adding a combination of nucleotide and colorspace alignment threshholding to Li&Durbin's BWA algorithm
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bwt_gen
COPYING
ChangeLog
Makefile
NEWS
README
bntseq.c
bntseq.h
btp324.pdf
bwa.1
bwa.txt
bwape.c
bwase.c
bwaseqio.c
bwt.c
bwt.h
bwt_lite.c
bwt_lite.h
bwtaln.c
bwtaln.h
bwtgap.c
bwtgap.h
bwtindex.c
bwtio.c
bwtmisc.c
bwtsw2.h
bwtsw2_aux.c
bwtsw2_chain.c
bwtsw2_core.c
bwtsw2_main.c
cs2nt.c
is.c
khash.h
kseq.h
ksort.h
kstring.c
kstring.h
kvec.h
main.c
main.h
simple_dp.c
solid2fastq.pl
stdaln.c
stdaln.h
utils.c
utils.h

README

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?