smalt - amd64
Documentation
./doc/changelog.Debian.gz
./doc/copyright
Binaries
simqual
compile units
simqual.c
Gimple
./simqual.c.004t.gimple
GKD
./simqual.o.gkd
OBJ
obj: ./simqual.o
basqual.c
Gimple
./basqual.c.004t.gimple
GKD
./basqual.o.gkd
OBJ
obj: ./basqual.o
diffstr.c
elib.c
Gimple
./elib.c.004t.gimple
GKD
./elib.o.gkd
OBJ
obj: ./elib.o
filio.c
Gimple
./filio.c.004t.gimple
GKD
./filio.o.gkd
OBJ
obj: ./filio.o
sequence.c
Gimple
./sequence.c.004t.gimple
GKD
./sequence.o.gkd
OBJ
obj: ./sequence.o
includes
simqual.c
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/../src/elib.h
../headers/../src/sequence.h
../headers/../src/diffstr.h
./basqual.h
basqual.c
../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/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
../headers/../src/elib.h
../headers/../src/filio.h
../headers/../src/sequence.h
./basqual.h
../headers//usr/include/stdlib.h
diffstr.c
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.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/../src/elib.h
../headers/../src/diffstr.h
../headers//usr/include/ctype.h
elib.c
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.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
./elib.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
filio.c
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
../headers//usr/include/string.h
./elib.h
sequence.c
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/zlib.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./filio.h
./elib.h
./sequence.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.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
sequenceReverseComplement_test
compile units
sequenceReverseComplement_test.c
Gimple
./sequenceReverseComplement_test.c.004t.gimple
GKD
./sequenceReverseComplement_test.o.gkd
OBJ
obj: ./sequenceReverseComplement_test.o
elib.c
Gimple
./elib.c.004t.gimple
GKD
./elib.o.gkd
OBJ
obj: ./elib.o
sequence.c
Gimple
./sequence.c.004t.gimple
GKD
./sequence.o.gkd
OBJ
obj: ./sequence.o
filio.c
Gimple
./filio.c.004t.gimple
GKD
./filio.o.gkd
OBJ
obj: ./filio.o
includes
sequenceReverseComplement_test.c
../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/libio.h
../headers/../src/elib.h
../headers/../src/sequence.h
../headers//usr/include/stdio.h
../headers//usr/include/stdlib.h
elib.c
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.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
./elib.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
sequence.c
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/zlib.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./filio.h
./elib.h
./sequence.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
filio.c
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
../headers//usr/include/string.h
./elib.h
libraries
../libs/lib/x86_64-linux-gnu/libz.so.1
../libs/lib/x86_64-linux-gnu/libc.so.6
manual
readstats
compile units
readstats.c
Gimple
./readstats.c.004t.gimple
GKD
./readstats.o.gkd
OBJ
obj: ./readstats.o
elib.c
Gimple
./elib.c.004t.gimple
GKD
./elib.o.gkd
OBJ
obj: ./elib.o
sequence.c
Gimple
./sequence.c.004t.gimple
GKD
./sequence.o.gkd
OBJ
obj: ./sequence.o
filio.c
Gimple
./filio.c.004t.gimple
GKD
./filio.o.gkd
OBJ
obj: ./filio.o
includes
readstats.c
../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/libio.h
../headers/../src/elib.h
../headers//usr/include/stdint.h
../headers/../src/sequence.h
../headers//usr/include/stdio.h
../headers//usr/include/stdlib.h
elib.c
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.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
./elib.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
sequence.c
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/zlib.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./filio.h
./elib.h
./sequence.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
filio.c
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
../headers//usr/include/string.h
./elib.h
libraries
../libs/lib/x86_64-linux-gnu/libz.so.1
../libs/lib/x86_64-linux-gnu/libc.so.6
manual
splitmates
compile units
splitmates.c
Gimple
./splitmates.c.004t.gimple
GKD
./splitmates.o.gkd
OBJ
obj: ./splitmates.o
elib.c
Gimple
