJ
obj: ./segment_juncs.o
unassigned
reads.cpp
Gimple
./reads.cpp.004t.gimple
GKD
./reads.o.gkd
OBJ
obj: ./reads.o
unassigned
bwt_map.cpp
Gimple
./bwt_map.cpp.004t.gimple
GKD
./bwt_map.o.gkd
OBJ
obj: ./bwt_map.o
unassigned
common.cpp
Gimple
./common.cpp.004t.gimple
GKD
./common.o.gkd
OBJ
obj: ./common.o
unassigned
fusions.cpp
Gimple
./fusions.cpp.004t.gimple
GKD
./fusions.o.gkd
OBJ
obj: ./fusions.o
unassigned
tokenize.cpp
Gimple
./tokenize.cpp.004t.gimple
GKD
./tokenize.o.gkd
OBJ
obj: ./tokenize.o
unassigned
utils.cpp
Gimple
./utils.cpp.004t.gimple
GKD
./utils.o.gkd
OBJ
obj: ./utils.o
bgzf.c
Gimple
./bgzf.c.004t.gimple
GKD
./bgzf.o.gkd
OBJ
obj: ./bgzf.o
bam_aux.c
Gimple
./bam_aux.c.004t.gimple
GKD
./bam_aux.o.gkd
OBJ
obj: ./bam_aux.o
unassigned
bam.c
Gimple
./bam.c.004t.gimple
GKD
./bam.o.gkd
OBJ
obj: ./bam.o
bam_import.c
Gimple
./bam_import.c.004t.gimple
GKD
./bam_import.o.gkd
OBJ
obj: ./bam_import.o
sam.c
Gimple
./sam.c.004t.gimple
GKD
./sam.o.gkd
OBJ
obj: ./sam.o
bam_pileup.c
Gimple
./bam_pileup.c.004t.gimple
GKD
./bam_pileup.o.gkd
OBJ
obj: ./bam_pileup.o
faidx.c
Gimple
./faidx.c.004t.gimple
GKD
./faidx.o.gkd
OBJ
obj: ./faidx.o
knetfile.c
Gimple
./knetfile.c.004t.gimple
GKD
./knetfile.o.gkd
OBJ
obj: ./knetfile.o
sam_header.c
Gimple
./sam_header.c.004t.gimple
GKD
./sam_header.o.gkd
OBJ
obj: ./sam_header.o
kstring.c
Gimple
./kstring.c.004t.gimple
GKD
./kstring.o.gkd
OBJ
obj: ./kstring.o
razf.c
Gimple
./razf.c.004t.gimple
GKD
./razf.o.gkd
OBJ
obj: ./razf.o
includes
unassigned
../headers//usr/include/boost/smart_ptr/detail/sp_counted_base_gcc_x86.hpp
../headers//usr/include/boost/exception/info.hpp
../headers//usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp
../headers//usr/include/boost/checked_delete.hpp
segment_juncs.cpp
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/boost/system/system_error.hpp
./fusions.h
../headers//usr/include/c++/4.9/bitset
../headers//usr/include/c++/4.9/bits/stl_algo.h
../headers//usr/include/c++/4.9/typeinfo
../headers//usr/include/boost/exception/detail/exception_ptr.hpp
../headers//usr/include/c++/4.9/bits/stl_tree.h
./segments.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/boost/system/error_code.hpp
../headers//usr/include/boost/thread/exceptions.hpp
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/boost/smart_ptr/shared_ptr.hpp
../headers//usr/include/boost/smart_ptr/detail/shared_count.hpp
../headers//usr/include/boost/thread/detail/thread.hpp
../headers//usr/include/c++/4.9/ostream
../headers//usr/include/c++/4.9/sstream
../headers//usr/include/c++/4.9/streambuf
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/boost/exception/exception.hpp
../headers//usr/include/c++/4.9/stdexcept
../headers//usr/include/c++/4.9/bits/stl_bvector.h
../headers//usr/include/c++/4.9/bits/stl_algobase.h
./common.h
./reads.h
./bwt_map.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
./junctions.h
../headers//usr/include/c++/4.9/bits/stl_pair.h
../headers//usr/include/seqan/sequence/string_base.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/seqan/modifier/modifier_shortcuts.h
../headers//usr/include/seqan/modifier/modifier_view.h
../headers//usr/include/seqan/basic/alphabet_residue.h
../headers//usr/include/seqan/basic/alphabet_simple_type.h
../headers//usr/include/seqan/modifier/modifier_reverse.h
../headers//usr/include/boost/thread/pthread/thread_data.hpp
../headers//usr/include/c++/4.9/bits/stl_map.h
../headers//usr/include/c++/4.9/bits/stl_set.h
../headers//usr/include/boost/throw_exception.hpp
../headers//usr/include/boost/thread/pthread/thread_heap_alloc.hpp
../headers//usr/include/boost/thread/pthread/mutex.hpp
../headers//usr/include/boost/smart_ptr/weak_ptr.hpp
../headers//usr/include/boost/thread/pthread/condition_variable_fwd.hpp
../headers//usr/include/boost/smart_ptr/enable_shared_from_this.hpp
../headers//usr/include/seqan/file/file_format_fasta.h
../headers//usr/include/seqan/file/stream.h
../headers//usr/include/seqan/sequence/string_packed.h
../headers//usr/include/seqan/sequence/string_alloc.h
../headers//usr/include/seqan/basic/iterator_adaptor.h
../headers//usr/include/seqan/basic/iterator_interface.h
../headers//usr/include/seqan/sequence/sequence_interface.h
../headers//usr/include/seqan/basic/allocator_interface.h
./insertions.h
../headers//usr/include/c++/4.9/bits/stl_heap.h
../headers//usr/include/c++/4.9/bits/stl_queue.h
../headers//usr/include/c++/4.9/bits/stl_function.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/seqan/sequence/sequence_lexical.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/seqan/sequence/segment_base.h
../headers//usr/include/seqan/basic/array_construct_destruct.h
../headers//usr/include/seqan/stream/adapt_fstream.h
../headers//usr/include/seqan/sequence/segment_infix.h
../headers//usr/include/seqan/file/stream_algorithms.h
../headers//usr/include/seqan/stream/adapt_sstream.h
../headers//usr/include/c++/4.9/istream
../headers//usr/include/seqan/sequence/string_cstyle.h
../headers//usr/include/seqan/sequence/adapt_std_string.h
../headers//usr/include/seqan/sequence/adapt_array_pointer.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/wchar.h
../headers//usr/include/_G_config.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/new
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/ostream.tcc
../headers//usr/include/c++/4.9/bits/locale_facets.h
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/iomanip
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/limits
../headers//usr/include/c++/4.9/bits/stl_list.h
../headers//usr/include/c++/4.9/fstream
../headers//usr/include/c++/4.9/exception
../headers//usr/include/c++/4.9/bits/list.tcc
../headers//usr/include/c++/4.9/bits/basic_ios.tcc
../headers//usr/include/c++/4.9/bits/stl_iterator_base_funcs.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/c++/4.9/bits/ostream_insert.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/c++/4.9/ext/type_traits.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/bits/pthreadtypes.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/wctype.h
../headers//usr/include/string.h
../headers//usr/include/stdint.h
../headers//usr/include/seqan/platform/platform_gcc.h
../headers//usr/include/seqan/basic/debug_test_system.h
../headers//usr/include/seqan/basic/profiling.h
../headers//usr/include/seqan/basic/metaprogramming_logic.h
../headers//usr/include/seqan/basic/fundamental_tags.h
../headers//usr/include/seqan/basic/alphabet_residue_tabs.h
../headers//usr/include/seqan/basic/container_concept.h
../headers//usr/include/seqan/modifier/modifier_functors.h
../headers//usr/include/seqan/basic/basic_type.h
../headers//usr/include/seqan/stream/adapt_iostream.h
../headers//usr/include/seqan/basic/alphabet_math.h
../headers//usr/include/seqan/basic/metaprogramming_type.h
../headers//usr/include/seqan/basic/proxy_iterator.h
../headers//usr/include/seqan/modifier/modifier_string.h
../headers//usr/include/seqan/basic/metaprogramming_enable_if.h
../headers//usr/include/seqan/basic/iterator_adapt_std.h
../headers//usr/include/seqan/basic/holder_base.h
../headers//usr/include/seqan/basic/holder_simple.h
../headers//usr/include/seqan/basic/fundamental_conversion.h
../headers//usr/include/seqan/modifier/modifier_iterator.h
../headers//usr/include/seqan/basic/alphabet_adapt_builtins.h
../headers//usr/include/seqan/basic/concept_checking.h
../headers//usr/include/seqan/basic/fundamental_transport.h
../headers//usr/include/seqan/basic/iterator_base.h
../headers//usr/include/seqan/file/file_format_raw.h
../headers//usr/include/seqan/file/file_format_mmap.h
../headers//usr/include/seqan/basic/hosted_type_interface.h
../headers//usr/include/seqan/sequence/sequence_shortcuts.h
../headers//usr/include/seqan/basic/metaprogramming_control.h
../headers//usr/include/seqan/random/random_normal.h
../headers//usr/include/boost/config/suffix.hpp
../headers//usr/include/boost/cstdint.hpp
../headers//usr/include/boost/iterator.hpp
../headers//usr/include/boost/operators.hpp
../headers//usr/include/boost/detail/sp_typeinfo.hpp
../headers//usr/include/boost/smart_ptr/detail/sp_convertible.hpp
../headers//usr/include/boost/smart_ptr/detail/spinlock_sync.hpp
../headers//usr/include/boost/smart_ptr/detail/spinlock_pool.hpp
../headers//usr/include/boost/integer_traits.hpp
../headers//usr/include/boost/none_t.hpp
../headers//usr/include/boost/thread/tss.hpp
../headers//usr/include/boost/thread/future.hpp
../headers//usr/include/boost/integer/static_log2.hpp
../headers//usr/include/boost/thread/detail/move.hpp
../headers//usr/include/boost/function/function_base.hpp
../headers//usr/include/boost/function/function_template.hpp
../headers//usr/include/boost/noncopyable.hpp
../headers//usr/include/boost/thread/future_error_code.hpp
../headers//usr/include/boost/mpl/aux_/adl_barrier.hpp
../headers//usr/include/boost/mpl/integral_c_tag.hpp
../headers//usr/include/boost/mpl/bool_fwd.hpp
../headers//usr/include/boost/mpl/void_fwd.hpp
../headers//usr/include/boost/mpl/aux_/na_fwd.hpp
../headers//usr/include/boost/type_traits/detail/yes_no_type.hpp
../headers//usr/include/boost/move/detail/meta_utils.hpp
../headers//usr/include/boost/thread/lock_options.hpp
../headers//usr/include/boost/exception/detail/type_info.hpp
../headers//usr/include/boost/exception/detail/error_info_impl.hpp
../headers//usr/include/boost/exception/to_string_stub.hpp
../headers//usr/include/boost/exception/detail/clone_current_exception.hpp
../headers//usr/include/boost/date_time/c_time.hpp
../headers//usr/include/boost/date_time/time_defs.hpp
../headers//usr/include/boost/date_time/special_defs.hpp
../headers//usr/include/boost/date_time/time_resolution_traits.hpp
../headers//usr/include/boost/date_time/int_adapter.hpp
../headers//usr/include/boost/date_time/date_defs.hpp
../headers//usr/include/boost/date_time/year_month_day.hpp
../headers//usr/include/boost/date_time/gregorian_calendar.hpp
../headers//usr/include/boost/date_time/gregorian_calendar.ipp
../headers//usr/include/boost/date_time/date_duration.hpp
../headers//usr/include/boost/date_time/date.hpp
../headers//usr/include/boost/date_time/time_duration.hpp
../headers//usr/include/boost/date_time/time_system_counted.hpp
../headers//usr/include/boost/date_time/time.hpp
../headers//usr/include/boost/date_time/constrained_value.hpp
../headers//usr/include/boost/date_time/gregorian/greg_weekday.hpp
../headers//usr/include/boost/date_time/gregorian/greg_day.hpp
../headers//usr/include/boost/date_time/gregorian/greg_year.hpp
../headers//usr/include/boost/date_time/gregorian/greg_month.hpp
../headers//usr/include/boost/date_time/gregorian/greg_calendar.hpp
../headers//usr/include/boost/date_time/gregorian/greg_day_of_year.hpp
../headers//usr/include/boost/date_time/gregorian/greg_duration.hpp
../headers//usr/include/boost/date_time/gregorian/greg_date.hpp
../headers//usr/include/boost/date_time/posix_time/posix_time_config.hpp
../headers//usr/include/boost/date_time/posix_time/ptime.hpp
../headers//usr/include/boost/ratio/detail/overflow_helpers.hpp
../headers//usr/include/boost/type_traits/add_rvalue_reference.hpp
../headers//usr/include/boost/chrono/detail/is_evenly_divisible_by.hpp
../headers//usr/include/boost/chrono/duration.hpp
../headers//usr/include/boost/chrono/system_clocks.hpp
../headers//usr/include/boost/chrono/time_point.hpp
../headers//usr/include/boost/thread/xtime.hpp
../headers//usr/include/boost/thread/thread_time.hpp
../headers//usr/include/boost/ratio/ratio.hpp
../headers//usr/include/boost/thread/pthread/pthread_mutex_scoped_lock.hpp
../headers//usr/include/boost/thread/lock_types.hpp
../headers//usr/include/boost/thread/cv_status.hpp
../headers//usr/include/boost/type_traits/type_with_alignment.hpp
../headers//usr/include/boost/optional/optional.hpp
../headers//usr/include/boost/smart_ptr/detail/operator_bool.hpp
../headers//usr/include/boost/thread/lock_guard.hpp
../headers//usr/include/seqan/random/ext_MersenneTwister.h
../headers//usr/include/boost/bind/storage.hpp
../headers//usr/include/boost/bind/arg.hpp
../headers//usr/include/boost/io_fwd.hpp
../headers//usr/include/boost/integer_fwd.hpp
../headers//usr/include/boost/functional/hash/detail/float_functions.hpp
../headers//usr/include/boost/thread/pthread/condition_variable.hpp
../headers//usr/include/boost/atomic/detail/gcc-atomic.hpp
../headers//usr/include/boost/thread/lockable_traits.hpp
../headers//usr/include/boost/tuple/detail/tuple_basic.hpp
../headers//usr/include/boost/exception/detail/is_output_streamable.hpp
../headers//usr/include/boost/exception/to_string.hpp
../headers//usr/include/boost/utility/enable_if.hpp
../headers//usr/include/boost/smart_ptr/bad_weak_ptr.hpp
../headers//usr/include/boost/detail/scoped_enum_emulation.hpp
../headers//usr/include/boost/none.hpp
../headers//usr/include/boost/mpl/bool.hpp
../headers//usr/include/boost/mpl/void.hpp
../headers//usr/include/boost/mpl/aux_/integral_wrapper.hpp
../headers//usr/include/boost/bind/placeholders.hpp
../headers//usr/include/samtools/bgzf.h
../headers//usr/include/samtools/bam.h
../headers//usr/include/samtools/sam.h
./utils.h
./deletions.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/getopt.h
../headers//usr/include/ctype.h
../headers//usr/include/pthread.h
./tokenize.h
../headers//usr/include/c++/4.9/cxxabi.h
unassigned
./reads.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
./common.h
reads.cpp
../headers//usr/include/c++/4.9/bits/stl_algo.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/stdlib.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers//usr/include/c++/4.9/bits/stl_heap.h
../headers//usr/include/c++/4.9/bits/stl_queue.h
../headers//usr/include/seqan/sequence/string_base.h
../headers//usr/include/seqan/sequence/sequence_interface.h
../headers//usr/include/seqan/sequence/string_alloc.h
../headers//usr/include/seqan/basic/allocator_interface.h
../headers//usr/include/seqan/sequence/adapt_array_pointer.h
../headers//usr/include/seqan/sequence/adapt_std_string.h
../headers//usr/include/seqan/basic/array_construct_destruct.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/libio.h
../headers//usr/include/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/new
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/stl_list.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/stdint.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/seqan/basic/debug_test_system.h
../headers//usr/include/seqan/basic/profiling.h
../headers//usr/include/seqan/basic/metaprogramming_logic.h
../headers//usr/include/seqan/basic/alphabet_residue_tabs.h
../headers//usr/include/seqan/basic/fundamental_tags.h
../headers//usr/include/seqan/basic/container_concept.h
../headers//usr/include/seqan/basic/iterator_interface.h
../headers//usr/include/seqan/modifier/modifier_functors.h
../headers//usr/include/seqan/basic/basic_type.h
../headers//usr/include/seqan/basic/alphabet_math.h
../headers//usr/include/seqan/basic/iterator_adapt_std.h
../headers//usr/include/seqan/basic/iterator_base.h
../headers//usr/include/seqan/basic/metaprogramming_control.h
../headers//usr/include/seqan/basic/alphabet_residue.h
../headers//usr/include/seqan/random/random_normal.h
../headers//usr/include/samtools/bgzf.h
../headers//usr/include/samtools/bam.h
../headers//usr/include/samtools/sam.h
./bwt_map.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
./tokenize.h
../headers//usr/include/ctype.h
../headers//usr/include/c++/4.9/cxxabi.h
../headers//usr/include/seqan/random/ext_MersenneTwister.h
unassigned
../headers//usr/include/c++/4.9/bits/locale_facets.h
./bwt_map.h
bwt_map.cpp
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/string.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
./common.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_tree.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/c++/4.9/bits/stl_bvector.h
../headers//usr/include/stdlib.h
../headers//usr/include/c++/4.9/bits/stl_algo.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_pair.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/bits/stl_map.h
../headers//usr/include/c++/4.9/bits/stl_heap.h
../headers//usr/include/seqan/sequence/string_base.h
../headers//usr/include/seqan/sequence/sequence_interface.h
../headers//usr/include/seqan/sequence/string_alloc.h
../headers//usr/include/seqan/basic/allocator_interface.h
../headers//usr/include/seqan/basic/alphabet_simple_type.h
../headers//usr/include/seqan/sequence/segment_base.h
../headers//usr/include/seqan/sequence/string_packed.h
../headers//usr/include/seqan/basic/iterator_adaptor.h
../headers//usr/include/seqan/basic/array_construct_destruct.h
../headers//usr/include/seqan/basic/iterator_interface.h
../headers//usr/include/seqan/sequence/segment_infix.h
../headers//usr/include/seqan/basic/alphabet_residue.h
../headers//usr/include/c++/4.9/ostream
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/seqan/modifier/modifier_view.h
../headers//usr/include/seqan/modifier/modifier_reverse.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/time.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/new
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/ostream.tcc
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/backward/auto_ptr.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/stl_list.h
../headers//usr/include/c++/4.9/bits/stl_function.h
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_funcs.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/c++/4.9/bits/ostream_insert.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/c++/4.9/ext/type_traits.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/wchar.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/stdint.h
../headers//usr/include/seqan/platform/platform_gcc.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/seqan/basic/debug_test_system.h
../headers//usr/include/seqan/basic/profiling.h
../headers//usr/include/seqan/basic/metaprogramming_logic.h
../headers//usr/include/seqan/basic/test_system.h
../headers//usr/include/seqan/basic/alphabet_residue_tabs.h
../headers//usr/include/seqan/basic/fundamental_tags.h
../headers//usr/include/seqan/basic/container_concept.h
../headers//usr/include/seqan/modifier/modifier_functors.h
../headers//usr/include/seqan/basic/alphabet_math.h
