perm - amd64

unassigned

AlignmentsQ.cpp

Gimple

./AlignmentsQ.cpp.004t.gimple

GKD

./AlignmentsQ.o.gkd

OBJ

obj: ./AlignmentsQ.o

unassigned

Filename.cpp

Gimple

./Filename.cpp.004t.gimple

GKD

./Filename.o.gkd

OBJ

obj: ./Filename.o

unassigned

GenomeNTdata.cpp

Gimple

./GenomeNTdata.cpp.004t.gimple

GKD

./GenomeNTdata.o.gkd

OBJ

obj: ./GenomeNTdata.o

unassigned

ReadInBits.cpp

Gimple

./ReadInBits.cpp.004t.gimple

GKD

./ReadInBits.o.gkd

OBJ

obj: ./ReadInBits.o

unassigned

PerM.cpp

Gimple

./PerM.cpp.004t.gimple

GKD

./PerM.o.gkd

OBJ

obj: ./PerM.o

unassigned

chromosomeNTdata.cpp

Gimple

./chromosomeNTdata.cpp.004t.gimple

GKD

./chromosomeNTdata.o.gkd

OBJ

obj: ./chromosomeNTdata.o

unassigned

bitsOperationUtil.cpp

Gimple

./bitsOperationUtil.cpp.004t.gimple

GKD

./bitsOperationUtil.o.gkd

OBJ

obj: ./bitsOperationUtil.o

unassigned

FileOutputBuffer.cpp

Gimple

./FileOutputBuffer.cpp.004t.gimple

GKD

./FileOutputBuffer.o.gkd

OBJ

obj: ./FileOutputBuffer.o

HashIndexT.cpp

Gimple

./HashIndexT.cpp.004t.gimple

GKD

./HashIndexT.o.gkd

OBJ

obj: ./HashIndexT.o

unassigned

ReadInBitsSet.cpp

Gimple

./ReadInBitsSet.cpp.004t.gimple

GKD

./ReadInBitsSet.o.gkd

OBJ

obj: ./ReadInBitsSet.o

SeedPattern.cpp

Gimple

./SeedPattern.cpp.004t.gimple

GKD

./SeedPattern.o.gkd

OBJ

obj: ./SeedPattern.o

unassigned

boolFlagArray.cpp

Gimple

./boolFlagArray.cpp.004t.gimple

GKD

./boolFlagArray.o.gkd

OBJ

obj: ./boolFlagArray.o

unassigned

GenomeInBits.cpp

Gimple

./GenomeInBits.cpp.004t.gimple

GKD

./GenomeInBits.o.gkd

OBJ

obj: ./GenomeInBits.o

unassigned

Index_Table.cpp

Gimple

./Index_Table.cpp.004t.gimple

GKD

./Index_Table.o.gkd

OBJ

obj: ./Index_Table.o

ReadsMapping.cpp

Gimple

./ReadsMapping.cpp.004t.gimple

GKD

./ReadsMapping.o.gkd

OBJ

obj: ./ReadsMapping.o

unassigned

PairedReadsMapping.cpp

Gimple

./PairedReadsMapping.cpp.004t.gimple

GKD

./PairedReadsMapping.o.gkd

OBJ

obj: ./PairedReadsMapping.o

unassigned

ShortReadUtil.cpp

Gimple

./ShortReadUtil.cpp.004t.gimple

GKD

./ShortReadUtil.o.gkd

OBJ

obj: ./ShortReadUtil.o

unassigned

chdir.cpp

Gimple

./chdir.cpp.004t.gimple

GKD

./chdir.o.gkd

OBJ

obj: ./chdir.o

unassigned

Genome_Index.cpp

Gimple

./Genome_Index.cpp.004t.gimple

GKD

./Genome_Index.o.gkd

OBJ

obj: ./Genome_Index.o

unassigned

MismatchScores.cpp

Gimple

./MismatchScores.cpp.004t.gimple

GKD

./MismatchScores.o.gkd

OBJ

obj: ./MismatchScores.o

unassigned

Flags.cpp

Gimple

./Flags.cpp.004t.gimple

GKD

./Flags.o.gkd

OBJ

obj: ./Flags.o

ParseReadsOpts.cpp

Gimple

./ParseReadsOpts.cpp.004t.gimple

GKD

./ParseReadsOpts.o.gkd

OBJ

obj: ./ParseReadsOpts.o

unassigned

ColorSpaceRead.cpp

Gimple

./ColorSpaceRead.cpp.004t.gimple