./elib.c.004t.gimple
GKD
./elib.o.gkd
OBJ
obj: ./elib.o
sequence.c
Gimple
./sequence.c.004t.gimple
GKD
./sequence.o.gkd
OBJ
obj: ./sequence.o
filio.c
Gimple
./filio.c.004t.gimple
GKD
./filio.o.gkd
OBJ
obj: ./filio.o
includes
splitmates.c
../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/libio.h
../headers/../src/elib.h
../headers/../src/sequence.h
../headers//usr/include/stdio.h
../headers//usr/include/string.h
../headers//usr/include/stdlib.h
elib.c
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.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
./elib.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
sequence.c
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/zlib.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./filio.h
./elib.h
./sequence.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
filio.c
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
../headers//usr/include/string.h
./elib.h
libraries
../libs/lib/x86_64-linux-gnu/libz.so.1
../libs/lib/x86_64-linux-gnu/libc.so.6
manual
trunkreads
compile units
trunkreads.c
Gimple
./trunkreads.c.004t.gimple
GKD
./trunkreads.o.gkd
OBJ
obj: ./trunkreads.o
elib.c
Gimple
./elib.c.004t.gimple
GKD
./elib.o.gkd
OBJ
obj: ./elib.o
sequence.c
Gimple
./sequence.c.004t.gimple
GKD
./sequence.o.gkd
OBJ
obj: ./sequence.o
filio.c
Gimple
./filio.c.004t.gimple
GKD
./filio.o.gkd
OBJ
obj: ./filio.o
includes
trunkreads.c
../headers//usr/include/stdlib.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/libio.h
../headers/../src/elib.h
../headers//usr/include/stdint.h
../headers/../src/sequence.h
../headers//usr/include/stdio.h
elib.c
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.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
./elib.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
sequence.c
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/zlib.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./filio.h
./elib.h
./sequence.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
filio.c
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
../headers//usr/include/string.h
./elib.h
libraries
../libs/lib/x86_64-linux-gnu/libz.so.1
../libs/lib/x86_64-linux-gnu/libc.so.6
manual
mixreads
compile units
mixreads.c
Gimple
./mixreads.c.004t.gimple
GKD
./mixreads.o.gkd
OBJ
obj: ./mixreads.o
elib.c
Gimple
./elib.c.004t.gimple
GKD
./elib.o.gkd
OBJ
obj: ./elib.o
sequence.c
Gimple
./sequence.c.004t.gimple
GKD
./sequence.o.gkd
OBJ
obj: ./sequence.o
filio.c
Gimple
./filio.c.004t.gimple
GKD
./filio.o.gkd
OBJ
obj: ./filio.o
includes
mixreads.c
../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/libio.h
../headers/../src/elib.h
../headers/../src/sequence.h
../headers//usr/include/stdio.h
../headers//usr/include/stdlib.h
elib.c
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.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
./elib.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
sequence.c
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/zlib.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./filio.h
./elib.h
./sequence.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
filio.c
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
../headers//usr/include/string.h
./elib.h
libraries
../libs/lib/x86_64-linux-gnu/libz.so.1
../libs/lib/x86_64-linux-gnu/libc.so.6
manual
splitreads
compile units
splitreads.c
Gimple
./splitreads.c.004t.gimple
GKD
./splitreads.o.gkd
OBJ
obj: ./splitreads.o
elib.c
Gimple
./elib.c.004t.gimple
GKD
./elib.o.gkd
OBJ
obj: ./elib.o
sequence.c
Gimple
./sequence.c.004t.gimple
GKD
./sequence.o.gkd
OBJ
obj: ./sequence.o
filio.c
Gimple
./filio.c.004t.gimple
GKD
./filio.o.gkd
OBJ
obj: ./filio.o
includes
splitreads.c
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/../src/elib.h
../headers/../src/sequence.h
../headers//usr/include/stdio.h
../headers//usr/include/string.h
../headers//usr/include/ctype.h
elib.c
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.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
./elib.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
sequence.c
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/zlib.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./filio.h