../headers//usr/include/seqan/basic/metaprogramming_type.h
../headers//usr/include/seqan/basic/basic_type.h
../headers//usr/include/seqan/basic/fundamental_conversion.h
../headers//usr/include/seqan/basic/iterator_base.h
../headers//usr/include/seqan/modifier/modifier_shortcuts.h
../headers//usr/include/seqan/sequence/sequence_shortcuts.h
../headers//usr/include/seqan/basic/metaprogramming_control.h
../headers//usr/include/seqan/random/random_normal.h
../headers//usr/include/samtools/bgzf.h
../headers//usr/include/samtools/bam.h
../headers//usr/include/samtools/sam.h
./reads.h
./junctions.h
./insertions.h
./deletions.h
./fusions.h
./align_status.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/ctype.h
./tokenize.h
../headers//usr/include/c++/4.9/cxxabi.h
../headers//usr/include/seqan/random/ext_MersenneTwister.h
unassigned
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
common.cpp
../headers//usr/include/c++/4.9/ostream
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
./common.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.h
../headers//usr/include/samtools/bam.h
../headers//usr/include/stdlib.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/libio.h
../headers//usr/include/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/locale_facets.h
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/getopt.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/samtools/bgzf.h
../headers//usr/include/samtools/sam.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/new
./tokenize.h
../headers//usr/include/ctype.h
unassigned
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/bits/stl_algo.h
./fusions.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_tree.h
fusions.cpp
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
./reads.h
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/c++/4.9/istream
../headers//usr/include/c++/4.9/ostream
../headers//usr/include/c++/4.9/streambuf
../headers//usr/include/c++/4.9/sstream
../headers//usr/include/seqan/stream/adapt_fstream.h
../headers//usr/include/seqan/file/stream_algorithms.h
../headers//usr/include/seqan/basic/alphabet_residue.h
../headers//usr/include/seqan/stream/adapt_sstream.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/c++/4.9/bits/stl_pair.h
../headers//usr/include/c++/4.9/bits/stl_map.h
./bwt_map.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/bits/stl_heap.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/seqan/sequence/string_base.h
../headers//usr/include/seqan/sequence/sequence_interface.h
../headers//usr/include/seqan/sequence/string_alloc.h
../headers//usr/include/seqan/basic/allocator_interface.h
../headers//usr/include/seqan/basic/alphabet_simple_type.h
../headers//usr/include/seqan/sequence/segment_base.h
../headers//usr/include/seqan/sequence/string_packed.h
../headers//usr/include/seqan/basic/iterator_adaptor.h
../headers//usr/include/seqan/basic/array_construct_destruct.h
../headers//usr/include/seqan/basic/iterator_interface.h
../headers//usr/include/seqan/sequence/segment_infix.h
../headers//usr/include/seqan/modifier/modifier_view.h
../headers//usr/include/seqan/modifier/modifier_reverse.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/wchar.h
../headers//usr/include/_G_config.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/new
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/ostream.tcc
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/stl_list.h
../headers//usr/include/c++/4.9/bits/stl_function.h
../headers//usr/include/c++/4.9/bits/basic_ios.tcc
../headers//usr/include/c++/4.9/bits/stl_iterator_base_funcs.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/string.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/c++/4.9/ext/type_traits.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/wctype.h
../headers//usr/include/stdint.h
../headers//usr/include/seqan/platform/platform_gcc.h
../headers//usr/include/seqan/basic/debug_test_system.h
../headers//usr/include/seqan/basic/profiling.h
../headers//usr/include/seqan/basic/metaprogramming_logic.h
../headers//usr/include/seqan/basic/alphabet_residue_tabs.h
../headers//usr/include/seqan/basic/fundamental_tags.h
../headers//usr/include/seqan/basic/container_concept.h
../headers//usr/include/seqan/modifier/modifier_functors.h
../headers//usr/include/seqan/basic/alphabet_math.h
../headers//usr/include/seqan/basic/metaprogramming_type.h
../headers//usr/include/seqan/basic/basic_type.h
../headers//usr/include/seqan/sequence/adapt_std_string.h
../headers//usr/include/seqan/basic/fundamental_conversion.h
../headers//usr/include/seqan/basic/iterator_base.h
../headers//usr/include/seqan/file/file_format_raw.h
../headers//usr/include/seqan/modifier/modifier_shortcuts.h
../headers//usr/include/seqan/sequence/sequence_shortcuts.h
../headers//usr/include/seqan/basic/metaprogramming_control.h
../headers//usr/include/seqan/random/random_normal.h
./junctions.h
./insertions.h
./deletions.h
./align_status.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
./common.h
../headers//usr/include/c++/4.9/cxxabi.h
../headers//usr/include/seqan/random/ext_MersenneTwister.h
../headers//usr/include/seqan/align/align_base.h
unassigned
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
tokenize.cpp
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/new
unassigned
../headers//usr/include/c++/4.9/bits/locale_facets.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/sstream
../headers//usr/include/c++/4.9/streambuf
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
utils.cpp
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/c++/4.9/istream
../headers//usr/include/c++/4.9/fstream
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/c++/4.9/bits/stl_algo.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/libio.h
../headers//usr/include/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/new
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/istream.tcc
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/bits/stl_pair.h
../headers//usr/include/c++/4.9/bits/basic_ios.tcc
../headers//usr/include/c++/4.9/bits/fstream.tcc
../headers//usr/include/c++/4.9/bits/sstream.tcc
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/bits/pthreadtypes.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
./utils.h
../headers//usr/include/stdint.h
../headers//usr/include/string.h
./common.h
bgzf.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./bgzf.h
./khash.h
../headers//usr/include/stdlib.h
../headers//usr/include/fcntl.h
../headers//usr/include/string.h
bam_aux.c
./khash.h
./bam.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdint.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/string.h
../headers//usr/include/ctype.h
unassigned
./kstring.h
bam.c
./bam_endian.h
./bam.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./knetfile.h
./bgzf.h
../headers//usr/include/stdlib.h
./sam_header.h
../headers//usr/include/ctype.h
../headers//usr/include/x86_64-linux-gnu/bits/errno.h
../headers//usr/include/string.h
bam_import.c
../headers//usr/include/stdlib.h
./khash.h
./bam.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/zlib.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./kstring.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
./sam_header.h
../headers//usr/include/ctype.h
sam.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdint.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
./knetfile.h
./bgzf.h
./bam.h
./sam.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/string.h
../headers//usr/include/unistd.h
./faidx.h
bam_pileup.c
./bam.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
./knetfile.h
./bgzf.h
../headers//usr/include/stdlib.h
../headers//usr/include/assert.h
faidx.c
./khash.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./faidx.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./razf.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/ctype.h
knetfile.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/x86_64-linux-gnu/bits/time.h
../headers//usr/include/x86_64-linux-gnu/sys/select.h
../headers//usr/include/unistd.h
../headers//usr/include/x86_64-linux-gnu/bits/sockaddr.h
../headers//usr/include/x86_64-linux-gnu/bits/socket.h
../headers//usr/include/netdb.h
./knetfile.h
../headers//usr/include/x86_64-linux-gnu/sys/socket.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/ctype.h
../headers//usr/include/x86_64-linux-gnu/bits/errno.h
../headers//usr/include/fcntl.h
../headers//usr/include/x86_64-linux-gnu/bits/socket_type.h
sam_header.c
./khash.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/string.h
kstring.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./kstring.h
../headers//usr/include/stdio.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/ctype.h
razf.c
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/fcntl.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./razf.h
../headers//usr/include/unistd.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
libraries
../libs/usr/lib/x86_64-linux-gnu/libboost_thread.so.1.55.0
../libs/usr/lib/x86_64-linux-gnu/libboost_system.so.1.55.0
../libs/lib/x86_64-linux-gnu/libz.so.1
../libs/usr/lib/x86_64-linux-gnu/libstdc++.so.6
../libs/lib/x86_64-linux-gnu/libm.so.6
../libs/lib/x86_64-linux-gnu/libgcc_s.so.1
../libs/lib/x86_64-linux-gnu/libpthread.so.0
../libs/lib/x86_64-linux-gnu/libc.so.6
manual
sam_juncs
compile units
sam_juncs.cpp
Gimple
./sam_juncs.cpp.004t.gimple
GKD
./sam_juncs.o.gkd
OBJ
obj: ./sam_juncs.o
unassigned
bwt_map.cpp
Gimple
./bwt_map.cpp.004t.gimple
GKD
./bwt_map.o.gkd
OBJ
obj: ./bwt_map.o
unassigned
common.cpp
Gimple
./common.cpp.004t.gimple
GKD
./common.o.gkd
OBJ
obj: ./common.o
unassigned
junctions.cpp
Gimple
./junctions.cpp.004t.gimple
GKD
./junctions.o.gkd
OBJ
obj: ./junctions.o
unassigned
tokenize.cpp
Gimple
./tokenize.cpp.004t.gimple
GKD
./tokenize.o.gkd
OBJ
obj: ./tokenize.o
unassigned
reads.cpp
Gimple
./reads.cpp.004t.gimple
GKD
./reads.o.gkd
OBJ
obj: ./reads.o
bgzf.c
Gimple
./bgzf.c.004t.gimple
GKD
./bgzf.o.gkd
OBJ
obj: ./bgzf.o
bam_aux.c
Gimple
./bam_aux.c.004t.gimple
GKD
./bam_aux.o.gkd
OBJ
obj: ./bam_aux.o
unassigned
bam.c
Gimple
./bam.c.004t.gimple
GKD
./bam.o.gkd
OBJ
obj: ./bam.o
bam_import.c
Gimple
./bam_import.c.004t.gimple
GKD
./bam_import.o.gkd
OBJ
obj: ./bam_import.o
sam.c
Gimple
./sam.c.004t.gimple
GKD
./sam.o.gkd
OBJ
obj: ./sam.o
bam_pileup.c
Gimple
./bam_pileup.c.004t.gimple
GKD
./bam_pileup.o.gkd
OBJ
obj: ./bam_pileup.o
faidx.c
Gimple
./faidx.c.004t.gimple
GKD
./faidx.o.gkd
OBJ
obj: ./faidx.o
knetfile.c
Gimple
./knetfile.c.004t.gimple
GKD
./knetfile.o.gkd
OBJ
obj: ./knetfile.o
sam_header.c
Gimple
./sam_header.c.004t.gimple
GKD
./sam_header.o.gkd
OBJ
obj: ./sam_header.o
kstring.c
Gimple
./kstring.c.004t.gimple
GKD
./kstring.o.gkd
OBJ
obj: ./kstring.o
razf.c
Gimple
./razf.c.004t.gimple
GKD
./razf.o.gkd
OBJ
obj: ./razf.o
includes
sam_juncs.cpp
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
./bwt_map.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_tree.h
../headers//usr/include/c++/4.9/bits/stl_map.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/string.h
../headers//usr/include/c++/4.9/bits/stl_pair.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdint.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/stl_list.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/stl_function.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/new
../headers//usr/include/stdlib.h
../headers//usr/include/time.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/wchar.h
../headers//usr/include/_G_config.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/samtools/bgzf.h
../headers//usr/include/samtools/bam.h
../headers//usr/include/samtools/sam.h
./common.h
../headers//usr/include/wctype.h
../headers//usr/include/seqan/basic/debug_test_system.h
../headers//usr/include/seqan/basic/profiling.h
../headers//usr/include/seqan/basic/alphabet_residue_tabs.h
../headers//usr/include/seqan/modifier/modifier_functors.h
../headers//usr/include/seqan/basic/alphabet_math.h
../headers//usr/include/seqan/basic/metaprogramming_control.h
../headers//usr/include/seqan/basic/alphabet_residue.h
../headers//usr/include/seqan/random/random_normal.h
./reads.h
./junctions.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/getopt.h
../headers//usr/include/c++/4.9/cxxabi.h
../headers//usr/include/seqan/random/ext_MersenneTwister.h
unassigned
../headers//usr/include/c++/4.9/bits/locale_facets.h
./bwt_map.h
bwt_map.cpp
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/string.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
./common.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_tree.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/c++/4.9/bits/stl_bvector.h
../headers//usr/include/stdlib.h
../headers//usr/include/c++/4.9/bits/stl_algo.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_pair.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/bits/stl_map.h
../headers//usr/include/c++/4.9/bits/stl_heap.h
../headers//usr/include/seqan/sequence/string_base.h
../headers//usr/include/seqan/sequence/sequence_interface.h
../headers//usr/include/seqan/sequence/string_alloc.h
../headers//usr/include/seqan/basic/allocator_interface.h
../headers//usr/include/seqan/basic/alphabet_simple_type.h
../headers//usr/include/seqan/sequence/segment_base.h
../headers//usr/include/seqan/sequence/string_packed.h
../headers//usr/include/seqan/basic/iterator_adaptor.h
../headers//usr/include/seqan/basic/array_construct_destruct.h
../headers//usr/include/seqan/basic/iterator_interface.h
../headers//usr/include/seqan/sequence/segment_infix.h
../headers//usr/include/seqan/basic/alphabet_residue.h
../headers//usr/include/c++/4.9/ostream
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/seqan/modifier/modifier_view.h
../headers//usr/include/seqan/modifier/modifier_reverse.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/time.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/new
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/ostream.tcc
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/backward/auto_ptr.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/stl_list.h
../headers//usr/include/c++/4.9/bits/stl_function.h
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_funcs.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/c++/4.9/bits/ostream_insert.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/c++/4.9/ext/type_traits.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/wchar.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/stdint.h
../headers//usr/include/seqan/platform/platform_gcc.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/seqan/basic/debug_test_system.h
../headers//usr/include/seqan/basic/profiling.h
../headers//usr/include/seqan/basic/metaprogramming_logic.h
../headers//usr/include/seqan/basic/test_system.h
../headers//usr/include/seqan/basic/alphabet_residue_tabs.h
../headers//usr/include/seqan/basic/fundamental_tags.h
../headers//usr/include/seqan/basic/container_concept.h
../headers//usr/include/seqan/modifier/modifier_functors.h
../headers//usr/include/seqan/basic/alphabet_math.h
../headers//usr/include/seqan/basic/metaprogramming_type.h
../headers//usr/include/seqan/basic/basic_type.h
../headers//usr/include/seqan/basic/fundamental_conversion.h
../headers//usr/include/seqan/basic/iterator_base.h
../headers//usr/include/seqan/modifier/modifier_shortcuts.h
../headers//usr/include/seqan/sequence/sequence_shortcuts.h
../headers//usr/include/seqan/basic/metaprogramming_control.h
../headers//usr/include/seqan/random/random_normal.h
../headers//usr/include/samtools/bgzf.h
../headers//usr/include/samtools/bam.h
../headers//usr/include/samtools/sam.h
./reads.h
./junctions.h
./insertions.h
./deletions.h
./fusions.h
./align_status.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/ctype.h
./tokenize.h
../headers//usr/include/c++/4.9/cxxabi.h
../headers//usr/include/seqan/random/ext_MersenneTwister.h
unassigned
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
common.cpp
../headers//usr/include/c++/4.9/ostream
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
./common.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.h
../headers//usr/include/samtools/bam.h
../headers//usr/include/stdlib.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/libio.h
../headers//usr/include/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/locale_facets.h
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/getopt.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/samtools/bgzf.h
../headers//usr/include/samtools/sam.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/new
./tokenize.h
../headers//usr/include/ctype.h
unassigned
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/bits/stl_tree.h
./junctions.h
./bwt_map.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
junctions.cpp
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/c++/4.9/bits/stl_pair.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_algo.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/bits/stl_map.h
../headers//usr/include/c++/4.9/bits/stl_heap.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/stdint.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/stl_list.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/stl_function.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/new
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdlib.h
../headers//usr/include/time.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/wchar.h
../headers//usr/include/_G_config.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/samtools/bgzf.h
../headers//usr/include/samtools/bam.h
../headers//usr/include/samtools/sam.h
./common.h
../headers//usr/include/wctype.h
../headers//usr/include/seqan/basic/debug_test_system.h
../headers//usr/include/seqan/basic/profiling.h
../headers//usr/include/seqan/basic/alphabet_residue_tabs.h
../headers//usr/include/seqan/modifier/modifier_functors.h
../headers//usr/include/seqan/basic/alphabet_math.h
../headers//usr/include/seqan/basic/metaprogramming_control.h
../headers//usr/include/seqan/basic/alphabet_residue.h
../headers//usr/include/seqan/random/random_normal.h
./reads.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/cxxabi.h