GKD

./ColorSpaceRead.o.gkd

OBJ

obj: ./ColorSpaceRead.o

unassigned

Genome_Index_Table.cpp

Gimple

./Genome_Index_Table.cpp.004t.gimple

GKD

./Genome_Index_Table.o.gkd

OBJ

obj: ./Genome_Index_Table.o

unassigned

ParameterList.cpp

Gimple

./ParameterList.cpp.004t.gimple

GKD

./ParameterList.o.gkd

OBJ

obj: ./ParameterList.o

unassigned

ReadsMappingStats.cpp

Gimple

./ReadsMappingStats.cpp.004t.gimple

GKD

./ReadsMappingStats.o.gkd

OBJ

obj: ./ReadsMappingStats.o

unassigned

FileInputBuffer.cpp

Gimple

./FileInputBuffer.cpp.004t.gimple

GKD

./FileInputBuffer.o.gkd

OBJ

obj: ./FileInputBuffer.o

unassigned

Genome_Index_TableQ.cpp

Gimple

./Genome_Index_TableQ.cpp.004t.gimple

GKD

./Genome_Index_TableQ.o.gkd

OBJ

obj: ./Genome_Index_TableQ.o

unassigned

ReadsQualScores.cpp

Gimple

./ReadsQualScores.cpp.004t.gimple

GKD

./ReadsQualScores.o.gkd

OBJ

obj: ./ReadsQualScores.o

ChrIndex2GeneName.cpp

Gimple

./ChrIndex2GeneName.cpp.004t.gimple

GKD

./ChrIndex2GeneName.o.gkd

OBJ

obj: ./ChrIndex2GeneName.o

unassigned

ReadsFileParser.cpp

Gimple

./ReadsFileParser.cpp.004t.gimple

GKD

./ReadsFileParser.o.gkd

OBJ

obj: ./ReadsFileParser.o

unassigned

PairedReadsSet.cpp

Gimple

./PairedReadsSet.cpp.004t.gimple

GKD

./PairedReadsSet.o.gkd

OBJ

obj: ./PairedReadsSet.o

MappingResult.cpp

Gimple

./MappingResult.cpp.004t.gimple

GKD

./MappingResult.o.gkd

OBJ

obj: ./MappingResult.o

unassigned

refInBinFile.cpp

Gimple

./refInBinFile.cpp.004t.gimple

GKD

./refInBinFile.o.gkd

OBJ

obj: ./refInBinFile.o

LongReadsSet.cpp

Gimple

./LongReadsSet.cpp.004t.gimple

GKD

./LongReadsSet.o.gkd

OBJ

obj: ./LongReadsSet.o

includes

unassigned

../headers//usr/include/c++/4.9/bits/stl_algo.h ../headers//usr/include/c++/4.9/bits/stl_pair.h

AlignmentsQ.cpp

../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 ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/bits/stl_heap.h ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/c++/4.9/limits ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.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/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/cstdlib ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.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/include/c++/4.9/debug/debug.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.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/_G_config.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio.h ../headers//usr/include/stdlib.h ./Filename.h ./stdafx.h ./ReadInBits.h ../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h ../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h ./AlignmentsQ.h ./bitsOperationUtil.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h