./elib.h
./sequence.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
filio.c
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
../headers//usr/include/string.h
./elib.h
libraries
../libs/lib/x86_64-linux-gnu/libz.so.1
../libs/lib/x86_64-linux-gnu/libc.so.6
manual
smalt_Xali_test
compile units
smalt.c
menu.c
threads.c
infmt.c
results.c
resultpairs.c
insert.c
report.c
rmap.c
score.c
Gimple
./score.c.004t.gimple
GKD
./score.o.gkd
OBJ
obj: ./score.o
diffstr.c
Gimple
./diffstr.c.004t.gimple
GKD
./diffstr.o.gkd
OBJ
obj: ./diffstr.o
alibuffer.c
Gimple
./alibuffer.c.004t.gimple
GKD
./alibuffer.o.gkd
OBJ
obj: ./alibuffer.o
alignment.c
Gimple
./alignment.c.004t.gimple
GKD
./alignment.o.gkd
OBJ
obj: ./alignment.o
swsimd.c
Gimple
./swsimd.c.004t.gimple
GKD
./swsimd.o.gkd
OBJ
obj: ./swsimd.o
sort.c
Gimple
./sort.c.004t.gimple
GKD
./sort.o.gkd
OBJ
obj: ./sort.o
array.c
Gimple
./array.c.004t.gimple
GKD
./array.o.gkd
OBJ
obj: ./array.o
interval.c
Gimple
./interval.c.004t.gimple
GKD
./interval.o.gkd
OBJ
obj: ./interval.o
hashidx.c
Gimple
./hashidx.c.004t.gimple
GKD
./hashidx.o.gkd
OBJ
obj: ./hashidx.o
hashhit.c
Gimple
./hashhit.c.004t.gimple
GKD
./hashhit.o.gkd
OBJ
obj: ./hashhit.o
segment.c
Gimple
./segment.c.004t.gimple
GKD
./segment.o.gkd
OBJ
obj: ./segment.o
elib.c
Gimple
./elib.c.004t.gimple
GKD
./elib.o.gkd
OBJ
obj: ./elib.o
filio.c
Gimple
./filio.c.004t.gimple
GKD
./filio.o.gkd
OBJ
obj: ./filio.o
sequence.c
Gimple
./sequence.c.004t.gimple
GKD
./sequence.o.gkd
OBJ
obj: ./sequence.o
includes
smalt.c
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/time.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
../headers/../src/elib.h
../headers/../src/threads.h
../headers/../src/sequence.h
../headers/../src/infmt.h
../headers/../src/hashidx.h
../headers/../src/score.h
../headers/../src/insert.h
../headers/../src/report.h
../headers/../src/results.h
../headers/../src/resultpairs.h
../headers/../src/rmap.h
../headers/../src/menu.h
../headers//usr/include/assert.h
../headers//usr/include/stdlib.h
menu.c
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/time.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers/../src/elib.h
../headers//usr/include/stdint.h
../headers/../src/menu.h
../headers//usr/include/ctype.h
../headers//usr/include/string.h
threads.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/bits/pthreadtypes.h
../headers//usr/include/x86_64-linux-gnu/bits/semaphore.h
../headers//usr/include/stdint.h
../headers//usr/include/libio.h
../headers/../src/elib.h
../headers/../src/threads.h
../headers//usr/include/stdio.h
../headers//usr/include/pthread.h
../headers//usr/include/semaphore.h
../headers//usr/include/stdlib.h
infmt.c
../headers//usr/include/bambamc/BamBam_FastQRead.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/libio.h
../headers/../src/elib.h
../headers//usr/include/stdint.h
../headers/../src/sequence.h
../headers/../src/infmt.h
../headers//usr/include/stdio.h
../headers//usr/include/bambamc/BamBam_BamCollatorInterface.h
../headers//usr/include/stdlib.h
results.c
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers/../src/elib.h
../headers/../src/array.h
../headers//usr/include/stdint.h
../headers/../src/diffstr.h
../headers/../src/sequence.h
../headers/../src/report.h
../headers/../src/score.h
../headers/../src/alignment.h
../headers/../src/results.h
../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h
../headers//usr/include/stdlib.h
resultpairs.c
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdlib.h
../headers/../src/elib.h
../headers/../src/array.h
../headers//usr/include/stdint.h
../headers/../src/insert.h
../headers/../src/sequence.h
../headers/../src/report.h
../headers/../src/results.h
../headers/../src/resultpairs.h
../headers//usr/include/stdio.h
insert.c
../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/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers/../src/elib.h
../headers/../src/vdef.h
../headers//usr/include/stdint.h
../headers/../src/insert.h
../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h
../headers//usr/include/stdlib.h
report.c
../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/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
