diff --git a/bwase.c b/bwase.c index 746add5..540aa6a 100644 --- a/bwase.c +++ b/bwase.c @@ -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); rseq = bns_get_seq(l_pac, pacseq, rb, re, &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); 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 diff --git a/main.c b/main.c index 6d3e301..4ebdfe8 100644 --- a/main.c +++ b/main.c @@ -4,7 +4,7 @@ #include "utils.h" #ifndef PACKAGE_VERSION -#define PACKAGE_VERSION "0.7.5a-r423" +#define PACKAGE_VERSION "0.7.5a-r424" #endif int bwa_fa2pac(int argc, char *argv[]);