Filename.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/char_traits.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/streambuf ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/stdlib.h ../headers//usr/include/x86_64-linux-gnu/sys/stat.h ../headers//usr/include/c++/4.9/iostream ../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/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/basic_ios.tcc ../headers//usr/include/c++/4.9/bits/fstream.tcc ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/bits/ostream_insert.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/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/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/c++/4.9/bits/functexcept.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/_G_config.h ../headers//usr/include/wctype.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio.h ../headers//usr/include/x86_64-linux-gnu/bits/stat.h ./Filename.h ../headers//usr/include/string.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

GenomeNTdata.cpp

./stdafx.h ./ShortReadUtil.h ../headers//usr/include/c++/4.9/ostream ../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/basic_ios.h ../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/stl_vector.h ../headers//usr/include/c++/4.9/bits/stl_iterator.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/vector.tcc ./ChrIndex2GeneName.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/iostream ./GenomeNTdata.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_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/new ../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/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/bits/locale_facets.h ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/limits ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/bits/stl_pair.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/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/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/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.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/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/_G_config.h ../headers//usr/include/wctype.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio.h ./Filename.h ./chromosomeNTdata.h ./ReadInBits.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h ./bitsOperationUtil.h ./SeedPattern.h ../headers//usr/include/string.h ./chdir.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h

ReadInBits.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/char_traits.h ../headers//usr/include/c++/4.9/bits/ios_base.h ./bitsOperationUtil.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/cwchar ../headers//usr/include/c++/4.9/clocale ../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/basic_ios.tcc ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/bits/ostream_insert.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/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/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/c++/4.9/bits/functexcept.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/_G_config.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio.h ./Filename.h ./stdafx.h ./ReadInBits.h ../headers//usr/include/string.h

unassigned

./ParameterList.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h

PerM.cpp

../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/stdlib.h ./ParseReadsOpts.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/iostream ./GenomeNTdata.h ../headers//usr/include/c++/4.9/ostream ../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/cpp_type_traits.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/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/limits ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/cstdlib ../headers//usr/include/c++/4.9/bits/vector.tcc ../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/new ../headers//usr/include/c++/4.9/bits/functexcept.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/_G_config.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio.h ./Filename.h ./stdafx.h ./FileInputBuffer.h ./ReadsQualScores.h ./ShortReadUtil.h ./ReadsFileParser.h ./ReadInBits.h ./MismatchScores.h ./ReadInBitsSet.h ./PairedReadsSet.h ../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h ../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h ./ChrIndex2GeneName.h ./chromosomeNTdata.h ./boolFlagArray.h ./seedOptions.h ./Index_Table.h ./Genome_Index_Table.h ./Flags.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h ./Genome_Index_TableQ.h ./FileOutputBuffer.h ./bitsOperationUtil.h ./ColorSpaceRead.h ./SeedPattern.h ./AlignmentsQ.h ./MappingResult.h ./Genome_Index.h ./ReadsMapping.h ./PairedReadsMapping.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

chromosomeNTdata.cpp

../headers//usr/include/c++/4.9/istream ../headers//usr/include/c++/4.9/bits/basic_ios.h ./stdafx.h ../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/bits/vector.tcc ../headers//usr/include/c++/4.9/ext/new_allocator.h ./ChrIndex2GeneName.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 ../headers//usr/include/c++/4.9/iostream ../headers//usr/include/c++/4.9/cwchar ../headers//usr/include/c++/4.9/bits/char_traits.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/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/cstdlib ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.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/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/include/libio.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/bits/functexcept.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/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/_G_config.h ../headers//usr/include/wctype.h ./ShortReadUtil.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio.h ./Filename.h ./chromosomeNTdata.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/string.h ../headers//usr/include/ctype.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h

bitsOperationUtil.cpp

../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.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/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/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/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/bits/ostream_insert.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/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/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/c++/4.9/bits/functexcept.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/_G_config.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio.h ./Filename.h ./stdafx.h ./bitsOperationUtil.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h

FileOutputBuffer.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/char_traits.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/fstream ../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/cwchar ../headers//usr/include/c++/4.9/clocale ../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/ostream_insert.h ../headers//usr/include/c++/4.9/bits/fstream.tcc ../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/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/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/c++/4.9/bits/functexcept.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/_G_config.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio.h ./Filename.h ./stdafx.h ./FileOutputBuffer.h ../headers//usr/include/c++/4.9/new