../headers//usr/include/seqan/random/ext_MersenneTwister.h
unassigned
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
tokenize.cpp
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/new
unassigned
./reads.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
./common.h
reads.cpp
../headers//usr/include/c++/4.9/bits/stl_algo.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/stdlib.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers//usr/include/c++/4.9/bits/stl_heap.h
../headers//usr/include/c++/4.9/bits/stl_queue.h
../headers//usr/include/seqan/sequence/string_base.h
../headers//usr/include/seqan/sequence/sequence_interface.h
../headers//usr/include/seqan/sequence/string_alloc.h
../headers//usr/include/seqan/basic/allocator_interface.h
../headers//usr/include/seqan/sequence/adapt_array_pointer.h
../headers//usr/include/seqan/sequence/adapt_std_string.h
../headers//usr/include/seqan/basic/array_construct_destruct.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/libio.h
../headers//usr/include/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/new
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/stl_list.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/stdint.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/seqan/basic/debug_test_system.h
../headers//usr/include/seqan/basic/profiling.h
../headers//usr/include/seqan/basic/metaprogramming_logic.h
../headers//usr/include/seqan/basic/alphabet_residue_tabs.h
../headers//usr/include/seqan/basic/fundamental_tags.h
../headers//usr/include/seqan/basic/container_concept.h
../headers//usr/include/seqan/basic/iterator_interface.h
../headers//usr/include/seqan/modifier/modifier_functors.h
../headers//usr/include/seqan/basic/basic_type.h
../headers//usr/include/seqan/basic/alphabet_math.h
../headers//usr/include/seqan/basic/iterator_adapt_std.h
../headers//usr/include/seqan/basic/iterator_base.h
../headers//usr/include/seqan/basic/metaprogramming_control.h
../headers//usr/include/seqan/basic/alphabet_residue.h
../headers//usr/include/seqan/random/random_normal.h
../headers//usr/include/samtools/bgzf.h
../headers//usr/include/samtools/bam.h
../headers//usr/include/samtools/sam.h
./bwt_map.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
./tokenize.h
../headers//usr/include/ctype.h
../headers//usr/include/c++/4.9/cxxabi.h
../headers//usr/include/seqan/random/ext_MersenneTwister.h
bgzf.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./bgzf.h
./khash.h
../headers//usr/include/stdlib.h
../headers//usr/include/fcntl.h
../headers//usr/include/string.h
bam_aux.c
./khash.h
./bam.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdint.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/string.h
../headers//usr/include/ctype.h
unassigned
./kstring.h
bam.c
./bam_endian.h
./bam.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./knetfile.h
./bgzf.h
../headers//usr/include/stdlib.h
./sam_header.h
../headers//usr/include/ctype.h
../headers//usr/include/x86_64-linux-gnu/bits/errno.h
../headers//usr/include/string.h
bam_import.c
../headers//usr/include/stdlib.h
./khash.h
./bam.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/zlib.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./kstring.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
./sam_header.h
../headers//usr/include/ctype.h
sam.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdint.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
./knetfile.h
./bgzf.h
./bam.h
./sam.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/string.h
../headers//usr/include/unistd.h
./faidx.h
bam_pileup.c
./bam.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
./knetfile.h
./bgzf.h
../headers//usr/include/stdlib.h
../headers//usr/include/assert.h
faidx.c
./khash.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./faidx.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./razf.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/ctype.h
knetfile.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/x86_64-linux-gnu/bits/time.h
../headers//usr/include/x86_64-linux-gnu/sys/select.h
../headers//usr/include/unistd.h
../headers//usr/include/x86_64-linux-gnu/bits/sockaddr.h
../headers//usr/include/x86_64-linux-gnu/bits/socket.h
../headers//usr/include/netdb.h
./knetfile.h
../headers//usr/include/x86_64-linux-gnu/sys/socket.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/ctype.h
../headers//usr/include/x86_64-linux-gnu/bits/errno.h
../headers//usr/include/fcntl.h
../headers//usr/include/x86_64-linux-gnu/bits/socket_type.h
sam_header.c
./khash.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/string.h
kstring.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./kstring.h
../headers//usr/include/stdio.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/ctype.h
razf.c
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/fcntl.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./razf.h
../headers//usr/include/unistd.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
libraries
../libs/lib/x86_64-linux-gnu/libz.so.1
../libs/usr/lib/x86_64-linux-gnu/libstdc++.so.6
../libs/lib/x86_64-linux-gnu/libm.so.6
../libs/lib/x86_64-linux-gnu/libgcc_s.so.1
../libs/lib/x86_64-linux-gnu/libpthread.so.0
../libs/lib/x86_64-linux-gnu/libc.so.6
manual
bam2fastx
compile units
unassigned
bam2fastx.cpp
Gimple
./bam2fastx.cpp.004t.gimple
GKD
./bam2fastx.o.gkd
OBJ
obj: ./bam2fastx.o
bam_aux.c
Gimple
./bam_aux.c.004t.gimple
GKD
./bam_aux.o.gkd
OBJ
obj: ./bam_aux.o
unassigned
bam.c
Gimple
./bam.c.004t.gimple
GKD
./bam.o.gkd
OBJ
obj: ./bam.o
bam_import.c
Gimple
./bam_import.c.004t.gimple
GKD
./bam_import.o.gkd
OBJ
obj: ./bam_import.o
sam.c
Gimple
./sam.c.004t.gimple
GKD
./sam.o.gkd
OBJ
obj: ./sam.o
bam_pileup.c
Gimple
./bam_pileup.c.004t.gimple
GKD
./bam_pileup.o.gkd
OBJ
obj: ./bam_pileup.o
faidx.c
Gimple
./faidx.c.004t.gimple
GKD
./faidx.o.gkd
OBJ
obj: ./faidx.o
knetfile.c
Gimple
./knetfile.c.004t.gimple
GKD
./knetfile.o.gkd
OBJ
obj: ./knetfile.o
sam_header.c
Gimple
./sam_header.c.004t.gimple
GKD
./sam_header.o.gkd
OBJ
obj: ./sam_header.o
bgzf.c
Gimple
./bgzf.c.004t.gimple
GKD
./bgzf.o.gkd
OBJ
obj: ./bgzf.o
kstring.c
Gimple
./kstring.c.004t.gimple
GKD
./kstring.o.gkd
OBJ
obj: ./kstring.o
razf.c
Gimple
./razf.c.004t.gimple
GKD
./razf.o.gkd
OBJ
obj: ./razf.o
includes
unassigned
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
bam2fastx.cpp
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/type_traits.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/wchar.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/string.h
../headers//usr/include/getopt.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/stdint.h
../headers//usr/include/samtools/bgzf.h
../headers//usr/include/samtools/bam.h
../headers//usr/include/samtools/sam.h
../headers//usr/include/x86_64-linux-gnu/bits/confname.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/ctype.h
bam_aux.c
./khash.h
./bam.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdint.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/string.h
../headers//usr/include/ctype.h
unassigned
./kstring.h
bam.c
./bam_endian.h
./bam.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./knetfile.h
./bgzf.h
../headers//usr/include/stdlib.h
./sam_header.h
../headers//usr/include/ctype.h
../headers//usr/include/x86_64-linux-gnu/bits/errno.h
../headers//usr/include/string.h
bam_import.c
../headers//usr/include/stdlib.h
./khash.h
./bam.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/zlib.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./kstring.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
./sam_header.h
../headers//usr/include/ctype.h
sam.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdint.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
./knetfile.h
./bgzf.h
./bam.h
./sam.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/string.h
../headers//usr/include/unistd.h
./faidx.h
bam_pileup.c
./bam.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
./knetfile.h
./bgzf.h
../headers//usr/include/stdlib.h
../headers//usr/include/assert.h
faidx.c
./khash.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./faidx.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./razf.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/ctype.h
knetfile.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/x86_64-linux-gnu/bits/time.h
../headers//usr/include/x86_64-linux-gnu/sys/select.h
../headers//usr/include/unistd.h
../headers//usr/include/x86_64-linux-gnu/bits/sockaddr.h
../headers//usr/include/x86_64-linux-gnu/bits/socket.h
../headers//usr/include/netdb.h
./knetfile.h
../headers//usr/include/x86_64-linux-gnu/sys/socket.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/ctype.h
../headers//usr/include/x86_64-linux-gnu/bits/errno.h
../headers//usr/include/fcntl.h
../headers//usr/include/x86_64-linux-gnu/bits/socket_type.h
sam_header.c
./khash.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/string.h
bgzf.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./bgzf.h
./khash.h
../headers//usr/include/stdlib.h
../headers//usr/include/fcntl.h
../headers//usr/include/string.h
kstring.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./kstring.h
../headers//usr/include/stdio.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/ctype.h
razf.c
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/fcntl.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./razf.h
../headers//usr/include/unistd.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
libraries
../libs/lib/x86_64-linux-gnu/libz.so.1
../libs/usr/lib/x86_64-linux-gnu/libstdc++.so.6
../libs/lib/x86_64-linux-gnu/libm.so.6
../libs/lib/x86_64-linux-gnu/libgcc_s.so.1
../libs/lib/x86_64-linux-gnu/libpthread.so.0
../libs/lib/x86_64-linux-gnu/libc.so.6
manual
../man/bam2fastx.1.gz
map2gtf
compile units
unassigned
map2gtf.cpp
Gimple
./map2gtf.cpp.004t.gimple
GKD
./map2gtf.o.gkd
OBJ
obj: ./map2gtf.o
unassigned
common.cpp
Gimple
./common.cpp.004t.gimple
GKD
./common.o.gkd
OBJ
obj: ./common.o
unassigned
tokenize.cpp
Gimple
./tokenize.cpp.004t.gimple
GKD
./tokenize.o.gkd
OBJ
obj: ./tokenize.o
GBase.cpp
Gimple
./GBase.cpp.004t.gimple
GKD
./GBase.o.gkd
OBJ
obj: ./GBase.o
bam_aux.c
Gimple
./bam_aux.c.004t.gimple
GKD
./bam_aux.o.gkd
OBJ
obj: ./bam_aux.o
unassigned
bam.c
Gimple
./bam.c.004t.gimple
GKD
./bam.o.gkd
OBJ
obj: ./bam.o
bam_import.c
Gimple
./bam_import.c.004t.gimple
GKD
./bam_import.o.gkd
OBJ
obj: ./bam_import.o
sam.c
Gimple
./sam.c.004t.gimple
GKD
./sam.o.gkd
OBJ
obj: ./sam.o
bam_pileup.c
Gimple
./bam_pileup.c.004t.gimple
GKD
./bam_pileup.o.gkd
OBJ
obj: ./bam_pileup.o
faidx.c
Gimple
./faidx.c.004t.gimple
GKD
./faidx.o.gkd
OBJ
obj: ./faidx.o
knetfile.c
Gimple
./knetfile.c.004t.gimple
GKD
./knetfile.o.gkd
OBJ
obj: ./knetfile.o
sam_header.c
Gimple
./sam_header.c.004t.gimple
GKD
./sam_header.o.gkd
OBJ
obj: ./sam_header.o
bgzf.c
Gimple
./bgzf.c.004t.gimple
GKD
./bgzf.o.gkd
OBJ
obj: ./bgzf.o
kstring.c
Gimple
./kstring.c.004t.gimple
GKD
./kstring.o.gkd
OBJ
obj: ./kstring.o
razf.c
Gimple
./razf.c.004t.gimple
GKD
./razf.o.gkd
OBJ
obj: ./razf.o
includes
unassigned
../headers//usr/include/c++/4.9/bits/locale_facets.h
./GVec.hh
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
map2gtf.cpp
../headers//usr/include/c++/4.9/ostream
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/c++/4.9/bits/stl_algo.h
./map2gtf.h
./bwt_map.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/bits/stl_tree.h
../headers//usr/include/c++/4.9/bits/stl_map.h
./GBase.h
../headers//usr/include/c++/4.9/fstream
../headers//usr/include/c++/4.9/streambuf
../headers//usr/include/c++/4.9/istream
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/stdlib.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers//usr/include/c++/4.9/sstream
../headers//usr/include/c++/4.9/bits/stl_pair.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.h
../headers//usr/include/c++/4.9/bits/stl_heap.h
../headers//usr/include/c++/4.9/bits/move.h
./common.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/time.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/ostream.tcc
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/backward/auto_ptr.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/stl_list.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/stl_function.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/basic_ios.tcc
../headers//usr/include/c++/4.9/bits/fstream.tcc
../headers//usr/include/c++/4.9/bits/sstream.tcc
../headers//usr/include/c++/4.9/new
../headers//usr/include/c++/4.9/bits/ostream_insert.h
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/string.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/wchar.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/stdint.h
../headers//usr/include/samtools/bgzf.h
../headers//usr/include/samtools/bam.h
../headers//usr/include/samtools/sam.h
../headers//usr/include/seqan/basic/debug_test_system.h
../headers//usr/include/seqan/basic/profiling.h
../headers//usr/include/seqan/basic/test_system.h
../headers//usr/include/seqan/basic/alphabet_residue_tabs.h
../headers//usr/include/seqan/basic/metaprogramming_control.h
../headers//usr/include/seqan/basic/alphabet_residue.h
./reads.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/getopt.h
../headers//usr/include/c++/4.9/cxxabi.h
unassigned
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
common.cpp
../headers//usr/include/c++/4.9/ostream
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
./common.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.h
../headers//usr/include/samtools/bam.h
../headers//usr/include/stdlib.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/libio.h
../headers//usr/include/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/locale_facets.h
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/getopt.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/samtools/bgzf.h
../headers//usr/include/samtools/sam.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/new
./tokenize.h
../headers//usr/include/ctype.h
unassigned
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
tokenize.cpp
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/new
GBase.cpp
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.h
../headers//usr/include/ctype.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/sys/stat.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/time.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/x86_64-linux-gnu/bits/stat.h
../headers//usr/include/stdint.h
./GBase.h
../headers//usr/include/stdlib.h
bam_aux.c
./khash.h
./bam.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdint.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/string.h
../headers//usr/include/ctype.h
unassigned
./kstring.h
bam.c
./bam_endian.h
./bam.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./knetfile.h
./bgzf.h
../headers//usr/include/stdlib.h
./sam_header.h
../headers//usr/include/ctype.h
../headers//usr/include/x86_64-linux-gnu/bits/errno.h
../headers//usr/include/string.h
bam_import.c
../headers//usr/include/stdlib.h
./khash.h
./bam.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/zlib.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./kstring.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
./sam_header.h
../headers//usr/include/ctype.h
sam.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdint.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
./knetfile.h
./bgzf.h
./bam.h
./sam.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/string.h
../headers//usr/include/unistd.h
./faidx.h
bam_pileup.c
./bam.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
./knetfile.h
./bgzf.h
../headers//usr/include/stdlib.h
../headers//usr/include/assert.h
faidx.c
./khash.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./faidx.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./razf.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/ctype.h
knetfile.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/x86_64-linux-gnu/bits/time.h
../headers//usr/include/x86_64-linux-gnu/sys/select.h
../headers//usr/include/unistd.h
../headers//usr/include/x86_64-linux-gnu/bits/sockaddr.h
../headers//usr/include/x86_64-linux-gnu/bits/socket.h
../headers//usr/include/netdb.h
./knetfile.h
../headers//usr/include/x86_64-linux-gnu/sys/socket.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/ctype.h
../headers//usr/include/x86_64-linux-gnu/bits/errno.h
../headers//usr/include/fcntl.h
../headers//usr/include/x86_64-linux-gnu/bits/socket_type.h
sam_header.c
./khash.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/string.h
bgzf.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./bgzf.h
./khash.h
../headers//usr/include/stdlib.h
../headers//usr/include/fcntl.h
../headers//usr/include/string.h
kstring.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./kstring.h
../headers//usr/include/stdio.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/ctype.h
razf.c
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/fcntl.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./razf.h
../headers//usr/include/unistd.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
libraries
../libs/lib/x86_64-linux-gnu/libz.so.1
../libs/usr/lib/x86_64-linux-gnu/libstdc++.so.6
../libs/lib/x86_64-linux-gnu/libm.so.6
../libs/lib/x86_64-linux-gnu/libgcc_s.so.1
../libs/lib/x86_64-linux-gnu/libpthread.so.0
../libs/lib/x86_64-linux-gnu/libc.so.6
manual
gtf_juncs
compile units
unassigned
gtf_juncs.cpp
Gimple
./gtf_juncs.cpp.004t.gimple
GKD
./gtf_juncs.o.gkd
OBJ
obj: ./gtf_juncs.o
unassigned
common.cpp
Gimple
./common.cpp.004t.gimple
GKD
./common.o.gkd
OBJ
obj: ./common.o
unassigned
tokenize.cpp
Gimple
./tokenize.cpp.004t.gimple
GKD
./tokenize.o.gkd
OBJ
obj: ./tokenize.o
GBase.cpp
Gimple
./GBase.cpp.004t.gimple
GKD
./GBase.o.gkd
OBJ
obj: ./GBase.o
unassigned
gff.cpp
Gimple
./gff.cpp.004t.gimple
GKD
./gff.o.gkd
OBJ
obj: ./gff.o
codons.cpp
Gimple
./codons.cpp.004t.gimple
GKD
./codons.o.gkd
OBJ
obj: ./codons.o
gdna.cpp
Gimple
./gdna.cpp.004t.gimple
GKD
./gdna.o.gkd
OBJ
obj: ./gdna.o
GFaSeqGet.cpp
Gimple
./GFaSeqGet.cpp.004t.gimple
GKD
./GFaSeqGet.o.gkd
OBJ
obj: ./GFaSeqGet.o
bam_aux.c
Gimple
./bam_aux.c.004t.gimple
GKD
./bam_aux.o.gkd
OBJ
obj: ./bam_aux.o
