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r730: more permissive about merging overlapping

This commit is contained in:
Heng Li 2014-04-28 10:01:54 -04:00
parent 76bb49e01b
commit dadd5d6281
2 changed files with 6 additions and 4 deletions
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8
bwamem.c
View File

@ -376,16 +376,18 @@ int mem_patch_reg(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac,
if (bwa_verbose >= 4)
printf("* potential hit merge between [%d,%d)<=>[%ld,%ld) and [%d,%d)<=>[%ld,%ld), @ %s; w=%d, r=%.4g\n",
a->qb, a->qe, (long)a->rb, (long)a->re, b->qb, b->qe, (long)b->rb, (long)b->re, bns->anns[a->rid].name, w, r);
if (w > opt->w<<1) return 0; // the bandwidth is too large
if (r >= PATCH_MAX_R_BW) return 0; // relative bandwidth is too large
if (a->re < b->rb || a->qe < b->qb) { // no overlap on query or on ref
if (w > opt->w<<1) return 0; // the bandwidth is too large
if (r >= PATCH_MAX_R_BW) return 0; // relative bandwidth is too large
}
// global alignment
w += a->w + b->w;
if (bwa_verbose >= 4) printf("* test potential hit merge with global alignment; w=%d\n", w);
bwa_gen_cigar2(opt->mat, opt->o_del, opt->e_del, opt->o_ins, opt->e_ins, w, bns->l_pac, pac, b->qe - a->qb, query + a->qb, a->rb, b->re, &score, 0, 0);
q_s = (int)((double)(b->qe - a->qb) / ((b->qe - b->qb) + (a->qe - a->qb)) * (b->score + a->score) + .499); // predicted score from query
r_s = (int)((double)(b->re - a->rb) / ((b->re - b->rb) + (a->re - a->rb)) * (b->score + a->score) + .499); // predicted score from ref
if (2. * score / (q_s + r_s) < PATCH_MIN_SC_RATIO) return 0;
if (bwa_verbose >= 4) printf("* score=%d;(%d,%d)\n", score, q_s, r_s);
if ((double)score / (q_s > r_s? q_s : r_s) < PATCH_MIN_SC_RATIO) return 0;
*_w = w;
return score;
}

2
main.c
View File

@ -4,7 +4,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.8-r729-dirty"
#define PACKAGE_VERSION "0.7.8-r730-dirty"
#endif
int bwa_fa2pac(int argc, char *argv[]);