HashIndexT.cpp

../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/cwchar ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/cstdio ../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/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/stddef.h ../headers//usr/include/wchar.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/_G_config.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio.h ./Filename.h ./stdafx.h ./HashIndexT.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h

ReadInBitsSet.cpp

../headers//usr/include/c++/4.9/bits/stl_vector.h ./ReadsQualScores.h ../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/fstream ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/streambuf ../headers//usr/include/c++/4.9/bits/ios_base.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_uninitialized.h ../headers//usr/include/c++/4.9/bits/stl_construct.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/iostream ./stdafx.h ../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/cwchar ../headers//usr/include/c++/4.9/clocale ../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/fstream.tcc ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.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/functexcept.h ../headers//usr/include/c++/4.9/bits/ostream_insert.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/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.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/_G_config.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio.h ./Filename.h ./FileInputBuffer.h ./FileOutputBuffer.h ./ShortReadUtil.h ./ReadsFileParser.h ./ReadInBits.h ./MismatchScores.h ./ReadInBitsSet.h ../headers//usr/include/c++/4.9/new ./bitsOperationUtil.h ./ColorSpaceRead.h ../headers//usr/include/ctype.h ../headers//usr/include/string.h

SeedPattern.cpp

./bitsOperationUtil.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/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/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/iosfwd ../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/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/stddef.h ../headers//usr/include/wchar.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/_G_config.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio.h ./Filename.h ./stdafx.h ./ReadInBits.h ./SeedPattern.h ../headers//usr/include/string.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h

boolFlagArray.cpp

../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.h ./boolFlagArray.h ../headers//usr/include/c++/4.9/iostream ../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/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/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/iosfwd ../headers//usr/include/c++/4.9/bits/ostream_insert.h ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/bits/functexcept.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/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_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/c++/4.9/new

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h

GenomeInBits.cpp

../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/c++/4.9/iostream ./GenomeNTdata.h ../headers//usr/include/c++/4.9/limits ../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.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/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/cstdlib ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../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/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/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/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/c++/4.9/bits/functexcept.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/_G_config.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio.h ../headers//usr/include/stdlib.h ./Filename.h ./stdafx.h ./ReadInBits.h ../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h ../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h ./ChrIndex2GeneName.h ./ShortReadUtil.h ./chromosomeNTdata.h ./boolFlagArray.h ./GenomeInBits.h ./bitsOperationUtil.h ./SeedPattern.h ../headers//usr/include/string.h

unassigned

./stdafx.h

Index_Table.cpp

../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/iostream ./HashIndexT.h ../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/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/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/cstdio ../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/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_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 ./boolFlagArray.h ../headers//usr/include/_G_config.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio.h ./Filename.h ./seedOptions.h ./Index_Table.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h ../headers//usr/include/string.h ../headers//usr/include/c++/4.9/new

ReadsMapping.cpp

../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/fstream ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/bits/basic_ios.h ./MappingResult.h ./ColorSpaceRead.h ./ShortReadUtil.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ./ParseReadsOpts.h ./ParameterList.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/streambuf ../headers//usr/include/c++/4.9/bits/char_traits.h ./ReadsMapping.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/stl_construct.h ../headers//usr/include/c++/4.9/ext/new_allocator.h ./ReadsQualScores.h ./stdafx.h ./seedOptions.h ./ReadInBitsSet.h ../headers//usr/include/c++/4.9/iostream ./GenomeNTdata.h ../headers//usr/include/c++/4.9/istream ../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/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/limits ../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/fstream.tcc ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/cstdlib ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/basic_ios.tcc ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/move.h ../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/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/_G_config.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio.h ../headers//usr/include/stdlib.h ./Filename.h ./FileOutputBuffer.h ./FileInputBuffer.h ./ReadsFileParser.h ./ReadInBits.h ./MismatchScores.h ./PairedReadsSet.h ../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h ../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h ./ChrIndex2GeneName.h ./chromosomeNTdata.h ./AlignmentsQ.h ./boolFlagArray.h ./GenomeInBits.h ./Index_Table.h ./Genome_Index_Table.h ./Flags.h ./ReadsMappingStats.h ./Genome_Index_TableQ.h ./LongReadsSet.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h ./bitsOperationUtil.h ./SeedPattern.h ./Genome_Index.h ../headers//usr/include/string.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/omp.h ./chdir.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h