unassigned
bam.c
Gimple
./bam.c.004t.gimple
GKD
./bam.o.gkd
OBJ
obj: ./bam.o
bam_import.c
Gimple
./bam_import.c.004t.gimple
GKD
./bam_import.o.gkd
OBJ
obj: ./bam_import.o
sam.c
Gimple
./sam.c.004t.gimple
GKD
./sam.o.gkd
OBJ
obj: ./sam.o
bam_pileup.c
Gimple
./bam_pileup.c.004t.gimple
GKD
./bam_pileup.o.gkd
OBJ
obj: ./bam_pileup.o
faidx.c
Gimple
./faidx.c.004t.gimple
GKD
./faidx.o.gkd
OBJ
obj: ./faidx.o
knetfile.c
Gimple
./knetfile.c.004t.gimple
GKD
./knetfile.o.gkd
OBJ
obj: ./knetfile.o
sam_header.c
Gimple
./sam_header.c.004t.gimple
GKD
./sam_header.o.gkd
OBJ
obj: ./sam_header.o
bgzf.c
Gimple
./bgzf.c.004t.gimple
GKD
./bgzf.o.gkd
OBJ
obj: ./bgzf.o
kstring.c
Gimple
./kstring.c.004t.gimple
GKD
./kstring.o.gkd
OBJ
obj: ./kstring.o
razf.c
Gimple
./razf.c.004t.gimple
GKD
./razf.o.gkd
OBJ
obj: ./razf.o
includes
unassigned
./GHash.hh
./GList.hh
gtf_juncs.cpp
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
./GVec.hh
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
./gff.h
../headers//usr/include/c++/4.9/bits/stl_tree.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
./bwt_map.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/bits/stl_map.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
./GBase.h
../headers//usr/include/c++/4.9/bits/stl_pair.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/stl_list.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/stl_function.h
../headers//usr/include/c++/4.9/bits/stl_set.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/new
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
./GFaSeqGet.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/wctype.h
../headers//usr/include/seqan/basic/debug_test_system.h
../headers//usr/include/seqan/basic/profiling.h
../headers//usr/include/seqan/basic/alphabet_residue_tabs.h
../headers//usr/include/seqan/basic/metaprogramming_control.h
../headers//usr/include/seqan/basic/alphabet_residue.h
./reads.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/getopt.h
./common.h
../headers//usr/include/c++/4.9/cxxabi.h
unassigned
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
common.cpp
../headers//usr/include/c++/4.9/ostream
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
./common.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.h
../headers//usr/include/samtools/bam.h
../headers//usr/include/stdlib.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/libio.h
../headers//usr/include/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/locale_facets.h
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/getopt.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/samtools/bgzf.h
../headers//usr/include/samtools/sam.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/new
./tokenize.h
../headers//usr/include/ctype.h
unassigned
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
tokenize.cpp
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/new
GBase.cpp
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.h
../headers//usr/include/ctype.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/sys/stat.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/time.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/x86_64-linux-gnu/bits/stat.h
../headers//usr/include/stdint.h
./GBase.h
../headers//usr/include/stdlib.h
unassigned
./GList.hh
./GBase.h
./GVec.hh
./gff.h
./GHash.hh
gff.cpp
../headers//usr/include/x86_64-linux-gnu/bits/string3.h
./codons.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/ctype.h
../headers//usr/include/string.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/bits/confname.h
./GFaSeqGet.h
./gdna.h
../headers//usr/include/stdlib.h
codons.cpp
../headers//usr/include/x86_64-linux-gnu/bits/string3.h
../headers//usr/include/ctype.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/libio.h
./GBase.h
./codons.h
../headers//usr/include/stdio.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/confname.h
gdna.cpp
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/libio.h
./GBase.h
../headers//usr/include/stdio.h
../headers//usr/include/x86_64-linux-gnu/bits/confname.h
../headers//usr/include/string.h
GFaSeqGet.cpp
../headers//usr/include/x86_64-linux-gnu/bits/string3.h
./GFaSeqGet.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/ctype.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./GBase.h
./gdna.h
bam_aux.c
./khash.h
./bam.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdint.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/string.h
../headers//usr/include/ctype.h
unassigned
./kstring.h
bam.c
./bam_endian.h
./bam.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./knetfile.h
./bgzf.h
../headers//usr/include/stdlib.h
./sam_header.h
../headers//usr/include/ctype.h
../headers//usr/include/x86_64-linux-gnu/bits/errno.h
../headers//usr/include/string.h
bam_import.c
../headers//usr/include/stdlib.h
./khash.h
./bam.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/zlib.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./kstring.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
./sam_header.h
../headers//usr/include/ctype.h
sam.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdint.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
./knetfile.h
./bgzf.h
./bam.h
./sam.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/string.h
../headers//usr/include/unistd.h
./faidx.h
bam_pileup.c
./bam.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
./knetfile.h
./bgzf.h
../headers//usr/include/stdlib.h
../headers//usr/include/assert.h
faidx.c
./khash.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./faidx.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./razf.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/ctype.h
knetfile.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/x86_64-linux-gnu/bits/time.h
../headers//usr/include/x86_64-linux-gnu/sys/select.h
../headers//usr/include/unistd.h
../headers//usr/include/x86_64-linux-gnu/bits/sockaddr.h
../headers//usr/include/x86_64-linux-gnu/bits/socket.h
../headers//usr/include/netdb.h
./knetfile.h
../headers//usr/include/x86_64-linux-gnu/sys/socket.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/ctype.h
../headers//usr/include/x86_64-linux-gnu/bits/errno.h
../headers//usr/include/fcntl.h
../headers//usr/include/x86_64-linux-gnu/bits/socket_type.h
sam_header.c
./khash.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/string.h
bgzf.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./bgzf.h
./khash.h
../headers//usr/include/stdlib.h
../headers//usr/include/fcntl.h
../headers//usr/include/string.h
kstring.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./kstring.h
../headers//usr/include/stdio.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/ctype.h
razf.c
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/fcntl.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./razf.h
../headers//usr/include/unistd.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
libraries
../libs/lib/x86_64-linux-gnu/libz.so.1
../libs/usr/lib/x86_64-linux-gnu/libstdc++.so.6
../libs/lib/x86_64-linux-gnu/libm.so.6
../libs/lib/x86_64-linux-gnu/libgcc_s.so.1
../libs/lib/x86_64-linux-gnu/libpthread.so.0
../libs/lib/x86_64-linux-gnu/libc.so.6
manual
juncs_db
compile units
unassigned
juncs_db.cpp
Gimple
./juncs_db.cpp.004t.gimple
GKD
./juncs_db.o.gkd
OBJ
obj: ./juncs_db.o
unassigned
common.cpp
Gimple
./common.cpp.004t.gimple
GKD
./common.o.gkd
OBJ
obj: ./common.o
unassigned
tokenize.cpp
Gimple
./tokenize.cpp.004t.gimple
GKD
./tokenize.o.gkd
OBJ
obj: ./tokenize.o
bam_aux.c
Gimple
./bam_aux.c.004t.gimple
GKD
./bam_aux.o.gkd
OBJ
obj: ./bam_aux.o
unassigned
bam.c
Gimple
./bam.c.004t.gimple
GKD
./bam.o.gkd
OBJ
obj: ./bam.o
bam_import.c
Gimple
./bam_import.c.004t.gimple
GKD
./bam_import.o.gkd
OBJ
obj: ./bam_import.o
sam.c
Gimple
./sam.c.004t.gimple
GKD
./sam.o.gkd
OBJ
obj: ./sam.o
bam_pileup.c
Gimple
./bam_pileup.c.004t.gimple
GKD
./bam_pileup.o.gkd
OBJ
obj: ./bam_pileup.o
faidx.c
Gimple
./faidx.c.004t.gimple
GKD
./faidx.o.gkd
OBJ
obj: ./faidx.o
knetfile.c
Gimple
./knetfile.c.004t.gimple
GKD
./knetfile.o.gkd
OBJ
obj: ./knetfile.o
sam_header.c
Gimple
./sam_header.c.004t.gimple
GKD
./sam_header.o.gkd
OBJ
obj: ./sam_header.o
bgzf.c
Gimple
./bgzf.c.004t.gimple
GKD
./bgzf.o.gkd
OBJ
obj: ./bgzf.o
kstring.c
Gimple
./kstring.c.004t.gimple
GKD
./kstring.o.gkd
OBJ
obj: ./kstring.o
razf.c
Gimple
./razf.c.004t.gimple
GKD
./razf.o.gkd
OBJ
obj: ./razf.o
includes
unassigned
../headers//usr/include/c++/4.9/bits/locale_facets.h
juncs_db.cpp
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/ostream
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/seqan/sequence/string_packed.h
../headers//usr/include/seqan/basic/iterator_adaptor.h
../headers//usr/include/seqan/stream/adapt_fstream.h
../headers//usr/include/seqan/basic/alphabet_residue.h
../headers//usr/include/seqan/basic/iterator_interface.h
../headers//usr/include/c++/4.9/bits/stl_tree.h
./bwt_map.h
../headers//usr/include/c++/4.9/bits/stl_map.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/seqan/file/file_format_fasta.h
../headers//usr/include/seqan/file/stream.h
../headers//usr/include/seqan/sequence/string_alloc.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/seqan/sequence/string_base.h
../headers//usr/include/seqan/basic/alphabet_simple_type.h
../headers//usr/include/seqan/sequence/sequence_interface.h
../headers//usr/include/seqan/basic/allocator_interface.h
../headers//usr/include/c++/4.9/bits/stl_algobase.h
./junctions.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_iterator.h
./insertions.h
./fusions.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers//usr/include/c++/4.9/bits/stl_pair.h
../headers//usr/include/seqan/sequence/adapt_array_pointer.h
../headers//usr/include/seqan/sequence/segment_base.h
../headers//usr/include/seqan/basic/array_construct_destruct.h
../headers//usr/include/seqan/file/stream_algorithms.h
../headers//usr/include/seqan/modifier/modifier_view.h
../headers//usr/include/seqan/modifier/modifier_reverse.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/c++/4.9/bits/stl_set.h
../headers//usr/include/seqan/sequence/string_cstyle.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/wchar.h
../headers//usr/include/_G_config.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/ostream.tcc
../headers//usr/include/c++/4.9/istream
../headers//usr/include/c++/4.9/streambuf
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/stl_list.h
../headers//usr/include/c++/4.9/bits/stl_function.h
../headers//usr/include/c++/4.9/fstream
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/c++/4.9/bits/basic_ios.tcc
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/new
../headers//usr/include/c++/4.9/bits/ostream_insert.h
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/wctype.h
../headers//usr/include/stdint.h
../headers//usr/include/seqan/platform/platform_gcc.h
../headers//usr/include/seqan/basic/debug_test_system.h
../headers//usr/include/seqan/basic/profiling.h
../headers//usr/include/seqan/basic/metaprogramming_logic.h
../headers//usr/include/seqan/basic/alphabet_residue_tabs.h
../headers//usr/include/seqan/basic/fundamental_tags.h
../headers//usr/include/seqan/basic/container_concept.h
../headers//usr/include/seqan/modifier/modifier_functors.h
../headers//usr/include/seqan/basic/basic_type.h
../headers//usr/include/seqan/stream/adapt_iostream.h
../headers//usr/include/seqan/basic/alphabet_math.h
../headers//usr/include/seqan/basic/metaprogramming_type.h
../headers//usr/include/seqan/sequence/segment_infix.h
../headers//usr/include/seqan/basic/proxy_iterator.h
../headers//usr/include/seqan/basic/fundamental_conversion.h
../headers//usr/include/seqan/sequence/adapt_std_string.h
../headers//usr/include/seqan/basic/alphabet_adapt_builtins.h
../headers//usr/include/seqan/basic/fundamental_transport.h
../headers//usr/include/seqan/basic/iterator_base.h
../headers//usr/include/seqan/file/file_format_raw.h
../headers//usr/include/seqan/modifier/modifier_shortcuts.h
../headers//usr/include/seqan/sequence/sequence_shortcuts.h
../headers//usr/include/seqan/basic/metaprogramming_control.h
../headers//usr/include/seqan/random/random_normal.h
../headers//usr/include/samtools/bgzf.h
../headers//usr/include/samtools/bam.h
../headers//usr/include/samtools/sam.h
./reads.h
./deletions.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/getopt.h
./common.h
./tokenize.h
../headers//usr/include/c++/4.9/cxxabi.h
../headers//usr/include/seqan/random/ext_MersenneTwister.h
../headers//usr/include/seqan/file/file_format_mmap.h
unassigned
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
common.cpp
../headers//usr/include/c++/4.9/ostream
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
./common.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.h
../headers//usr/include/samtools/bam.h
../headers//usr/include/stdlib.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/libio.h
../headers//usr/include/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/locale_facets.h
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/getopt.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/samtools/bgzf.h
../headers//usr/include/samtools/sam.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/new
./tokenize.h
../headers//usr/include/ctype.h
unassigned
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
tokenize.cpp
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/new
bam_aux.c
./khash.h
./bam.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdint.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/string.h
../headers//usr/include/ctype.h
unassigned
./kstring.h
bam.c
./bam_endian.h
./bam.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./knetfile.h
./bgzf.h
../headers//usr/include/stdlib.h
./sam_header.h
../headers//usr/include/ctype.h
../headers//usr/include/x86_64-linux-gnu/bits/errno.h
../headers//usr/include/string.h
bam_import.c
../headers//usr/include/stdlib.h
./khash.h
./bam.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/zlib.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./kstring.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
./sam_header.h
../headers//usr/include/ctype.h
sam.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdint.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
./knetfile.h
./bgzf.h
./bam.h
./sam.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/string.h
../headers//usr/include/unistd.h
./faidx.h
bam_pileup.c
./bam.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
./knetfile.h
./bgzf.h
../headers//usr/include/stdlib.h
../headers//usr/include/assert.h
faidx.c
./khash.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./faidx.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./razf.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/ctype.h
knetfile.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/x86_64-linux-gnu/bits/time.h
../headers//usr/include/x86_64-linux-gnu/sys/select.h
../headers//usr/include/unistd.h
../headers//usr/include/x86_64-linux-gnu/bits/sockaddr.h
../headers//usr/include/x86_64-linux-gnu/bits/socket.h
../headers//usr/include/netdb.h
./knetfile.h
../headers//usr/include/x86_64-linux-gnu/sys/socket.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/ctype.h
../headers//usr/include/x86_64-linux-gnu/bits/errno.h
../headers//usr/include/fcntl.h
../headers//usr/include/x86_64-linux-gnu/bits/socket_type.h
sam_header.c
./khash.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/string.h
bgzf.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./bgzf.h
./khash.h
../headers//usr/include/stdlib.h
../headers//usr/include/fcntl.h
../headers//usr/include/string.h
kstring.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./kstring.h
../headers//usr/include/stdio.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/ctype.h
razf.c
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/fcntl.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./razf.h
../headers//usr/include/unistd.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
libraries
../libs/lib/x86_64-linux-gnu/libz.so.1
../libs/usr/lib/x86_64-linux-gnu/libstdc++.so.6
../libs/lib/x86_64-linux-gnu/libm.so.6
../libs/lib/x86_64-linux-gnu/libgcc_s.so.1
../libs/lib/x86_64-linux-gnu/libpthread.so.0
../libs/lib/x86_64-linux-gnu/libc.so.6
manual
tophat_reports
compile units
unassigned
tophat_reports.cpp
Gimple
./tophat_reports.cpp.004t.gimple
GKD
./tophat_reports.o.gkd
OBJ
obj: ./tophat_reports.o
unassigned
reads.cpp
Gimple
./reads.cpp.004t.gimple
GKD
./reads.o.gkd
OBJ
obj: ./reads.o
unassigned
bwt_map.cpp
Gimple
./bwt_map.cpp.004t.gimple
GKD
./bwt_map.o.gkd
OBJ
obj: ./bwt_map.o
unassigned
common.cpp
Gimple
./common.cpp.004t.gimple
GKD
./common.o.gkd
OBJ
obj: ./common.o
unassigned
junctions.cpp
Gimple
./junctions.cpp.004t.gimple
GKD
./junctions.o.gkd
OBJ
obj: ./junctions.o
unassigned
insertions.cpp
Gimple
./insertions.cpp.004t.gimple
GKD
./insertions.o.gkd
OBJ
obj: ./insertions.o
deletions.cpp
Gimple
./deletions.cpp.004t.gimple
GKD
./deletions.o.gkd
OBJ
obj: ./deletions.o
unassigned
fusions.cpp
Gimple
./fusions.cpp.004t.gimple
GKD
./fusions.o.gkd
OBJ
obj: ./fusions.o
align_status.cpp
Gimple
./align_status.cpp.004t.gimple
GKD
./align_status.o.gkd
OBJ
obj: ./align_status.o
unassigned
tokenize.cpp
Gimple
./tokenize.cpp.004t.gimple
GKD
./tokenize.o.gkd
OBJ
obj: ./tokenize.o
inserts.cpp
Gimple
./inserts.cpp.004t.gimple
GKD
./inserts.o.gkd
OBJ
obj: ./inserts.o
bam_merge_impl.cpp
Gimple
./bam_merge_impl.cpp.004t.gimple
GKD
./bam_merge_impl.o.gkd
OBJ
obj: ./bam_merge_impl.o
unassigned
utils.cpp
Gimple
./utils.cpp.004t.gimple
GKD
./utils.o.gkd
OBJ
obj: ./utils.o
coverage.cpp
Gimple
./coverage.cpp.004t.gimple
GKD
./coverage.o.gkd
OBJ
obj: ./coverage.o
bgzf.c
Gimple
./bgzf.c.004t.gimple
GKD
./bgzf.o.gkd
OBJ
obj: ./bgzf.o
bam_aux.c
Gimple
./bam_aux.c.004t.gimple
GKD
./bam_aux.o.gkd
OBJ
obj: ./bam_aux.o
unassigned
bam.c
Gimple
./bam.c.004t.gimple
GKD
./bam.o.gkd
OBJ
obj: ./bam.o
bam_import.c
Gimple
./bam_import.c.004t.gimple
GKD
./bam_import.o.gkd
OBJ
obj: ./bam_import.o
sam.c
Gimple
./sam.c.004t.gimple
GKD
./sam.o.gkd
OBJ
obj: ./sam.o
bam_pileup.c
Gimple
./bam_pileup.c.004t.gimple
GKD
./bam_pileup.o.gkd
OBJ
obj: ./bam_pileup.o
faidx.c
Gimple
./faidx.c.004t.gimple
GKD