../headers//usr/include/bambamc/BamBam_CharBuffer.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/bambamc/BamBam_ListNode.h
../headers//usr/include/bambamc/BamBam_List.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/bambamc/BamBam_BgzfCompressor.h
../headers//usr/include/bambamc/BamBam_BamSingleAlignment.h
../headers//usr/include/bambamc/BamBam_BamAlignmentPut.h
../headers//usr/include/bambamc/BamBam_BamHeaderInfo.h
../headers//usr/include/bambamc/BamBam_BamWriter.h
../headers//usr/include/bambamc/BamBam_BamFlagBase.h
../headers/../src/elib.h
../headers/../src/array.h
../headers/../src/sequence.h
../headers/../src/diffstr.h
../headers/../src/report.h
../headers//usr/include/stdlib.h
../headers//usr/include/ctype.h
rmap.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/libio.h
../headers/../src/elib.h
../headers/../src/array.h
../headers/../src/sequence.h
../headers/../src/interval.h
../headers/../src/hashidx.h
../headers/../src/hashhit.h
../headers/../src/segment.h
../headers/../src/score.h
../headers/../src/alibuffer.h
../headers/../src/alignment.h
../headers/../src/results.h
../headers/../src/resultpairs.h
../headers/../src/rmap.h
../headers//usr/include/stdio.h
../headers//usr/include/stdlib.h
score.c
../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/stdio.h
../headers//usr/include/libio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/emmintrin.h
../headers//usr/include/stdint.h
./elib.h
./sequence.h
./score.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h
diffstr.c
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.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
./elib.h
./diffstr.h
../headers//usr/include/ctype.h
alibuffer.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
./alibuffer.h
./alibuffer_struct.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/emmintrin.h
./score.h
./elib.h
../headers//usr/include/stdio.h
../headers//usr/include/stdlib.h
alignment.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/lib/gcc/x86_64-linux-gnu/4.9/include/emmintrin.h
../headers//usr/include/stdint.h
./elib.h
./sequence.h
./score.h
./diffstr.h
./alibuffer.h
./alibuffer_struct.h
./alignment.h
../headers//usr/include/stdio.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h
swsimd.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/emmintrin.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
./elib.h
./sequence.h
./score.h
./alibuffer.h
./alibuffer_struct.h
../headers//usr/include/stdio.h
sort.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
../headers//usr/include/stdio.h
./elib.h
../headers//usr/include/stdlib.h
array.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
./array.h
./elib.h
interval.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/stdlib.h
../headers//usr/include/libio.h
./elib.h
./vdef.h
../headers//usr/include/stdint.h
./sequence.h
./interval.h
../headers//usr/include/stdio.h
hashidx.c
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.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
./elib.h
./filio.h
./sequence.h
./interval.h
./hashidx.h
../headers//usr/include/stdlib.h
hashhit.c
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdlib.h
../headers//usr/include/stdint.h
./elib.h
./sequence.h
./hashidx.h
./hashhit.h
./sort.h
../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h
segment.c
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.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
./elib.h
./array.h
../headers//usr/include/stdint.h
./sequence.h
./hashhit.h
./segment.h
../headers//usr/include/stdlib.h
./sort.h
elib.c
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.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
./elib.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
filio.c
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
../headers//usr/include/string.h
./elib.h
sequence.c
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/zlib.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./filio.h
./elib.h
./sequence.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
libraries
../libs/usr/lib/x86_64-linux-gnu/libbambamc.so.0
../libs/lib/x86_64-linux-gnu/libz.so.1