PairedReadsMapping.cpp

../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/istream ../headers//usr/include/c++/4.9/bits/basic_ios.h ./ParseReadsOpts.h ./ParameterList.h ./MappingResult.h ./ReadsMapping.h ./stdafx.h ./PairedReadsMapping.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ./ReadInBitsSet.h ./ReadsQualScores.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/bits/ios_base.h ./seedOptions.h ../headers//usr/include/c++/4.9/iostream ./GenomeNTdata.h ../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/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/limits ../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/vector.tcc ../headers//usr/include/c++/4.9/cstdlib ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/basic_ios.tcc ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../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/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/new_allocator.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/_G_config.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio.h ../headers//usr/include/stdlib.h ./Filename.h ./FileOutputBuffer.h ./FileInputBuffer.h ./ShortReadUtil.h ./ReadsFileParser.h ./ReadInBits.h ./MismatchScores.h ./PairedReadsSet.h ../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h ../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h ./ChrIndex2GeneName.h ./chromosomeNTdata.h ./AlignmentsQ.h ./boolFlagArray.h ./GenomeInBits.h ./Index_Table.h ./Genome_Index_Table.h ./Flags.h ./Genome_Index_TableQ.h ./ReadsMappingStats.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h ./bitsOperationUtil.h ./ColorSpaceRead.h ./SeedPattern.h ./Genome_Index.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/omp.h ../headers//usr/include/string.h ./LongReadsSet.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h

ShortReadUtil.cpp

../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.h ./ShortReadUtil.h ../headers//usr/include/c++/4.9/bits/move.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/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/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/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/bits/ostream_insert.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/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/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/c++/4.9/bits/functexcept.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/_G_config.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio.h ./Filename.h ./stdafx.h ../headers//usr/include/stdlib.h ../headers//usr/include/string.h ../headers//usr/include/ctype.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h

chdir.cpp

../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/char_traits.h ../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/x86_64-linux-gnu/sys/stat.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/cwchar ../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/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/ostream_insert.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/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/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/c++/4.9/bits/functexcept.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/_G_config.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio.h ../headers//usr/include/x86_64-linux-gnu/bits/stat.h ./Filename.h ./stdafx.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h ../headers//usr/include/unistd.h ../headers//usr/include/string.h ../headers//usr/include/stdlib.h

unassigned

./SeedPattern.h

Genome_Index.cpp

../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h ./seedOptions.h ../headers//usr/include/c++/4.9/iostream ./GenomeNTdata.h ../headers//usr/include/c++/4.9/limits ../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/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/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/cstdlib ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/new ../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/alloc_traits.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.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/_G_config.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio.h ../headers//usr/include/stdlib.h ./Filename.h ./stdafx.h ../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h ../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h ./ChrIndex2GeneName.h ./ShortReadUtil.h ./chromosomeNTdata.h ./ReadInBits.h ./boolFlagArray.h ./GenomeInBits.h ./Genome_Index.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h ./bitsOperationUtil.h ../headers//usr/include/string.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h

MismatchScores.cpp

../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/c++/4.9/ostream ../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/bits/char_traits.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/x86_64-linux-gnu/c++/4.9/bits/c++config.h ../headers//usr/include/c++/4.9/clocale ../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/basic_ios.tcc ../headers//usr/include/c++/4.9/bits/fstream.tcc ../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/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/new_allocator.h ../headers//usr/include/c++/4.9/ext/numeric_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/_G_config.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio.h ./MismatchScores.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/string.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