./faidx.o.gkd
OBJ
obj: ./faidx.o
knetfile.c
Gimple
./knetfile.c.004t.gimple
GKD
./knetfile.o.gkd
OBJ
obj: ./knetfile.o
sam_header.c
Gimple
./sam_header.c.004t.gimple
GKD
./sam_header.o.gkd
OBJ
obj: ./sam_header.o
kstring.c
Gimple
./kstring.c.004t.gimple
GKD
./kstring.o.gkd
OBJ
obj: ./kstring.o
razf.c
Gimple
./razf.c.004t.gimple
GKD
./razf.o.gkd
OBJ
obj: ./razf.o
includes
unassigned
../headers//usr/include/c++/4.9/bits/locale_facets.h
../headers//usr/include/boost/smart_ptr/detail/sp_counted_base_gcc_x86.hpp
../headers//usr/include/boost/exception/info.hpp
./reads.h
../headers//usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp
tophat_reports.cpp
../headers//usr/include/boost/checked_delete.hpp
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/boost/system/system_error.hpp
./bwt_map.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_algo.h
../headers//usr/include/c++/4.9/typeinfo
../headers//usr/include/boost/exception/detail/exception_ptr.hpp
../headers//usr/include/c++/4.9/bits/stl_tree.h
./junctions.h
../headers//usr/include/boost/thread/exceptions.hpp
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/boost/system/error_code.hpp
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_pair.h
./fusions.h
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/boost/smart_ptr/shared_ptr.hpp
../headers//usr/include/boost/smart_ptr/detail/shared_count.hpp
../headers//usr/include/c++/4.9/ostream
../headers//usr/include/c++/4.9/sstream
../headers//usr/include/c++/4.9/streambuf
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/boost/exception/exception.hpp
../headers//usr/include/c++/4.9/stdexcept
./common.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.h
../headers//usr/include/boost/thread/detail/thread.hpp
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/boost/random/mersenne_twister.hpp
../headers//usr/include/boost/thread/pthread/thread_data.hpp
../headers//usr/include/c++/4.9/bits/stl_map.h
./inserts.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/boost/throw_exception.hpp
../headers//usr/include/boost/thread/pthread/mutex.hpp
../headers//usr/include/boost/smart_ptr/weak_ptr.hpp
../headers//usr/include/boost/thread/pthread/condition_variable_fwd.hpp
../headers//usr/include/seqan/file/file_format_fasta.h
../headers//usr/include/seqan/file/stream.h
../headers//usr/include/seqan/sequence/string_packed.h
../headers//usr/include/seqan/sequence/string_alloc.h
../headers//usr/include/seqan/sequence/string_base.h
../headers//usr/include/seqan/basic/iterator_adaptor.h
../headers//usr/include/seqan/basic/alphabet_simple_type.h
../headers//usr/include/seqan/basic/iterator_interface.h
../headers//usr/include/seqan/sequence/sequence_interface.h
../headers//usr/include/seqan/basic/allocator_interface.h
../headers//usr/include/c++/4.9/bits/stl_heap.h
../headers//usr/include/c++/4.9/bits/stl_queue.h
./bam_merge.h
../headers//usr/include/c++/4.9/bits/stl_function.h
../headers//usr/include/c++/4.9/fstream
../headers//usr/include/c++/4.9/istream
../headers//usr/include/c++/4.9/bits/move.h
./insertions.h
../headers//usr/include/boost/thread/pthread/thread_heap_alloc.hpp
../headers//usr/include/boost/smart_ptr/enable_shared_from_this.hpp
./coverage.h
../headers//usr/include/string.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/wchar.h
../headers//usr/include/_G_config.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/new
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/istream.tcc
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h
../headers//usr/include/c++/4.9/iomanip
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/limits
../headers//usr/include/c++/4.9/bits/stl_list.h
../headers//usr/include/c++/4.9/exception
../headers//usr/include/c++/4.9/bits/list.tcc
../headers//usr/include/c++/4.9/bits/basic_ios.tcc
../headers//usr/include/c++/4.9/bits/sstream.tcc
../headers//usr/include/c++/4.9/bits/stl_iterator_base_funcs.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/ostream_insert.h
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/c++/4.9/ext/type_traits.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/bits/pthreadtypes.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/wctype.h
../headers//usr/include/stdint.h
../headers//usr/include/seqan/platform/platform_gcc.h
../headers//usr/include/seqan/basic/debug_test_system.h
../headers//usr/include/seqan/basic/profiling.h
../headers//usr/include/seqan/basic/metaprogramming_logic.h
../headers//usr/include/seqan/basic/alphabet_residue.h
../headers//usr/include/seqan/basic/alphabet_residue_tabs.h
../headers//usr/include/seqan/basic/fundamental_tags.h
../headers//usr/include/seqan/basic/container_concept.h
../headers//usr/include/seqan/modifier/modifier_functors.h
../headers//usr/include/seqan/stream/adapt_iostream.h
../headers//usr/include/seqan/basic/alphabet_math.h
../headers//usr/include/seqan/basic/basic_type.h
../headers//usr/include/seqan/basic/proxy_iterator.h
../headers//usr/include/seqan/sequence/adapt_std_string.h
../headers//usr/include/seqan/basic/metaprogramming_type.h
../headers//usr/include/seqan/basic/alphabet_adapt_builtins.h
../headers//usr/include/seqan/basic/array_construct_destruct.h
../headers//usr/include/seqan/basic/fundamental_transport.h
../headers//usr/include/seqan/basic/iterator_base.h
../headers//usr/include/seqan/basic/metaprogramming_control.h
../headers//usr/include/seqan/random/random_normal.h
../headers//usr/include/boost/config/suffix.hpp
../headers//usr/include/boost/cstdint.hpp
../headers//usr/include/boost/iterator.hpp
../headers//usr/include/boost/operators.hpp
../headers//usr/include/boost/detail/sp_typeinfo.hpp
../headers//usr/include/boost/smart_ptr/detail/sp_convertible.hpp
../headers//usr/include/boost/smart_ptr/detail/spinlock_sync.hpp
../headers//usr/include/boost/smart_ptr/detail/spinlock_pool.hpp
../headers//usr/include/boost/integer_traits.hpp
../headers//usr/include/boost/none_t.hpp
../headers//usr/include/boost/thread/tss.hpp
../headers//usr/include/boost/thread/future.hpp
../headers//usr/include/boost/integer/static_log2.hpp
../headers//usr/include/boost/thread/detail/move.hpp
../headers//usr/include/boost/function/function_base.hpp
../headers//usr/include/boost/function/function_template.hpp
../headers//usr/include/boost/noncopyable.hpp
../headers//usr/include/boost/thread/future_error_code.hpp
../headers//usr/include/boost/mpl/aux_/adl_barrier.hpp
../headers//usr/include/boost/mpl/integral_c_tag.hpp
../headers//usr/include/boost/mpl/bool_fwd.hpp
../headers//usr/include/boost/mpl/void_fwd.hpp
../headers//usr/include/boost/mpl/aux_/na_fwd.hpp
../headers//usr/include/boost/type_traits/detail/yes_no_type.hpp
../headers//usr/include/boost/move/detail/meta_utils.hpp
../headers//usr/include/boost/thread/lock_options.hpp
../headers//usr/include/boost/exception/detail/type_info.hpp
../headers//usr/include/boost/exception/detail/error_info_impl.hpp
../headers//usr/include/boost/exception/to_string_stub.hpp
../headers//usr/include/boost/exception/detail/clone_current_exception.hpp
../headers//usr/include/boost/date_time/c_time.hpp
../headers//usr/include/boost/date_time/time_defs.hpp
../headers//usr/include/boost/date_time/special_defs.hpp
../headers//usr/include/boost/date_time/time_resolution_traits.hpp
../headers//usr/include/boost/date_time/int_adapter.hpp
../headers//usr/include/boost/date_time/date_defs.hpp
../headers//usr/include/boost/date_time/year_month_day.hpp
../headers//usr/include/boost/date_time/gregorian_calendar.hpp
../headers//usr/include/boost/date_time/gregorian_calendar.ipp
../headers//usr/include/boost/date_time/date_duration.hpp
../headers//usr/include/boost/date_time/date.hpp
../headers//usr/include/boost/date_time/time_duration.hpp
../headers//usr/include/boost/date_time/time_system_counted.hpp
../headers//usr/include/boost/date_time/time.hpp
../headers//usr/include/boost/date_time/constrained_value.hpp
../headers//usr/include/boost/date_time/gregorian/greg_weekday.hpp
../headers//usr/include/boost/date_time/gregorian/greg_day.hpp
../headers//usr/include/boost/date_time/gregorian/greg_year.hpp
../headers//usr/include/boost/date_time/gregorian/greg_month.hpp
../headers//usr/include/boost/date_time/gregorian/greg_calendar.hpp
../headers//usr/include/boost/date_time/gregorian/greg_day_of_year.hpp
../headers//usr/include/boost/date_time/gregorian/greg_duration.hpp
../headers//usr/include/boost/date_time/gregorian/greg_date.hpp
../headers//usr/include/boost/date_time/posix_time/posix_time_config.hpp
../headers//usr/include/boost/date_time/posix_time/ptime.hpp
../headers//usr/include/boost/ratio/detail/overflow_helpers.hpp
../headers//usr/include/boost/type_traits/add_rvalue_reference.hpp
../headers//usr/include/boost/chrono/detail/is_evenly_divisible_by.hpp
../headers//usr/include/boost/chrono/duration.hpp
../headers//usr/include/boost/chrono/system_clocks.hpp
../headers//usr/include/boost/chrono/time_point.hpp
../headers//usr/include/boost/thread/xtime.hpp
../headers//usr/include/boost/thread/thread_time.hpp
../headers//usr/include/boost/ratio/ratio.hpp
../headers//usr/include/boost/thread/pthread/pthread_mutex_scoped_lock.hpp
../headers//usr/include/boost/thread/lock_types.hpp
../headers//usr/include/boost/thread/cv_status.hpp
../headers//usr/include/boost/type_traits/type_with_alignment.hpp
../headers//usr/include/boost/optional/optional.hpp
../headers//usr/include/boost/smart_ptr/detail/operator_bool.hpp
../headers//usr/include/boost/thread/lock_guard.hpp
../headers//usr/include/seqan/random/ext_MersenneTwister.h
../headers//usr/include/boost/bind/storage.hpp
../headers//usr/include/boost/bind/arg.hpp
../headers//usr/include/boost/io_fwd.hpp
../headers//usr/include/boost/integer_fwd.hpp
../headers//usr/include/boost/functional/hash/detail/float_functions.hpp
../headers//usr/include/boost/thread/pthread/condition_variable.hpp
../headers//usr/include/boost/atomic/detail/gcc-atomic.hpp
../headers//usr/include/boost/thread/lockable_traits.hpp
../headers//usr/include/boost/tuple/detail/tuple_basic.hpp
../headers//usr/include/boost/exception/detail/is_output_streamable.hpp
../headers//usr/include/boost/exception/to_string.hpp
../headers//usr/include/boost/utility/enable_if.hpp
../headers//usr/include/boost/random/detail/ptr_helper.hpp
../headers//usr/include/boost/smart_ptr/bad_weak_ptr.hpp
../headers//usr/include/boost/detail/scoped_enum_emulation.hpp
../headers//usr/include/boost/none.hpp
../headers//usr/include/boost/mpl/bool.hpp
../headers//usr/include/boost/mpl/void.hpp
../headers//usr/include/boost/mpl/aux_/integral_wrapper.hpp
../headers//usr/include/boost/bind/placeholders.hpp
../headers//usr/include/samtools/bgzf.h
../headers//usr/include/samtools/bam.h
../headers//usr/include/samtools/sam.h
./utils.h
./deletions.h
./align_status.h
../headers//usr/include/getopt.h
../headers//usr/include/pthread.h
./tokenize.h
../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h
../headers//usr/include/c++/4.9/cxxabi.h
unassigned
./reads.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
./common.h
reads.cpp
../headers//usr/include/c++/4.9/bits/stl_algo.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/stdlib.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers//usr/include/c++/4.9/bits/stl_heap.h
../headers//usr/include/c++/4.9/bits/stl_queue.h
../headers//usr/include/seqan/sequence/string_base.h
../headers//usr/include/seqan/sequence/sequence_interface.h
../headers//usr/include/seqan/sequence/string_alloc.h
../headers//usr/include/seqan/basic/allocator_interface.h
../headers//usr/include/seqan/sequence/adapt_array_pointer.h
../headers//usr/include/seqan/sequence/adapt_std_string.h
../headers//usr/include/seqan/basic/array_construct_destruct.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/libio.h
../headers//usr/include/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/new
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/stl_list.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/stdint.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/seqan/basic/debug_test_system.h
../headers//usr/include/seqan/basic/profiling.h
../headers//usr/include/seqan/basic/metaprogramming_logic.h
../headers//usr/include/seqan/basic/alphabet_residue_tabs.h
../headers//usr/include/seqan/basic/fundamental_tags.h
../headers//usr/include/seqan/basic/container_concept.h
../headers//usr/include/seqan/basic/iterator_interface.h
../headers//usr/include/seqan/modifier/modifier_functors.h
../headers//usr/include/seqan/basic/basic_type.h
../headers//usr/include/seqan/basic/alphabet_math.h
../headers//usr/include/seqan/basic/iterator_adapt_std.h
../headers//usr/include/seqan/basic/iterator_base.h
../headers//usr/include/seqan/basic/metaprogramming_control.h
../headers//usr/include/seqan/basic/alphabet_residue.h
../headers//usr/include/seqan/random/random_normal.h
../headers//usr/include/samtools/bgzf.h
../headers//usr/include/samtools/bam.h
../headers//usr/include/samtools/sam.h
./bwt_map.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
./tokenize.h
../headers//usr/include/ctype.h
../headers//usr/include/c++/4.9/cxxabi.h
../headers//usr/include/seqan/random/ext_MersenneTwister.h
unassigned
../headers//usr/include/c++/4.9/bits/locale_facets.h
./bwt_map.h
bwt_map.cpp
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/string.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
./common.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_tree.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/c++/4.9/bits/stl_bvector.h
../headers//usr/include/stdlib.h
../headers//usr/include/c++/4.9/bits/stl_algo.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_pair.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/bits/stl_map.h
../headers//usr/include/c++/4.9/bits/stl_heap.h
../headers//usr/include/seqan/sequence/string_base.h
../headers//usr/include/seqan/sequence/sequence_interface.h
../headers//usr/include/seqan/sequence/string_alloc.h
../headers//usr/include/seqan/basic/allocator_interface.h
../headers//usr/include/seqan/basic/alphabet_simple_type.h
../headers//usr/include/seqan/sequence/segment_base.h
../headers//usr/include/seqan/sequence/string_packed.h
../headers//usr/include/seqan/basic/iterator_adaptor.h
../headers//usr/include/seqan/basic/array_construct_destruct.h
../headers//usr/include/seqan/basic/iterator_interface.h
../headers//usr/include/seqan/sequence/segment_infix.h
../headers//usr/include/seqan/basic/alphabet_residue.h
../headers//usr/include/c++/4.9/ostream
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/seqan/modifier/modifier_view.h
../headers//usr/include/seqan/modifier/modifier_reverse.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/time.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/new
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/ostream.tcc
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/backward/auto_ptr.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/stl_list.h
../headers//usr/include/c++/4.9/bits/stl_function.h
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_funcs.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/c++/4.9/bits/ostream_insert.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/c++/4.9/ext/type_traits.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/wchar.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/stdint.h
../headers//usr/include/seqan/platform/platform_gcc.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/seqan/basic/debug_test_system.h
../headers//usr/include/seqan/basic/profiling.h
../headers//usr/include/seqan/basic/metaprogramming_logic.h
../headers//usr/include/seqan/basic/test_system.h
../headers//usr/include/seqan/basic/alphabet_residue_tabs.h
../headers//usr/include/seqan/basic/fundamental_tags.h
../headers//usr/include/seqan/basic/container_concept.h
../headers//usr/include/seqan/modifier/modifier_functors.h
../headers//usr/include/seqan/basic/alphabet_math.h
../headers//usr/include/seqan/basic/metaprogramming_type.h
../headers//usr/include/seqan/basic/basic_type.h
../headers//usr/include/seqan/basic/fundamental_conversion.h
../headers//usr/include/seqan/basic/iterator_base.h
../headers//usr/include/seqan/modifier/modifier_shortcuts.h
../headers//usr/include/seqan/sequence/sequence_shortcuts.h
../headers//usr/include/seqan/basic/metaprogramming_control.h
../headers//usr/include/seqan/random/random_normal.h
../headers//usr/include/samtools/bgzf.h
../headers//usr/include/samtools/bam.h
../headers//usr/include/samtools/sam.h
./reads.h
./junctions.h
./insertions.h
./deletions.h
./fusions.h
./align_status.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/ctype.h
./tokenize.h
../headers//usr/include/c++/4.9/cxxabi.h
../headers//usr/include/seqan/random/ext_MersenneTwister.h
unassigned
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
common.cpp
../headers//usr/include/c++/4.9/ostream
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
./common.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.h
../headers//usr/include/samtools/bam.h
../headers//usr/include/stdlib.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/libio.h
../headers//usr/include/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/locale_facets.h
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/getopt.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/samtools/bgzf.h
../headers//usr/include/samtools/sam.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/new
./tokenize.h
../headers//usr/include/ctype.h
unassigned
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/bits/stl_tree.h
./junctions.h
./bwt_map.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
junctions.cpp
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/c++/4.9/bits/stl_pair.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_algo.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/bits/stl_map.h
../headers//usr/include/c++/4.9/bits/stl_heap.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/stdint.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/stl_list.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/stl_function.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/new
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdlib.h