../libs/lib/x86_64-linux-gnu/libm.so.6
../libs/lib/x86_64-linux-gnu/libpthread.so.0
../libs/lib/x86_64-linux-gnu/libc.so.6
manual
smalt
compile units
smalt.c
Gimple
./smalt.c.004t.gimple
GKD
./smalt.o.gkd
OBJ
obj: ./smalt.o
menu.c
Gimple
./menu.c.004t.gimple
GKD
./menu.o.gkd
OBJ
obj: ./menu.o
threads.c
Gimple
./threads.c.004t.gimple
GKD
./threads.o.gkd
OBJ
obj: ./threads.o
infmt.c
Gimple
./infmt.c.004t.gimple
GKD
./infmt.o.gkd
OBJ
obj: ./infmt.o
results.c
Gimple
./results.c.004t.gimple
GKD
./results.o.gkd
OBJ
obj: ./results.o
resultpairs.c
Gimple
./resultpairs.c.004t.gimple
GKD
./resultpairs.o.gkd
OBJ
obj: ./resultpairs.o
report.c
Gimple
./report.c.004t.gimple
GKD
./report.o.gkd
OBJ
obj: ./report.o
rmap.c
Gimple
./rmap.c.004t.gimple
GKD
./rmap.o.gkd
OBJ
obj: ./rmap.o
insert.c
Gimple
./insert.c.004t.gimple
GKD
./insert.o.gkd
OBJ
obj: ./insert.o
score.c
Gimple
./score.c.004t.gimple
GKD
./score.o.gkd
OBJ
obj: ./score.o
diffstr.c
Gimple
./diffstr.c.004t.gimple
GKD
./diffstr.o.gkd
OBJ
obj: ./diffstr.o
alibuffer.c
Gimple
./alibuffer.c.004t.gimple
GKD
./alibuffer.o.gkd
OBJ
obj: ./alibuffer.o
alignment.c
Gimple
./alignment.c.004t.gimple
GKD
./alignment.o.gkd
OBJ
obj: ./alignment.o
swsimd.c
Gimple
./swsimd.c.004t.gimple
GKD
./swsimd.o.gkd
OBJ
obj: ./swsimd.o
sort.c
Gimple
./sort.c.004t.gimple
GKD
./sort.o.gkd
OBJ
obj: ./sort.o
array.c
Gimple
./array.c.004t.gimple
GKD
./array.o.gkd
OBJ
obj: ./array.o
interval.c
Gimple
./interval.c.004t.gimple
GKD
./interval.o.gkd
OBJ
obj: ./interval.o
hashidx.c
Gimple
./hashidx.c.004t.gimple
GKD
./hashidx.o.gkd
OBJ
obj: ./hashidx.o
hashhit.c
Gimple
./hashhit.c.004t.gimple
GKD
./hashhit.o.gkd
OBJ
obj: ./hashhit.o
segment.c
Gimple
./segment.c.004t.gimple
GKD
./segment.o.gkd
OBJ
obj: ./segment.o
elib.c
Gimple
./elib.c.004t.gimple
GKD
./elib.o.gkd
OBJ
obj: ./elib.o
filio.c
Gimple
./filio.c.004t.gimple
GKD
./filio.o.gkd
OBJ
obj: ./filio.o
sequence.c
Gimple
./sequence.c.004t.gimple
GKD
./sequence.o.gkd
OBJ
obj: ./sequence.o
includes
smalt.c
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/time.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
./elib.h
./threads.h
./sequence.h
./infmt.h
./hashidx.h
./score.h
./insert.h
./report.h
./results.h
./resultpairs.h
./rmap.h
./menu.h
../headers//usr/include/assert.h
../headers//usr/include/stdlib.h
menu.c
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/stdlib-float.h
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/time.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
./elib.h
../headers//usr/include/stdint.h
./menu.h
../headers//usr/include/ctype.h
../headers//usr/include/string.h
threads.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/bits/pthreadtypes.h
../headers//usr/include/x86_64-linux-gnu/bits/semaphore.h
../headers//usr/include/stdint.h
../headers//usr/include/libio.h
./elib.h
./threads.h
../headers//usr/include/stdio.h
../headers//usr/include/pthread.h
../headers//usr/include/semaphore.h
../headers//usr/include/stdlib.h
infmt.c
../headers//usr/include/bambamc/BamBam_FastQRead.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/libio.h
./elib.h
../headers//usr/include/stdint.h
./sequence.h
./infmt.h
../headers//usr/include/stdio.h
../headers//usr/include/bambamc/BamBam_BamCollatorInterface.h
../headers//usr/include/stdlib.h
results.c
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
./elib.h
./array.h
../headers//usr/include/stdint.h
./diffstr.h
./sequence.h
./report.h
./score.h
./alignment.h
./results.h
../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h
../headers//usr/include/stdlib.h
resultpairs.c
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdlib.h
./elib.h
./array.h
../headers//usr/include/stdint.h
./insert.h
./sequence.h
./report.h
./results.h
./resultpairs.h
../headers//usr/include/stdio.h
report.c
../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/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
../headers//usr/include/bambamc/BamBam_CharBuffer.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/bambamc/BamBam_ListNode.h
../headers//usr/include/bambamc/BamBam_List.h
../headers//usr/include/x86_64-linux-gnu/zconf.h
../headers//usr/include/bambamc/BamBam_BgzfCompressor.h