Flags.cpp

../headers//usr/include/c++/4.9/bits/stl_iterator.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_uninitialized.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.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/cwchar ../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/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_iterator_base_types.h ../headers//usr/include/c++/4.9/bits/move.h ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/bits/ostream_insert.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/include/libio.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/bits/functexcept.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/_G_config.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio.h ./Filename.h ./stdafx.h ./Flags.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/string.h ../headers//usr/include/stdlib.h

ParseReadsOpts.cpp

../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/cwchar ../headers//usr/include/c++/4.9/clocale ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/bits/cpp_type_traits.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/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.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/_G_config.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio.h ./Filename.h ./stdafx.h ./ParseReadsOpts.h ../headers//usr/include/c++/4.9/new

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h

ColorSpaceRead.cpp

./ReadInBits.h ./ColorSpaceRead.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/c++/4.9/istream ./bitsOperationUtil.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/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.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/cstdio ../headers//usr/include/c++/4.9/bits/postypes.h ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/bits/ostream_insert.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/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/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/c++/4.9/bits/functexcept.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/_G_config.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio.h ./Filename.h ./stdafx.h ./ShortReadUtil.h ../headers//usr/include/ctype.h ../headers//usr/include/string.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h

Genome_Index_Table.cpp

../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h ./ColorSpaceRead.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/stl_algo.h ./Genome_Index_Table.h ../headers//usr/include/c++/4.9/bits/stl_algobase.h ../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/c++/4.9/bits/char_traits.h ../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/istream ../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 ./GenomeNTdata.h ../headers//usr/include/c++/4.9/bits/cpp_type_traits.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/cstdlib ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../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/limits ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.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/new ../headers//usr/include/c++/4.9/bits/ostream_insert.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/alloc_traits.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.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/bits/functexcept.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/stdlib.h ../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h ../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h ./ChrIndex2GeneName.h ../headers//usr/include/_G_config.h ../headers//usr/include/wctype.h ./ShortReadUtil.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio.h ./Filename.h ./stdafx.h ./chromosomeNTdata.h ./ReadInBits.h ./boolFlagArray.h ./GenomeInBits.h ./seedOptions.h ./HashIndexT.h ./Index_Table.h ./Genome_Index.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h ./bitsOperationUtil.h ./SeedPattern.h ./chdir.h ./refInBinFile.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/omp.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h

ParameterList.cpp

../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h ./ParameterList.h ../headers//usr/include/c++/4.9/ostream ../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/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/stdlib.h ../headers//usr/include/c++/4.9/bits/stl_iterator.h ../headers//usr/include/c++/4.9/bits/char_traits.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/iostream ../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/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/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/fstream.tcc ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/cstdlib ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.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/new ../headers//usr/include/c++/4.9/bits/ostream_insert.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/stdio.h ../headers//usr/include/libio.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/bits/functexcept.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/_G_config.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio.h ./Filename.h ./stdafx.h ./Flags.h ./ShortReadUtil.h ./FileInputBuffer.h ./ReadsQualScores.h ./ReadsFileParser.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/c++/4.9/bits/gthr-default.h ./FileOutputBuffer.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/omp.h ../headers//usr/include/string.h ../headers//usr/include/ctype.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h

ReadsMappingStats.cpp

../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/basic_ios.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/iostream ./GenomeNTdata.h ../headers//usr/include/c++/4.9/limits ../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/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/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/cstdlib ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/bits/basic_ios.tcc ../headers//usr/include/c++/4.9/new ../headers//usr/include/c++/4.9/bits/ostream_insert.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/stdio.h ../headers//usr/include/libio.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/bits/functexcept.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/_G_config.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio.h ../headers//usr/include/stdlib.h ./Filename.h ./stdafx.h ../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h ../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h ./ChrIndex2GeneName.h ./ShortReadUtil.h ./chromosomeNTdata.h ./ReadInBits.h ./AlignmentsQ.h ./ReadsMappingStats.h ./bitsOperationUtil.h ./SeedPattern.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h