../headers//usr/include/time.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/wchar.h
../headers//usr/include/_G_config.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/samtools/bgzf.h
../headers//usr/include/samtools/bam.h
../headers//usr/include/samtools/sam.h
./common.h
../headers//usr/include/wctype.h
../headers//usr/include/seqan/basic/debug_test_system.h
../headers//usr/include/seqan/basic/profiling.h
../headers//usr/include/seqan/basic/alphabet_residue_tabs.h
../headers//usr/include/seqan/modifier/modifier_functors.h
../headers//usr/include/seqan/basic/alphabet_math.h
../headers//usr/include/seqan/basic/metaprogramming_control.h
../headers//usr/include/seqan/basic/alphabet_residue.h
../headers//usr/include/seqan/random/random_normal.h
./reads.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/cxxabi.h
../headers//usr/include/seqan/random/ext_MersenneTwister.h
unassigned
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
insertions.cpp
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/c++/4.9/bits/stl_tree.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
./bwt_map.h
../headers//usr/include/c++/4.9/bits/char_traits.h
./insertions.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_pair.h
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers//usr/include/c++/4.9/bits/stl_map.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/wchar.h
../headers//usr/include/_G_config.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/stl_list.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/stl_function.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/new
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/string.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/wctype.h
../headers//usr/include/stdint.h
../headers//usr/include/seqan/basic/debug_test_system.h
../headers//usr/include/seqan/basic/profiling.h
../headers//usr/include/seqan/basic/alphabet_residue_tabs.h
../headers//usr/include/seqan/modifier/modifier_functors.h
../headers//usr/include/seqan/basic/alphabet_math.h
../headers//usr/include/seqan/basic/metaprogramming_control.h
../headers//usr/include/seqan/basic/alphabet_residue.h
../headers//usr/include/seqan/random/random_normal.h
./reads.h
./junctions.h
./deletions.h
./fusions.h
./align_status.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
./common.h
../headers//usr/include/c++/4.9/cxxabi.h
../headers//usr/include/seqan/random/ext_MersenneTwister.h
deletions.cpp
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/c++/4.9/bits/stl_tree.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
./bwt_map.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/bits/char_traits.h
./junctions.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
./deletions.h
../headers//usr/include/c++/4.9/bits/stl_pair.h
../headers//usr/include/c++/4.9/bits/stl_map.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/stdint.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/stl_list.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/stl_function.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/new
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdlib.h
../headers//usr/include/time.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/wchar.h
../headers//usr/include/_G_config.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/seqan/basic/debug_test_system.h
../headers//usr/include/seqan/basic/profiling.h
../headers//usr/include/seqan/basic/alphabet_residue_tabs.h
../headers//usr/include/seqan/modifier/modifier_functors.h
../headers//usr/include/seqan/basic/alphabet_math.h
../headers//usr/include/seqan/basic/metaprogramming_control.h
../headers//usr/include/seqan/basic/alphabet_residue.h
../headers//usr/include/seqan/random/random_normal.h
./reads.h
./common.h
../headers//usr/include/c++/4.9/cxxabi.h
../headers//usr/include/seqan/random/ext_MersenneTwister.h
unassigned
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/bits/stl_algo.h
./fusions.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_tree.h
fusions.cpp
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
./reads.h
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/c++/4.9/istream
../headers//usr/include/c++/4.9/ostream
../headers//usr/include/c++/4.9/streambuf
../headers//usr/include/c++/4.9/sstream
../headers//usr/include/seqan/stream/adapt_fstream.h
../headers//usr/include/seqan/file/stream_algorithms.h
../headers//usr/include/seqan/basic/alphabet_residue.h
../headers//usr/include/seqan/stream/adapt_sstream.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/c++/4.9/bits/stl_pair.h
../headers//usr/include/c++/4.9/bits/stl_map.h
./bwt_map.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/bits/stl_heap.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/seqan/sequence/string_base.h
../headers//usr/include/seqan/sequence/sequence_interface.h
../headers//usr/include/seqan/sequence/string_alloc.h
../headers//usr/include/seqan/basic/allocator_interface.h
../headers//usr/include/seqan/basic/alphabet_simple_type.h
../headers//usr/include/seqan/sequence/segment_base.h
../headers//usr/include/seqan/sequence/string_packed.h
../headers//usr/include/seqan/basic/iterator_adaptor.h
../headers//usr/include/seqan/basic/array_construct_destruct.h
../headers//usr/include/seqan/basic/iterator_interface.h
../headers//usr/include/seqan/sequence/segment_infix.h
../headers//usr/include/seqan/modifier/modifier_view.h
../headers//usr/include/seqan/modifier/modifier_reverse.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/wchar.h
../headers//usr/include/_G_config.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/new
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/ostream.tcc
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/stl_list.h
../headers//usr/include/c++/4.9/bits/stl_function.h
../headers//usr/include/c++/4.9/bits/basic_ios.tcc
../headers//usr/include/c++/4.9/bits/stl_iterator_base_funcs.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/string.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/c++/4.9/ext/type_traits.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/wctype.h
../headers//usr/include/stdint.h
../headers//usr/include/seqan/platform/platform_gcc.h
../headers//usr/include/seqan/basic/debug_test_system.h
../headers//usr/include/seqan/basic/profiling.h
../headers//usr/include/seqan/basic/metaprogramming_logic.h
../headers//usr/include/seqan/basic/alphabet_residue_tabs.h
../headers//usr/include/seqan/basic/fundamental_tags.h
../headers//usr/include/seqan/basic/container_concept.h
../headers//usr/include/seqan/modifier/modifier_functors.h
../headers//usr/include/seqan/basic/alphabet_math.h
../headers//usr/include/seqan/basic/metaprogramming_type.h
../headers//usr/include/seqan/basic/basic_type.h
../headers//usr/include/seqan/sequence/adapt_std_string.h
../headers//usr/include/seqan/basic/fundamental_conversion.h
../headers//usr/include/seqan/basic/iterator_base.h
../headers//usr/include/seqan/file/file_format_raw.h
../headers//usr/include/seqan/modifier/modifier_shortcuts.h
../headers//usr/include/seqan/sequence/sequence_shortcuts.h
../headers//usr/include/seqan/basic/metaprogramming_control.h
../headers//usr/include/seqan/random/random_normal.h
./junctions.h
./insertions.h
./deletions.h
./align_status.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
./common.h
../headers//usr/include/c++/4.9/cxxabi.h
../headers//usr/include/seqan/random/ext_MersenneTwister.h
../headers//usr/include/seqan/align/align_base.h
align_status.cpp
../headers//usr/include/c++/4.9/bits/stl_tree.h
./junctions.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
./bwt_map.h
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_map.h
../headers//usr/include/c++/4.9/iostream
./coverage.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdlib.h
../headers//usr/include/time.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/stl_pair.h
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/limits
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/stl_list.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/stl_function.h
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/new
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/wchar.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/stdint.h
../headers//usr/include/string.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/seqan/basic/debug_test_system.h
../headers//usr/include/seqan/basic/profiling.h
../headers//usr/include/seqan/basic/alphabet_residue_tabs.h
../headers//usr/include/seqan/modifier/modifier_functors.h
../headers//usr/include/seqan/basic/alphabet_math.h
../headers//usr/include/seqan/basic/metaprogramming_control.h
../headers//usr/include/seqan/basic/alphabet_residue.h
../headers//usr/include/seqan/random/random_normal.h
./reads.h
./insertions.h
./deletions.h
./fusions.h
./align_status.h
./common.h
../headers//usr/include/c++/4.9/cxxabi.h
../headers//usr/include/seqan/random/ext_MersenneTwister.h
unassigned
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
tokenize.cpp
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/new
inserts.cpp
../headers//usr/include/c++/4.9/bits/stl_vector.h
./bwt_map.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/bits/stl_tree.h
../headers//usr/include/c++/4.9/bits/stl_algo.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
./inserts.h
../headers//usr/include/c++/4.9/bits/stl_pair.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
./junctions.h
../headers//usr/include/c++/4.9/bits/stl_set.h
../headers//usr/include/c++/4.9/bits/stl_map.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/libio.h
../headers//usr/include/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/new
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/limits
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/stl_list.h
../headers//usr/include/c++/4.9/bits/stl_function.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_funcs.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/stdint.h
../headers//usr/include/_G_config.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/seqan/basic/debug_test_system.h
../headers//usr/include/seqan/basic/profiling.h
../headers//usr/include/seqan/basic/alphabet_residue_tabs.h
../headers//usr/include/seqan/modifier/modifier_functors.h
../headers//usr/include/seqan/basic/alphabet_math.h
../headers//usr/include/seqan/basic/metaprogramming_control.h
../headers//usr/include/seqan/basic/alphabet_residue.h
../headers//usr/include/seqan/random/random_normal.h
./reads.h
./common.h
../headers//usr/include/c++/4.9/cxxabi.h
../headers//usr/include/seqan/random/ext_MersenneTwister.h
bam_merge_impl.cpp
../headers//usr/include/stdlib.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers//usr/include/c++/4.9/bits/stl_heap.h
./bam_merge.h
../headers//usr/include/c++/4.9/bits/stl_queue.h
../headers//usr/include/c++/4.9/bits/stl_algo.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/bits/stl_bvector.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/new
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/wchar.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/string.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/x86_64-linux-gnu/bits/confname.h
../headers//usr/include/samtools/bgzf.h
../headers//usr/include/samtools/bam.h
../headers//usr/include/samtools/sam.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
./common.h
unassigned
../headers//usr/include/c++/4.9/bits/locale_facets.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/sstream
../headers//usr/include/c++/4.9/streambuf
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
utils.cpp
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/c++/4.9/istream
../headers//usr/include/c++/4.9/fstream
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/c++/4.9/bits/stl_algo.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/libio.h
../headers//usr/include/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/new
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/istream.tcc
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/bits/stl_pair.h
../headers//usr/include/c++/4.9/bits/basic_ios.tcc
../headers//usr/include/c++/4.9/bits/fstream.tcc
../headers//usr/include/c++/4.9/bits/sstream.tcc
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/bits/pthreadtypes.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
./utils.h
../headers//usr/include/stdint.h
../headers//usr/include/string.h
./common.h
coverage.cpp
../headers//usr/include/c++/4.9/bits/stl_tree.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_map.h
../headers//usr/include/c++/4.9/bits/stl_pair.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/iostream
./coverage.h
../headers//usr/include/libio.h
../headers//usr/include/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/c++/4.9/new
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/limits
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/stl_list.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/stl_function.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/c++/4.9/ext/type_traits.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/stdint.h
../headers//usr/include/string.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/seqan/basic/debug_test_system.h
../headers//usr/include/seqan/basic/profiling.h
../headers//usr/include/seqan/basic/alphabet_residue_tabs.h
../headers//usr/include/seqan/basic/metaprogramming_control.h
../headers//usr/include/seqan/basic/alphabet_residue.h
./bwt_map.h
./reads.h
./common.h
../headers//usr/include/c++/4.9/cxxabi.h
bgzf.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./bgzf.h
./khash.h
../headers//usr/include/stdlib.h
../headers//usr/include/fcntl.h
../headers//usr/include/string.h
bam_aux.c
./khash.h
./bam.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdint.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/string.h
../headers//usr/include/ctype.h
unassigned
./kstring.h
bam.c
./bam_endian.h
./bam.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./knetfile.h
./bgzf.h
../headers//usr/include/stdlib.h
./sam_header.h
../headers//usr/include/ctype.h
../headers//usr/include/x86_64-linux-gnu/bits/errno.h
../headers//usr/include/string.h
bam_import.c
../headers//usr/include/stdlib.h
./khash.h
./bam.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/zlib.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./kstring.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
./sam_header.h
../headers//usr/include/ctype.h
sam.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdint.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
./knetfile.h
./bgzf.h
./bam.h
./sam.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/string.h
../headers//usr/include/unistd.h
./faidx.h
bam_pileup.c
./bam.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
./knetfile.h
./bgzf.h
../headers//usr/include/stdlib.h
../headers//usr/include/assert.h
faidx.c
./khash.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./faidx.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./razf.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/ctype.h
knetfile.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/x86_64-linux-gnu/bits/time.h
../headers//usr/include/x86_64-linux-gnu/sys/select.h
../headers//usr/include/unistd.h
../headers//usr/include/x86_64-linux-gnu/bits/sockaddr.h
../headers//usr/include/x86_64-linux-gnu/bits/socket.h
../headers//usr/include/netdb.h
./knetfile.h
../headers//usr/include/x86_64-linux-gnu/sys/socket.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/ctype.h
../headers//usr/include/x86_64-linux-gnu/bits/errno.h
../headers//usr/include/fcntl.h
../headers//usr/include/x86_64-linux-gnu/bits/socket_type.h
sam_header.c
./khash.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/string.h
kstring.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./kstring.h
../headers//usr/include/stdio.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/ctype.h
razf.c
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/fcntl.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./razf.h
../headers//usr/include/unistd.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
libraries
../libs/usr/lib/x86_64-linux-gnu/libboost_thread.so.1.55.0
../libs/usr/lib/x86_64-linux-gnu/libboost_system.so.1.55.0
../libs/lib/x86_64-linux-gnu/libz.so.1
../libs/usr/lib/x86_64-linux-gnu/libstdc++.so.6
../libs/lib/x86_64-linux-gnu/libm.so.6
../libs/lib/x86_64-linux-gnu/libgcc_s.so.1
../libs/lib/x86_64-linux-gnu/libpthread.so.0
../libs/lib/x86_64-linux-gnu/libc.so.6
manual
long_spanning_reads
compile units
unassigned
long_spanning_reads.cpp
Gimple
./long_spanning_reads.cpp.004t.gimple
GKD
./long_spanning_reads.o.gkd
OBJ
obj: ./long_spanning_reads.o
unassigned
reads.cpp
Gimple
./reads.cpp.004t.gimple
GKD
./reads.o.gkd
OBJ
obj: ./reads.o
unassigned
bwt_map.cpp
Gimple
./bwt_map.cpp.004t.gimple
GKD
./bwt_map.o.gkd
OBJ
obj: ./bwt_map.o
unassigned
common.cpp
Gimple
./common.cpp.004t.gimple
GKD
./common.o.gkd
OBJ
obj: ./common.o
unassigned
fusions.cpp
Gimple
./fusions.cpp.004t.gimple
GKD
./fusions.o.gkd
OBJ
obj: ./fusions.o
unassigned
tokenize.cpp
Gimple
./tokenize.cpp.004t.gimple
GKD
./tokenize.o.gkd
OBJ
obj: ./tokenize.o
unassigned
utils.cpp
Gimple
./utils.cpp.004t.gimple
GKD
./utils.o.gkd
OBJ
obj: ./utils.o
bgzf.c
Gimple
./bgzf.c.004t.gimple
GKD
./bgzf.o.gkd
OBJ
obj: ./bgzf.o
bam_aux.c
Gimple
./bam_aux.c.004t.gimple
GKD
./bam_aux.o.gkd
OBJ
obj: ./bam_aux.o
unassigned
bam.c
Gimple
./bam.c.004t.gimple
GKD
./bam.o.gkd
OBJ
obj: ./bam.o
bam_import.c
Gimple
./bam_import.c.004t.gimple
GKD
./bam_import.o.gkd
OBJ
obj: ./bam_import.o
sam.c
Gimple
./sam.c.004t.gimple
GKD
./sam.o.gkd
OBJ
obj: ./sam.o
bam_pileup.c
Gimple
./bam_pileup.c.004t.gimple
GKD
./bam_pileup.o.gkd
OBJ
obj: ./bam_pileup.o
faidx.c
Gimple
./faidx.c.004t.gimple
GKD
./faidx.o.gkd
OBJ
obj: ./faidx.o
knetfile.c
Gimple
./knetfile.c.004t.gimple
GKD
./knetfile.o.gkd
OBJ
obj: ./knetfile.o
sam_header.c
Gimple
./sam_header.c.004t.gimple
GKD
./sam_header.o.gkd
OBJ
obj: ./sam_header.o
kstring.c
Gimple
./kstring.c.004t.gimple
GKD
./kstring.o.gkd
OBJ
obj: ./kstring.o
razf.c
Gimple
./razf.c.004t.gimple
GKD
./razf.o.gkd
OBJ
obj: ./razf.o
includes
unassigned
../headers//usr/include/boost/smart_ptr/detail/sp_counted_base_gcc_x86.hpp