../headers//usr/include/bambamc/BamBam_BamSingleAlignment.h
../headers//usr/include/bambamc/BamBam_BamAlignmentPut.h
../headers//usr/include/bambamc/BamBam_BamHeaderInfo.h
../headers//usr/include/bambamc/BamBam_BamWriter.h
../headers//usr/include/bambamc/BamBam_BamFlagBase.h
./elib.h
./array.h
./sequence.h
./diffstr.h
./report.h
../headers//usr/include/stdlib.h
../headers//usr/include/ctype.h
rmap.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/libio.h
./elib.h
./array.h
./sequence.h
./interval.h
./hashidx.h
./hashhit.h
./segment.h
./score.h
./alibuffer.h
./alignment.h
./results.h
./resultpairs.h
./rmap.h
../headers//usr/include/stdio.h
../headers//usr/include/stdlib.h
insert.c
../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/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
./elib.h
./vdef.h
../headers//usr/include/stdint.h
./insert.h
../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h
../headers//usr/include/stdlib.h
score.c
../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/stdio.h
../headers//usr/include/libio.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/emmintrin.h
../headers//usr/include/stdint.h
./elib.h
./sequence.h
./score.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h
diffstr.c
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.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
./elib.h
./diffstr.h
../headers//usr/include/ctype.h
alibuffer.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
./alibuffer.h
./alibuffer_struct.h
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/emmintrin.h
./score.h
./elib.h
../headers//usr/include/stdio.h
../headers//usr/include/stdlib.h
alignment.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/lib/gcc/x86_64-linux-gnu/4.9/include/emmintrin.h
../headers//usr/include/stdint.h
./elib.h
./sequence.h
./score.h
./diffstr.h
./alibuffer.h
./alibuffer_struct.h
./alignment.h
../headers//usr/include/stdio.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h
swsimd.c
../headers//usr/lib/gcc/x86_64-linux-gnu/4.9/include/emmintrin.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
./elib.h
./sequence.h
./score.h
./alibuffer.h
./alibuffer_struct.h
../headers//usr/include/stdio.h
sort.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
../headers//usr/include/stdio.h
./elib.h
../headers//usr/include/stdlib.h
array.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
./array.h
./elib.h
interval.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/stdlib.h
../headers//usr/include/libio.h
./elib.h
./vdef.h
../headers//usr/include/stdint.h
./sequence.h
./interval.h
../headers//usr/include/stdio.h
hashidx.c
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.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
./elib.h
./filio.h
./sequence.h
./interval.h
./hashidx.h
../headers//usr/include/stdlib.h
hashhit.c
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdlib.h
../headers//usr/include/stdint.h
./elib.h
./sequence.h
./hashidx.h
./hashhit.h
./sort.h
../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h
segment.c
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.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
./elib.h
./array.h
../headers//usr/include/stdint.h
./sequence.h
./hashhit.h
./segment.h
../headers//usr/include/stdlib.h
./sort.h
elib.c
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.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
./elib.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
filio.c
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
../headers//usr/include/string.h
./elib.h
sequence.c
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/zlib.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./filio.h
./elib.h
./sequence.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
libraries
../libs/usr/lib/x86_64-linux-gnu/libbambamc.so.0
../libs/lib/x86_64-linux-gnu/libz.so.1
../libs/lib/x86_64-linux-gnu/libm.so.6
../libs/lib/x86_64-linux-gnu/libpthread.so.0
../libs/lib/x86_64-linux-gnu/libc.so.6
manual
../man/smalt.1.gz
basqcol
compile units
basqcol.c
Gimple
./basqcol.c.004t.gimple
GKD
./basqcol.o.gkd
OBJ
obj: ./basqcol.o
basqual.c
Gimple
./basqual.c.004t.gimple
GKD