FileInputBuffer.cpp

../headers//usr/include/c++/4.9/fstream ../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/c++/4.9/istream ../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/iostream ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.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/cwctype ../headers//usr/include/c++/4.9/bits/ostream.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/iosfwd ../headers//usr/include/c++/4.9/bits/fstream.tcc ../headers//usr/include/c++/4.9/bits/basic_ios.tcc ../headers//usr/include/c++/4.9/bits/ostream_insert.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/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/stddef.h ../headers//usr/include/wchar.h ../headers//usr/include/c++/4.9/bits/functexcept.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/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 ./Filename.h ./stdafx.h ./FileInputBuffer.h ../headers//usr/include/c++/4.9/new

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h

Genome_Index_TableQ.cpp

../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/char_traits.h ../headers//usr/include/c++/4.9/bits/basic_ios.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/ext/atomicity.h ./stdafx.h ./ReadInBits.h ../headers//usr/include/c++/4.9/bits/stl_iterator_base_funcs.h ../headers//usr/include/c++/4.9/bits/stl_algobase.h ./Genome_Index_TableQ.h ./ColorSpaceRead.h ../headers//usr/include/c++/4.9/bits/stl_algo.h ./Genome_Index_Table.h ./AlignmentsQ.h ./bitsOperationUtil.h ../headers//usr/include/c++/4.9/iostream ./GenomeNTdata.h ../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/cwchar ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/c++config.h ../headers//usr/include/c++/4.9/new ../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/cstdlib ../headers//usr/include/c++/4.9/bits/stringfwd.h ../headers//usr/include/c++/4.9/bits/stl_vector.h ../headers//usr/include/c++/4.9/bits/vector.tcc ../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/limits ../headers//usr/include/c++/4.9/iosfwd ../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/ostream_insert.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/alloc_traits.h ../headers//usr/include/c++/4.9/debug/debug.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.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/bits/functexcept.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/stdlib.h ../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h ../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h ./ChrIndex2GeneName.h ../headers//usr/include/_G_config.h ../headers//usr/include/wctype.h ./ShortReadUtil.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio.h ./Filename.h ./chromosomeNTdata.h ./boolFlagArray.h ./GenomeInBits.h ./seedOptions.h ./Index_Table.h ./Genome_Index.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h ./SeedPattern.h ../headers//usr/include/string.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h

ReadsQualScores.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/bits/stl_vector.h ./stdafx.h ../headers//usr/include/stdlib.h ./ReadsQualScores.h ../headers//usr/include/c++/4.9/ostream ../headers//usr/include/c++/4.9/bits/char_traits.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/cwchar ../headers//usr/include/c++/4.9/clocale ../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/fstream.tcc ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/basic_ios.tcc ../headers//usr/include/c++/4.9/bits/functexcept.h ../headers//usr/include/c++/4.9/bits/ostream_insert.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/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/stddef.h ../headers//usr/include/wchar.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/_G_config.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio.h ./Filename.h ./FileInputBuffer.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/string.h ../headers//usr/include/ctype.h

ChrIndex2GeneName.cpp

../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/char_traits.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/vector.tcc ./ChrIndex2GeneName.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/iostream ../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/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/cstdio ../headers//usr/include/c++/4.9/cstdlib ../headers//usr/include/c++/4.9/bits/stl_iterator_base_funcs.h ../headers//usr/include/c++/4.9/bits/move.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/c++/4.9/debug/debug.h ../headers//usr/include/stdio.h ../headers//usr/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.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/_G_config.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio.h ../headers//usr/include/stdlib.h ./Filename.h ./stdafx.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/c++/4.9/bits/gthr-default.h

unassigned

../headers//usr/include/c++/4.9/bits/locale_facets.h

ReadsFileParser.cpp

../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/basic_ios.h ../headers//usr/include/c++/4.9/bits/ios_base.h ../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h ./stdafx.h ./ReadsFileParser.h ./ShortReadUtil.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/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/cpp_type_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/cwctype ../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/fstream.tcc ../headers//usr/include/c++/4.9/bits/basic_ios.tcc ../headers//usr/include/c++/4.9/bits/stl_algobase.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/stdio.h ../headers//usr/include/libio.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/bits/functexcept.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/_G_config.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio.h ./Filename.h ./FileInputBuffer.h ./ReadsQualScores.h ./FileOutputBuffer.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/string.h ./chdir.h

unassigned

../headers//usr/include/c++/4.9/bits/basic_string.h ../headers//usr/include/c++/4.9/ext/atomicity.h