../headers//usr/include/boost/exception/info.hpp
../headers//usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp
../headers//usr/include/boost/checked_delete.hpp
long_spanning_reads.cpp
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/boost/system/system_error.hpp
./bwt_map.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/seqan/file/stream_algorithms.h
../headers//usr/include/seqan/basic/alphabet_residue.h
../headers//usr/include/seqan/stream/adapt_fstream.h
../headers//usr/include/c++/4.9/typeinfo
../headers//usr/include/boost/exception/detail/exception_ptr.hpp
../headers//usr/include/c++/4.9/bits/stl_tree.h
./insertions.h
./junctions.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/boost/system/error_code.hpp
../headers//usr/include/boost/thread/exceptions.hpp
../headers//usr/include/boost/smart_ptr/shared_ptr.hpp
../headers//usr/include/boost/smart_ptr/detail/shared_count.hpp
../headers//usr/include/c++/4.9/sstream
../headers//usr/include/c++/4.9/streambuf
../headers//usr/include/c++/4.9/ostream
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/boost/exception/exception.hpp
../headers//usr/include/c++/4.9/stdexcept
./common.h
./reads.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_list.h
../headers//usr/include/boost/thread/detail/thread.hpp
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_algo.h
../headers//usr/include/c++/4.9/istream
../headers//usr/include/seqan/sequence/string_packed.h
../headers//usr/include/seqan/basic/iterator_adaptor.h
../headers//usr/include/seqan/stream/adapt_sstream.h
../headers//usr/include/seqan/basic/iterator_interface.h
../headers//usr/include/seqan/modifier/modifier_shortcuts.h
../headers//usr/include/seqan/modifier/modifier_view.h
../headers//usr/include/seqan/basic/alphabet_simple_type.h
../headers//usr/include/seqan/sequence/string_base.h
../headers//usr/include/seqan/modifier/modifier_reverse.h
../headers//usr/include/boost/thread/pthread/thread_data.hpp
../headers//usr/include/c++/4.9/bits/stl_pair.h
../headers//usr/include/c++/4.9/bits/stl_map.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/bits/list.tcc
./fusions.h
../headers//usr/include/boost/throw_exception.hpp
../headers//usr/include/boost/thread/pthread/condition_variable_fwd.hpp
../headers//usr/include/seqan/file/file_format_fasta.h
../headers//usr/include/seqan/file/stream.h
../headers//usr/include/seqan/sequence/string_alloc.h
../headers//usr/include/seqan/sequence/sequence_interface.h
../headers//usr/include/seqan/basic/allocator_interface.h
../headers//usr/include/c++/4.9/bits/stl_heap.h
../headers//usr/include/c++/4.9/bits/stl_queue.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/bits/stl_function.h
../headers//usr/include/seqan/sequence/segment_base.h
../headers//usr/include/seqan/basic/array_construct_destruct.h
../headers//usr/include/seqan/sequence/adapt_std_string.h
../headers//usr/include/seqan/sequence/segment_infix.h
../headers//usr/include/c++/4.9/bits/stl_set.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/boost/thread/pthread/thread_heap_alloc.hpp
../headers//usr/include/boost/smart_ptr/weak_ptr.hpp
../headers//usr/include/boost/thread/pthread/mutex.hpp
../headers//usr/include/boost/smart_ptr/enable_shared_from_this.hpp
../headers//usr/include/c++/4.9/iostream
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/wchar.h
../headers//usr/include/_G_config.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/new
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/ostream.tcc
../headers//usr/include/c++/4.9/bits/locale_facets.h
../headers//usr/include/c++/4.9/iomanip
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/limits
../headers//usr/include/c++/4.9/fstream
../headers//usr/include/c++/4.9/exception
../headers//usr/include/c++/4.9/bits/basic_ios.tcc
../headers//usr/include/c++/4.9/bits/stl_iterator_base_funcs.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/ostream_insert.h
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/c++/4.9/ext/type_traits.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/bits/pthreadtypes.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/wctype.h
../headers//usr/include/stdint.h
../headers//usr/include/seqan/platform/platform_gcc.h
../headers//usr/include/seqan/basic/debug_test_system.h
../headers//usr/include/seqan/basic/profiling.h
../headers//usr/include/seqan/basic/metaprogramming_logic.h
../headers//usr/include/seqan/basic/alphabet_residue_tabs.h
../headers//usr/include/seqan/basic/fundamental_tags.h
../headers//usr/include/seqan/basic/container_concept.h
../headers//usr/include/seqan/modifier/modifier_functors.h
../headers//usr/include/seqan/basic/basic_type.h
../headers//usr/include/seqan/stream/adapt_iostream.h
../headers//usr/include/seqan/basic/alphabet_math.h
../headers//usr/include/seqan/basic/metaprogramming_type.h
../headers//usr/include/seqan/basic/proxy_iterator.h
../headers//usr/include/seqan/basic/fundamental_conversion.h
../headers//usr/include/seqan/basic/iterator_adapt_std.h
../headers//usr/include/seqan/basic/alphabet_adapt_builtins.h
../headers//usr/include/seqan/basic/fundamental_transport.h
../headers//usr/include/seqan/basic/iterator_base.h
../headers//usr/include/seqan/file/file_format_raw.h
../headers//usr/include/seqan/sequence/sequence_shortcuts.h
../headers//usr/include/seqan/basic/metaprogramming_control.h
../headers//usr/include/seqan/random/random_normal.h
../headers//usr/include/boost/config/suffix.hpp
../headers//usr/include/boost/cstdint.hpp
../headers//usr/include/boost/iterator.hpp
../headers//usr/include/boost/operators.hpp
../headers//usr/include/boost/detail/sp_typeinfo.hpp
../headers//usr/include/boost/smart_ptr/detail/sp_convertible.hpp
../headers//usr/include/boost/smart_ptr/detail/spinlock_sync.hpp
../headers//usr/include/boost/smart_ptr/detail/spinlock_pool.hpp
../headers//usr/include/boost/integer_traits.hpp
../headers//usr/include/boost/none_t.hpp
../headers//usr/include/boost/thread/tss.hpp
../headers//usr/include/boost/thread/future.hpp
../headers//usr/include/boost/integer/static_log2.hpp
../headers//usr/include/boost/thread/detail/move.hpp
../headers//usr/include/boost/function/function_base.hpp
../headers//usr/include/boost/function/function_template.hpp
../headers//usr/include/seqan/file/file_format_mmap.h
../headers//usr/include/boost/noncopyable.hpp
../headers//usr/include/boost/thread/future_error_code.hpp
../headers//usr/include/boost/mpl/aux_/adl_barrier.hpp
../headers//usr/include/boost/mpl/integral_c_tag.hpp
../headers//usr/include/boost/mpl/bool_fwd.hpp
../headers//usr/include/boost/mpl/void_fwd.hpp
../headers//usr/include/boost/mpl/aux_/na_fwd.hpp
../headers//usr/include/boost/type_traits/detail/yes_no_type.hpp
../headers//usr/include/boost/move/detail/meta_utils.hpp
../headers//usr/include/boost/thread/lock_options.hpp
../headers//usr/include/boost/exception/detail/type_info.hpp
../headers//usr/include/boost/exception/detail/error_info_impl.hpp
../headers//usr/include/boost/exception/to_string_stub.hpp
../headers//usr/include/boost/exception/detail/clone_current_exception.hpp
../headers//usr/include/boost/date_time/c_time.hpp
../headers//usr/include/boost/date_time/time_defs.hpp
../headers//usr/include/boost/date_time/special_defs.hpp
../headers//usr/include/boost/date_time/time_resolution_traits.hpp
../headers//usr/include/boost/date_time/int_adapter.hpp
../headers//usr/include/boost/date_time/date_defs.hpp
../headers//usr/include/boost/date_time/year_month_day.hpp
../headers//usr/include/boost/date_time/gregorian_calendar.hpp
../headers//usr/include/boost/date_time/gregorian_calendar.ipp
../headers//usr/include/boost/date_time/date_duration.hpp
../headers//usr/include/boost/date_time/date.hpp
../headers//usr/include/boost/date_time/time_duration.hpp
../headers//usr/include/boost/date_time/time_system_counted.hpp
../headers//usr/include/boost/date_time/time.hpp
../headers//usr/include/boost/date_time/constrained_value.hpp
../headers//usr/include/boost/date_time/gregorian/greg_weekday.hpp
../headers//usr/include/boost/date_time/gregorian/greg_day.hpp
../headers//usr/include/boost/date_time/gregorian/greg_year.hpp
../headers//usr/include/boost/date_time/gregorian/greg_month.hpp
../headers//usr/include/boost/date_time/gregorian/greg_calendar.hpp
../headers//usr/include/boost/date_time/gregorian/greg_day_of_year.hpp
../headers//usr/include/boost/date_time/gregorian/greg_duration.hpp
../headers//usr/include/boost/date_time/gregorian/greg_date.hpp
../headers//usr/include/boost/date_time/posix_time/posix_time_config.hpp
../headers//usr/include/boost/date_time/posix_time/ptime.hpp
../headers//usr/include/boost/ratio/detail/overflow_helpers.hpp
../headers//usr/include/boost/type_traits/add_rvalue_reference.hpp
../headers//usr/include/boost/chrono/detail/is_evenly_divisible_by.hpp
../headers//usr/include/boost/chrono/duration.hpp
../headers//usr/include/boost/chrono/system_clocks.hpp
../headers//usr/include/boost/chrono/time_point.hpp
../headers//usr/include/boost/thread/xtime.hpp
../headers//usr/include/boost/thread/thread_time.hpp
../headers//usr/include/boost/ratio/ratio.hpp
../headers//usr/include/boost/thread/pthread/pthread_mutex_scoped_lock.hpp
../headers//usr/include/boost/thread/lock_types.hpp
../headers//usr/include/boost/thread/cv_status.hpp
../headers//usr/include/boost/type_traits/type_with_alignment.hpp
../headers//usr/include/boost/optional/optional.hpp
../headers//usr/include/boost/smart_ptr/detail/operator_bool.hpp
../headers//usr/include/boost/thread/lock_guard.hpp
../headers//usr/include/seqan/random/ext_MersenneTwister.h
../headers//usr/include/boost/bind/storage.hpp
../headers//usr/include/boost/bind/arg.hpp
../headers//usr/include/boost/io_fwd.hpp
../headers//usr/include/boost/integer_fwd.hpp
../headers//usr/include/boost/functional/hash/detail/float_functions.hpp
../headers//usr/include/boost/thread/pthread/condition_variable.hpp
../headers//usr/include/boost/atomic/detail/gcc-atomic.hpp
../headers//usr/include/boost/thread/lockable_traits.hpp
../headers//usr/include/boost/tuple/detail/tuple_basic.hpp
../headers//usr/include/boost/exception/detail/is_output_streamable.hpp
../headers//usr/include/boost/exception/to_string.hpp
../headers//usr/include/boost/utility/enable_if.hpp
../headers//usr/include/boost/smart_ptr/bad_weak_ptr.hpp
../headers//usr/include/boost/detail/scoped_enum_emulation.hpp
../headers//usr/include/boost/none.hpp
../headers//usr/include/boost/mpl/bool.hpp
../headers//usr/include/boost/mpl/void.hpp
../headers//usr/include/boost/mpl/aux_/integral_wrapper.hpp
../headers//usr/include/boost/bind/placeholders.hpp
../headers//usr/include/samtools/bgzf.h
../headers//usr/include/samtools/bam.h
../headers//usr/include/samtools/sam.h
./utils.h
./deletions.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/getopt.h
../headers//usr/include/pthread.h
./tokenize.h
../headers//usr/include/c++/4.9/cxxabi.h
unassigned
./reads.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
./common.h
reads.cpp
../headers//usr/include/c++/4.9/bits/stl_algo.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/stdlib.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers//usr/include/c++/4.9/bits/stl_heap.h
../headers//usr/include/c++/4.9/bits/stl_queue.h
../headers//usr/include/seqan/sequence/string_base.h
../headers//usr/include/seqan/sequence/sequence_interface.h
../headers//usr/include/seqan/sequence/string_alloc.h
../headers//usr/include/seqan/basic/allocator_interface.h
../headers//usr/include/seqan/sequence/adapt_array_pointer.h
../headers//usr/include/seqan/sequence/adapt_std_string.h
../headers//usr/include/seqan/basic/array_construct_destruct.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/libio.h
../headers//usr/include/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/new
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/stl_list.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/stdint.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/seqan/basic/debug_test_system.h
../headers//usr/include/seqan/basic/profiling.h
../headers//usr/include/seqan/basic/metaprogramming_logic.h
../headers//usr/include/seqan/basic/alphabet_residue_tabs.h
../headers//usr/include/seqan/basic/fundamental_tags.h
../headers//usr/include/seqan/basic/container_concept.h
../headers//usr/include/seqan/basic/iterator_interface.h
../headers//usr/include/seqan/modifier/modifier_functors.h
../headers//usr/include/seqan/basic/basic_type.h
../headers//usr/include/seqan/basic/alphabet_math.h
../headers//usr/include/seqan/basic/iterator_adapt_std.h
../headers//usr/include/seqan/basic/iterator_base.h
../headers//usr/include/seqan/basic/metaprogramming_control.h
../headers//usr/include/seqan/basic/alphabet_residue.h
../headers//usr/include/seqan/random/random_normal.h
../headers//usr/include/samtools/bgzf.h
../headers//usr/include/samtools/bam.h
../headers//usr/include/samtools/sam.h
./bwt_map.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
./tokenize.h
../headers//usr/include/ctype.h
../headers//usr/include/c++/4.9/cxxabi.h
../headers//usr/include/seqan/random/ext_MersenneTwister.h
unassigned
../headers//usr/include/c++/4.9/bits/locale_facets.h
./bwt_map.h
bwt_map.cpp
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/string.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
./common.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_tree.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/c++/4.9/bits/stl_bvector.h
../headers//usr/include/stdlib.h
../headers//usr/include/c++/4.9/bits/stl_algo.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_pair.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/bits/stl_map.h
../headers//usr/include/c++/4.9/bits/stl_heap.h
../headers//usr/include/seqan/sequence/string_base.h
../headers//usr/include/seqan/sequence/sequence_interface.h
../headers//usr/include/seqan/sequence/string_alloc.h
../headers//usr/include/seqan/basic/allocator_interface.h
../headers//usr/include/seqan/basic/alphabet_simple_type.h
../headers//usr/include/seqan/sequence/segment_base.h
../headers//usr/include/seqan/sequence/string_packed.h
../headers//usr/include/seqan/basic/iterator_adaptor.h
../headers//usr/include/seqan/basic/array_construct_destruct.h
../headers//usr/include/seqan/basic/iterator_interface.h
../headers//usr/include/seqan/sequence/segment_infix.h
../headers//usr/include/seqan/basic/alphabet_residue.h
../headers//usr/include/c++/4.9/ostream
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/seqan/modifier/modifier_view.h
../headers//usr/include/seqan/modifier/modifier_reverse.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/time.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/new
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/ostream.tcc
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/backward/auto_ptr.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/stl_list.h
../headers//usr/include/c++/4.9/bits/stl_function.h
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_funcs.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/c++/4.9/bits/ostream_insert.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/c++/4.9/ext/type_traits.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/wchar.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/stdint.h
../headers//usr/include/seqan/platform/platform_gcc.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/seqan/basic/debug_test_system.h
../headers//usr/include/seqan/basic/profiling.h
../headers//usr/include/seqan/basic/metaprogramming_logic.h
../headers//usr/include/seqan/basic/test_system.h
../headers//usr/include/seqan/basic/alphabet_residue_tabs.h
../headers//usr/include/seqan/basic/fundamental_tags.h
../headers//usr/include/seqan/basic/container_concept.h
../headers//usr/include/seqan/modifier/modifier_functors.h
../headers//usr/include/seqan/basic/alphabet_math.h
../headers//usr/include/seqan/basic/metaprogramming_type.h
../headers//usr/include/seqan/basic/basic_type.h
../headers//usr/include/seqan/basic/fundamental_conversion.h
../headers//usr/include/seqan/basic/iterator_base.h
../headers//usr/include/seqan/modifier/modifier_shortcuts.h
../headers//usr/include/seqan/sequence/sequence_shortcuts.h
../headers//usr/include/seqan/basic/metaprogramming_control.h
../headers//usr/include/seqan/random/random_normal.h
../headers//usr/include/samtools/bgzf.h
../headers//usr/include/samtools/bam.h
../headers//usr/include/samtools/sam.h
./reads.h
./junctions.h
./insertions.h
./deletions.h
./fusions.h
./align_status.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/ctype.h
./tokenize.h
../headers//usr/include/c++/4.9/cxxabi.h
../headers//usr/include/seqan/random/ext_MersenneTwister.h
unassigned
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
common.cpp
../headers//usr/include/c++/4.9/ostream
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
./common.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.h
../headers//usr/include/samtools/bam.h
../headers//usr/include/stdlib.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/libio.h
../headers//usr/include/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/locale_facets.h
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/getopt.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/samtools/bgzf.h
../headers//usr/include/samtools/sam.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/new
./tokenize.h
../headers//usr/include/ctype.h
unassigned
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/bits/stl_algo.h
./fusions.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_tree.h
fusions.cpp
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
./reads.h
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/c++/4.9/istream
../headers//usr/include/c++/4.9/ostream
../headers//usr/include/c++/4.9/streambuf
../headers//usr/include/c++/4.9/sstream
../headers//usr/include/seqan/stream/adapt_fstream.h
../headers//usr/include/seqan/file/stream_algorithms.h
../headers//usr/include/seqan/basic/alphabet_residue.h
../headers//usr/include/seqan/stream/adapt_sstream.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/c++/4.9/bits/stl_pair.h
../headers//usr/include/c++/4.9/bits/stl_map.h