./basqual.o.gkd
OBJ
obj: ./basqual.o
elib.c
Gimple
./elib.c.004t.gimple
GKD
./elib.o.gkd
OBJ
obj: ./elib.o
filio.c
Gimple
./filio.c.004t.gimple
GKD
./filio.o.gkd
OBJ
obj: ./filio.o
sequence.c
Gimple
./sequence.c.004t.gimple
GKD
./sequence.o.gkd
OBJ
obj: ./sequence.o
includes
basqcol.c
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.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/stdint.h
../headers/../src/elib.h
../headers/../src/sequence.h
./basqual.h
basqual.c
../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/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
../headers/../src/elib.h
../headers/../src/filio.h
../headers/../src/sequence.h
./basqual.h
../headers//usr/include/stdlib.h
elib.c
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.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
./elib.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
filio.c
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
../headers//usr/include/string.h
./elib.h
sequence.c
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/zlib.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./filio.h
./elib.h
./sequence.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
libraries
../libs/lib/x86_64-linux-gnu/libz.so.1
../libs/lib/x86_64-linux-gnu/libc.so.6
manual
fetchseq
compile units
fetchseq.c
Gimple
./fetchseq.c.004t.gimple
GKD
./fetchseq.o.gkd
OBJ
obj: ./fetchseq.o
elib.c
Gimple
./elib.c.004t.gimple
GKD
./elib.o.gkd
OBJ
obj: ./elib.o
sequence.c
Gimple
./sequence.c.004t.gimple
GKD
./sequence.o.gkd
OBJ
obj: ./sequence.o
filio.c
Gimple
./filio.c.004t.gimple
GKD
./filio.o.gkd
OBJ
obj: ./filio.o
includes
fetchseq.c
../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/libio.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers/../src/elib.h
../headers//usr/include/stdint.h
../headers/../src/sequence.h
../headers//usr/include/stdio.h
../headers//usr/include/ctype.h
elib.c
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.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
./elib.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
sequence.c
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/zlib.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./filio.h
./elib.h
./sequence.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
filio.c
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
../headers//usr/include/string.h
./elib.h
libraries
../libs/lib/x86_64-linux-gnu/libz.so.1
../libs/lib/x86_64-linux-gnu/libc.so.6
manual
simread
compile units
simread.c
Gimple
./simread.c.004t.gimple
GKD
./simread.o.gkd
OBJ
obj: ./simread.o
rsample.c
Gimple
./rsample.c.004t.gimple
GKD
./rsample.o.gkd
OBJ
obj: ./rsample.o
elib.c
Gimple
./elib.c.004t.gimple
GKD
./elib.o.gkd
OBJ
obj: ./elib.o
sequence.c
Gimple
./sequence.c.004t.gimple
GKD
./sequence.o.gkd
OBJ
obj: ./sequence.o
filio.c
Gimple
./filio.c.004t.gimple
GKD
./filio.o.gkd
OBJ
obj: ./filio.o
includes
simread.c
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.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/time.h
../headers//usr/include/x86_64-linux-gnu/sys/types.h
../headers//usr/include/stdint.h
../headers/../src/elib.h
../headers/../src/sequence.h
./rsample.h
../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h
rsample.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
../headers/../src/elib.h
../headers//usr/include/stdlib.h
../headers//usr/include/x86_64-linux-gnu/bits/mathcalls.h
elib.c
../headers//usr/include/x86_64-linux-gnu/bits/stdio2.h
../headers//usr/include/x86_64-linux-gnu/bits/string3.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
./elib.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
sequence.c
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/zlib.h
../headers//usr/include/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
./filio.h
./elib.h
./sequence.h
../headers//usr/include/stdlib.h
../headers//usr/include/string.h
filio.c
../headers//usr/include/x86_64-linux-gnu/bits/string3.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/stdio.h
../headers//usr/include/libio.h
../headers//usr/include/stdint.h
../headers//usr/include/string.h
./elib.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