PairedReadsSet.cpp

./stdafx.h ../headers//usr/include/c++/4.9/bits/stl_vector.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/cpp_type_traits.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/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/cstdio ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/bits/vector.tcc ../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/new_allocator.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/_G_config.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio.h ./Filename.h ./FileOutputBuffer.h ./FileInputBuffer.h ./ReadsQualScores.h ./ShortReadUtil.h ./ReadsFileParser.h ./ReadInBits.h ./MismatchScores.h ./ReadInBitsSet.h ./PairedReadsSet.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h ./bitsOperationUtil.h ./ColorSpaceRead.h ../headers//usr/include/string.h ../headers//usr/include/c++/4.9/new

MappingResult.cpp

./stdafx.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/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/bits/stl_construct.h ../headers//usr/include/c++/4.9/bits/stl_uninitialized.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.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/cstdio ../headers//usr/include/c++/4.9/cstdlib ../headers//usr/include/c++/4.9/bits/stl_iterator_base_types.h ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/new ../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/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.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/_G_config.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio.h ../headers//usr/include/stdlib.h ./Filename.h ./ReadInBits.h ../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h ../headers//usr/include/x86_64-linux-gnu/bits/stdlib-bsearch.h ./AlignmentsQ.h ./ShortReadUtil.h ./MappingResult.h ./FileOutputBuffer.h ./bitsOperationUtil.h ./ColorSpaceRead.h ../headers//usr/include/string.h

unassigned

./stdafx.h

refInBinFile.cpp

./boolFlagArray.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/vector.tcc ../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 ./ChrIndex2GeneName.h ../headers//usr/include/c++/4.9/bits/stl_algobase.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/iostream ./GenomeNTdata.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/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/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/cstdio ../headers//usr/include/c++/4.9/limits ../headers//usr/include/c++/4.9/iosfwd ../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/new ../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/include/libio.h ../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/stddef.h ../headers//usr/include/wchar.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/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/_G_config.h ../headers//usr/include/wctype.h ./ShortReadUtil.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio.h ./Filename.h ./chromosomeNTdata.h ./ReadInBits.h ./GenomeInBits.h ../headers//usr/include/x86_64-linux-gnu/c++/4.9/bits/gthr-default.h ./bitsOperationUtil.h ./SeedPattern.h ../headers//usr/include/string.h

LongReadsSet.cpp

../headers//usr/include/c++/4.9/bits/stl_vector.h ./ReadsQualScores.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/cpp_type_traits.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/bits/ios_base.h ../headers//usr/include/c++/4.9/cwctype ../headers//usr/include/c++/4.9/cstdio ../headers//usr/include/c++/4.9/iosfwd ../headers//usr/include/c++/4.9/bits/vector.tcc ../headers//usr/include/c++/4.9/bits/allocator.h ../headers//usr/include/c++/4.9/bits/stl_algobase.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/new_allocator.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/_G_config.h ../headers//usr/include/x86_64-linux-gnu/bits/stdio.h ./Filename.h ./stdafx.h ./FileOutputBuffer.h ./FileInputBuffer.h ./ShortReadUtil.h ./ReadsFileParser.h ./ReadInBits.h ./MismatchScores.h ./ReadInBitsSet.h ./PairedReadsSet.h ./LongReadsSet.h ./bitsOperationUtil.h ./ColorSpaceRead.h ../headers//usr/include/c++/4.9/new ../headers//usr/include/string.h