./bwt_map.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/bits/stl_heap.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/seqan/sequence/string_base.h
../headers//usr/include/seqan/sequence/sequence_interface.h
../headers//usr/include/seqan/sequence/string_alloc.h
../headers//usr/include/seqan/basic/allocator_interface.h
../headers//usr/include/seqan/basic/alphabet_simple_type.h
../headers//usr/include/seqan/sequence/segment_base.h
../headers//usr/include/seqan/sequence/string_packed.h
../headers//usr/include/seqan/basic/iterator_adaptor.h
../headers//usr/include/seqan/basic/array_construct_destruct.h
../headers//usr/include/seqan/basic/iterator_interface.h
../headers//usr/include/seqan/sequence/segment_infix.h
../headers//usr/include/seqan/modifier/modifier_view.h
../headers//usr/include/seqan/modifier/modifier_reverse.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/wchar.h
../headers//usr/include/_G_config.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/new
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/ostream.tcc
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/stl_list.h
../headers//usr/include/c++/4.9/bits/stl_function.h
../headers//usr/include/c++/4.9/bits/basic_ios.tcc
../headers//usr/include/c++/4.9/bits/stl_iterator_base_funcs.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/string.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/c++/4.9/ext/type_traits.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/wctype.h
../headers//usr/include/stdint.h
../headers//usr/include/seqan/platform/platform_gcc.h
../headers//usr/include/seqan/basic/debug_test_system.h
../headers//usr/include/seqan/basic/profiling.h
../headers//usr/include/seqan/basic/metaprogramming_logic.h
../headers//usr/include/seqan/basic/alphabet_residue_tabs.h
../headers//usr/include/seqan/basic/fundamental_tags.h
../headers//usr/include/seqan/basic/container_concept.h
../headers//usr/include/seqan/modifier/modifier_functors.h
../headers//usr/include/seqan/basic/alphabet_math.h
../headers//usr/include/seqan/basic/metaprogramming_type.h
../headers//usr/include/seqan/basic/basic_type.h
../headers//usr/include/seqan/sequence/adapt_std_string.h
../headers//usr/include/seqan/basic/fundamental_conversion.h
../headers//usr/include/seqan/basic/iterator_base.h
../headers//usr/include/seqan/file/file_format_raw.h
../headers//usr/include/seqan/modifier/modifier_shortcuts.h
../headers//usr/include/seqan/sequence/sequence_shortcuts.h
../headers//usr/include/seqan/basic/metaprogramming_control.h
../headers//usr/include/seqan/random/random_normal.h
./junctions.h
./insertions.h
./deletions.h
./align_status.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
./common.h
../headers//usr/include/c++/4.9/cxxabi.h
../headers//usr/include/seqan/random/ext_MersenneTwister.h
../headers//usr/include/seqan/align/align_base.h
unassigned
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
tokenize.cpp
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/new
unassigned
../headers//usr/include/c++/4.9/bits/locale_facets.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/sstream
../headers//usr/include/c++/4.9/streambuf
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
utils.cpp
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/c++/4.9/istream
../headers//usr/include/c++/4.9/fstream
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/c++/4.9/bits/stl_algo.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/libio.h
../headers//usr/include/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/new
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/istream.tcc
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/basic_file.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++io.h
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/bits/stl_pair.h
../headers//usr/include/c++/4.9/bits/basic_ios.tcc
../headers//usr/include/c++/4.9/bits/fstream.tcc
../headers//usr/include/c++/4.9/bits/sstream.tcc
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/bits/pthreadtypes.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
./utils.h
../headers//usr/include/stdint.h
../headers//usr/include/string.h
./common.h
bgzf.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./bgzf.h
./khash.h
../headers//usr/include/stdlib.h
../headers//usr/include/fcntl.h
../headers//usr/include/string.h
bam_aux.c
./khash.h
./bam.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdint.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/string.h
../headers//usr/include/ctype.h
unassigned
./kstring.h
bam.c
./bam_endian.h
./bam.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./knetfile.h
./bgzf.h
../headers//usr/include/stdlib.h
./sam_header.h
../headers//usr/include/ctype.h
../headers//usr/include/x86_64-linux-gnu/bits/errno.h
../headers//usr/include/string.h
bam_import.c
../headers//usr/include/stdlib.h
./khash.h
./bam.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/zlib.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./kstring.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
./sam_header.h
../headers//usr/include/ctype.h
sam.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdint.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
./knetfile.h
./bgzf.h
./bam.h
./sam.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/string.h
../headers//usr/include/unistd.h
./faidx.h
bam_pileup.c
./bam.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
./knetfile.h
./bgzf.h
../headers//usr/include/stdlib.h
../headers//usr/include/assert.h
faidx.c
./khash.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./faidx.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./razf.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/ctype.h
knetfile.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/x86_64-linux-gnu/bits/time.h
../headers//usr/include/x86_64-linux-gnu/sys/select.h
../headers//usr/include/unistd.h
../headers//usr/include/x86_64-linux-gnu/bits/sockaddr.h
../headers//usr/include/x86_64-linux-gnu/bits/socket.h
../headers//usr/include/netdb.h
./knetfile.h
../headers//usr/include/x86_64-linux-gnu/sys/socket.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/ctype.h
../headers//usr/include/x86_64-linux-gnu/bits/errno.h
../headers//usr/include/fcntl.h
../headers//usr/include/x86_64-linux-gnu/bits/socket_type.h
sam_header.c
./khash.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/string.h
kstring.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./kstring.h
../headers//usr/include/stdio.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/ctype.h
razf.c
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/fcntl.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./razf.h
../headers//usr/include/unistd.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
libraries
../libs/usr/lib/x86_64-linux-gnu/libboost_thread.so.1.55.0
../libs/usr/lib/x86_64-linux-gnu/libboost_system.so.1.55.0
../libs/lib/x86_64-linux-gnu/libz.so.1
../libs/usr/lib/x86_64-linux-gnu/libstdc++.so.6
../libs/lib/x86_64-linux-gnu/libm.so.6
../libs/lib/x86_64-linux-gnu/libgcc_s.so.1
../libs/lib/x86_64-linux-gnu/libpthread.so.0
../libs/lib/x86_64-linux-gnu/libc.so.6
manual
prep_reads
compile units
unassigned
prep_reads.cpp
Gimple
./prep_reads.cpp.004t.gimple
GKD
./prep_reads.o.gkd
OBJ
obj: ./prep_reads.o
unassigned
reads.cpp
Gimple
./reads.cpp.004t.gimple
GKD
./reads.o.gkd
OBJ
obj: ./reads.o
unassigned
common.cpp
Gimple
./common.cpp.004t.gimple
GKD
./common.o.gkd
OBJ
obj: ./common.o
unassigned
tokenize.cpp
Gimple
./tokenize.cpp.004t.gimple
GKD
./tokenize.o.gkd
OBJ
obj: ./tokenize.o
qual.cpp
Gimple
./qual.cpp.004t.gimple
GKD
./qual.o.gkd
OBJ
obj: ./qual.o
bam_aux.c
Gimple
./bam_aux.c.004t.gimple
GKD
./bam_aux.o.gkd
OBJ
obj: ./bam_aux.o
unassigned
bam.c
Gimple
./bam.c.004t.gimple
GKD
./bam.o.gkd
OBJ
obj: ./bam.o
bam_import.c
Gimple
./bam_import.c.004t.gimple
GKD
./bam_import.o.gkd
OBJ
obj: ./bam_import.o
sam.c
Gimple
./sam.c.004t.gimple
GKD
./sam.o.gkd
OBJ
obj: ./sam.o
bam_pileup.c
Gimple
./bam_pileup.c.004t.gimple
GKD
./bam_pileup.o.gkd
OBJ
obj: ./bam_pileup.o
faidx.c
Gimple
./faidx.c.004t.gimple
GKD
./faidx.o.gkd
OBJ
obj: ./faidx.o
knetfile.c
Gimple
./knetfile.c.004t.gimple
GKD
./knetfile.o.gkd
OBJ
obj: ./knetfile.o
sam_header.c
Gimple
./sam_header.c.004t.gimple
GKD
./sam_header.o.gkd
OBJ
obj: ./sam_header.o
bgzf.c
Gimple
./bgzf.c.004t.gimple
GKD
./bgzf.o.gkd
OBJ
obj: ./bgzf.o
kstring.c
Gimple
./kstring.c.004t.gimple
GKD
./kstring.o.gkd
OBJ
obj: ./kstring.o
razf.c
Gimple
./razf.c.004t.gimple
GKD
./razf.o.gkd
OBJ
obj: ./razf.o
includes
unassigned
../headers//usr/include/c++/4.9/bits/stl_bvector.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
prep_reads.cpp
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
./common.h
./reads.h
./qual.h
../headers//usr/include/c++/4.9/ostream
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.h
../headers//usr/include/c++/4.9/bits/stl_algo.h
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers//usr/include/c++/4.9/bits/stl_heap.h
../headers//usr/include/c++/4.9/bits/stl_queue.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/wchar.h
../headers//usr/include/_G_config.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/new
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/ostream.tcc
../headers//usr/include/c++/4.9/bits/locale_facets.h
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/stl_list.h
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/time.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/samtools/bgzf.h
../headers//usr/include/samtools/bam.h
../headers//usr/include/samtools/sam.h
../headers//usr/include/wctype.h
../headers//usr/include/seqan/basic/debug_test_system.h
../headers//usr/include/seqan/basic/profiling.h
../headers//usr/include/seqan/basic/alphabet_residue_tabs.h
../headers//usr/include/seqan/basic/metaprogramming_control.h
../headers//usr/include/seqan/basic/alphabet_residue.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/getopt.h
../headers//usr/include/ctype.h
./tokenize.h
../headers//usr/include/c++/4.9/cxxabi.h
unassigned
./reads.h
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
./common.h
reads.cpp
../headers//usr/include/c++/4.9/bits/stl_algo.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/stdlib.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
../headers//usr/include/c++/4.9/bits/stl_heap.h
../headers//usr/include/c++/4.9/bits/stl_queue.h
../headers//usr/include/seqan/sequence/string_base.h
../headers//usr/include/seqan/sequence/sequence_interface.h
../headers//usr/include/seqan/sequence/string_alloc.h
../headers//usr/include/seqan/basic/allocator_interface.h
../headers//usr/include/seqan/sequence/adapt_array_pointer.h
../headers//usr/include/seqan/sequence/adapt_std_string.h
../headers//usr/include/seqan/basic/array_construct_destruct.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/libio.h
../headers//usr/include/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/new
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/ctime
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/stl_list.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/stdint.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/seqan/basic/debug_test_system.h
../headers//usr/include/seqan/basic/profiling.h
../headers//usr/include/seqan/basic/metaprogramming_logic.h
../headers//usr/include/seqan/basic/alphabet_residue_tabs.h
../headers//usr/include/seqan/basic/fundamental_tags.h
../headers//usr/include/seqan/basic/container_concept.h
../headers//usr/include/seqan/basic/iterator_interface.h
../headers//usr/include/seqan/modifier/modifier_functors.h
../headers//usr/include/seqan/basic/basic_type.h
../headers//usr/include/seqan/basic/alphabet_math.h
../headers//usr/include/seqan/basic/iterator_adapt_std.h
../headers//usr/include/seqan/basic/iterator_base.h
../headers//usr/include/seqan/basic/metaprogramming_control.h
../headers//usr/include/seqan/basic/alphabet_residue.h
../headers//usr/include/seqan/random/random_normal.h
../headers//usr/include/samtools/bgzf.h
../headers//usr/include/samtools/bam.h
../headers//usr/include/samtools/sam.h
./bwt_map.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
./tokenize.h
../headers//usr/include/ctype.h
../headers//usr/include/c++/4.9/cxxabi.h
../headers//usr/include/seqan/random/ext_MersenneTwister.h
unassigned
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/ext/new_allocator.h
common.cpp
../headers//usr/include/c++/4.9/ostream
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
./common.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.h
../headers//usr/include/samtools/bam.h
../headers//usr/include/stdlib.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/iostream
../headers//usr/include/libio.h
../headers//usr/include/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/ios_base.h
../headers//usr/include/c++/4.9/cwctype
../headers//usr/include/c++/4.9/bits/locale_facets.h
../headers//usr/include/c++/4.9/cstdarg
../headers//usr/include/c++/4.9/cstdio
../headers//usr/include/c++/4.9/bits/postypes.h
../headers//usr/include/c++/4.9/cstring
../headers//usr/include/c++/4.9/cstdlib
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/basic_ios.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/iosfwd
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/wctype.h
../headers//usr/include/getopt.h
../headers//usr/include/_G_config.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib.h
../headers//usr/include/samtools/bgzf.h
../headers//usr/include/samtools/sam.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/new
./tokenize.h
../headers//usr/include/ctype.h
unassigned
../headers//usr/include/c++/4.9/bits/basic_string.h
../headers//usr/include/c++/4.9/ext/atomicity.h
../headers//usr/include/c++/4.9/bits/stl_construct.h
../headers//usr/include/c++/4.9/bits/vector.tcc
../headers//usr/include/c++/4.9/ext/new_allocator.h
../headers//usr/include/c++/4.9/bits/stl_algobase.h
../headers//usr/include/c++/4.9/bits/stl_vector.h
../headers//usr/include/c++/4.9/bits/stl_iterator.h
../headers//usr/include/c++/4.9/bits/stl_uninitialized.h
tokenize.cpp
../headers//usr/include/c++/4.9/cwchar
../headers//usr/include/c++/4.9/bits/char_traits.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h
../headers//usr/include/c++/4.9/bits/allocator.h
../headers//usr/include/c++/4.9/clocale
../headers//usr/include/c++/4.9/bits/basic_string.tcc
../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h
../headers//usr/include/c++/4.9/bits/move.h
../headers//usr/include/c++/4.9/bits/stringfwd.h
../headers//usr/include/c++/4.9/bits/functexcept.h
../headers//usr/include/c++/4.9/debug/debug.h
../headers//usr/include/c++/4.9/bits/predefined_ops.h
../headers//usr/include/c++/4.9/ext/numeric_traits.h
../headers//usr/include/c++/4.9/ext/alloc_traits.h
../headers//usr/include/c++/4.9/bits/cpp_type_traits.h
../headers//usr/include/stdio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/wchar.h
../headers//usr/include/x86_64-linux-gnu/bits/wchar2.h
../headers//usr/include/time.h
../headers//usr/include/locale.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/atomic_word.h
../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h
../headers//usr/include/c++/4.9/new
qual.cpp
bam_aux.c
./khash.h
./bam.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdint.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/string.h
../headers//usr/include/ctype.h
unassigned
./kstring.h
bam.c
./bam_endian.h
./bam.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./knetfile.h
./bgzf.h
../headers//usr/include/stdlib.h
./sam_header.h
../headers//usr/include/ctype.h
../headers//usr/include/x86_64-linux-gnu/bits/errno.h
../headers//usr/include/string.h
bam_import.c
../headers//usr/include/stdlib.h
./khash.h
./bam.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/zlib.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./kstring.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
./sam_header.h
../headers//usr/include/ctype.h
sam.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdint.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
./knetfile.h
./bgzf.h
./bam.h
./sam.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/string.h
../headers//usr/include/unistd.h
./faidx.h
bam_pileup.c
./bam.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
./knetfile.h
./bgzf.h
../headers//usr/include/stdlib.h
../headers//usr/include/assert.h
faidx.c
./khash.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./faidx.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./razf.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/ctype.h
knetfile.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/x86_64-linux-gnu/bits/time.h
../headers//usr/include/x86_64-linux-gnu/sys/select.h
../headers//usr/include/unistd.h
../headers//usr/include/x86_64-linux-gnu/bits/sockaddr.h
../headers//usr/include/x86_64-linux-gnu/bits/socket.h
../headers//usr/include/netdb.h
./knetfile.h
../headers//usr/include/x86_64-linux-gnu/sys/socket.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/ctype.h
../headers//usr/include/x86_64-linux-gnu/bits/errno.h
../headers//usr/include/fcntl.h
../headers//usr/include/x86_64-linux-gnu/bits/socket_type.h
sam_header.c
./khash.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/string2.h
../headers//usr/include/string.h
bgzf.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./bgzf.h
./khash.h
../headers//usr/include/stdlib.h
../headers//usr/include/fcntl.h
../headers//usr/include/string.h
kstring.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stdarg.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./kstring.h
../headers//usr/include/stdio.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
../headers//usr/include/ctype.h
razf.c
../headers//usr/include/x86_64-linux-gnu/bits/types.h
../headers//usr/include/fcntl.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/zlib.h
./knetfile.h
./razf.h
../headers//usr/include/unistd.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
libraries
../libs/lib/x86_64-linux-gnu/libz.so.1
../libs/usr/lib/x86_64-linux-gnu/libstdc++.so.6
../libs/lib/x86_64-linux-gnu/libm.so.6
../libs/lib/x86_64-linux-gnu/libgcc_s.so.1
../libs/lib/x86_64-linux-gnu/libpthread.so.0
../libs/lib/x86_64-linux-gnu/libc.so.6
manual