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r424: fixed a bw bug in samse/pe

This commit is contained in:
Heng Li 2013-11-25 15:48:04 -05:00
parent 4219e58623
commit 8b6ec74907
2 changed files with 2 additions and 2 deletions
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2
bwase.c
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@ -180,7 +180,7 @@ bwa_cigar_t *bwa_refine_gapped_core(bwtint_t l_pac, const ubyte_t *pacseq, int l
assert(re <= l_pac); assert(re <= l_pac);
rseq = bns_get_seq(l_pac, pacseq, rb, re, &rlen); rseq = bns_get_seq(l_pac, pacseq, rb, re, &rlen);
assert(re - rb == rlen); assert(re - rb == rlen);
ksw_global(len, seq, rlen, rseq, 5, mat, 5, 1, SW_BW, n_cigar, &cigar32); ksw_global(len, seq, rlen, rseq, 5, mat, 5, 1, SW_BW > abs(rlen - len) * 1.5? SW_BW : abs(rlen - len) * 1.5, n_cigar, &cigar32);
assert(*n_cigar > 0); assert(*n_cigar > 0);
if ((cigar32[*n_cigar - 1]&0xf) == 1) cigar32[*n_cigar - 1] = (cigar32[*n_cigar - 1]>>4<<4) | 3; // change endding ins to soft clipping if ((cigar32[*n_cigar - 1]&0xf) == 1) cigar32[*n_cigar - 1] = (cigar32[*n_cigar - 1]>>4<<4) | 3; // change endding ins to soft clipping
if ((cigar32[0]&0xf) == 1) cigar32[0] = (cigar32[0]>>4<<4) | 3; // change beginning ins to soft clipping if ((cigar32[0]&0xf) == 1) cigar32[0] = (cigar32[0]>>4<<4) | 3; // change beginning ins to soft clipping

2
main.c
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@ -4,7 +4,7 @@
#include "utils.h" #include "utils.h"
#ifndef PACKAGE_VERSION #ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.5a-r423" #define PACKAGE_VERSION "0.7.5a-r424"
#endif #endif
int bwa_fa2pac(int argc, char *argv[]); int bwa_fa2pac(int argc, char *argv[]);