GitHub - michaelglass/bwa-colorspace: adding a combination of nucleotide and colorspace alignment threshholding to Li&Durbin's BWA algorithm

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adding a combination of nucleotide and colorspace alignment threshholding to Li&Durbin's BWA algorithm

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Name		Name	Last commit message	Last commit date
Latest commit History 7 Commits
bwt_gen		bwt_gen
COPYING		COPYING
ChangeLog		ChangeLog
Makefile		Makefile
NEWS		NEWS
README		README
bntseq.c		bntseq.c
bntseq.h		bntseq.h
btp324.pdf		btp324.pdf
bwa.1		bwa.1
bwa.txt		bwa.txt
bwape.c		bwape.c
bwase.c		bwase.c
bwaseqio.c		bwaseqio.c
bwt.c		bwt.c
bwt.h		bwt.h
bwt_lite.c		bwt_lite.c
bwt_lite.h		bwt_lite.h
bwtaln.c		bwtaln.c
bwtaln.h		bwtaln.h
bwtgap.c		bwtgap.c
bwtgap.h		bwtgap.h
bwtindex.c		bwtindex.c
bwtio.c		bwtio.c
bwtmisc.c		bwtmisc.c
bwtsw2.h		bwtsw2.h
bwtsw2_aux.c		bwtsw2_aux.c
bwtsw2_chain.c		bwtsw2_chain.c
bwtsw2_core.c		bwtsw2_core.c
bwtsw2_main.c		bwtsw2_main.c
cs2nt.c		cs2nt.c
is.c		is.c
khash.h		khash.h
kseq.h		kseq.h
ksort.h		ksort.h
kstring.c		kstring.c
kstring.h		kstring.h
kvec.h		kvec.h
main.c		main.c
main.h		main.h
simple_dp.c		simple_dp.c
solid2fastq.pl		solid2fastq.pl
stdaln.c		stdaln.c
stdaln.h		stdaln.h
utils.c		utils.c
utils.h		utils.h

Repository files navigation

what's happening in this program. . .

1)
bntseq.c
#156 void bns_fasta2bntseq(gzFile fp_fa, const char *prefix) 
Takes a fasta database file (fp_fa) and converts it to a .pac (packed) binary with the filename prefix.

this code has lots of types defined at compile time.  for instance, various macros set types and variables in methods.
kseq.h defines various macros and inline functions.  type_t is gzFile, __read is gzread, buffer is 4096.  


kseq.h
looking through kseq_read up to ks_getuntil at this point.

WHAT IS A PAC FILE?
HOW DO I READ IT?