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r821: more relax on containing seeds

This commit is contained in:
Heng Li 2014-09-12 10:35:49 -04:00
parent f4aedddee6
commit 8d2b93156b
2 changed files with 3 additions and 3 deletions
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4
bwamem.c
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@ -627,12 +627,12 @@ void mem_chain2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac
// qd: distance ahead of the seed on query; rd: on reference
qd = s->qbeg - p->qb; rd = s->rbeg - p->rb;
max_gap = cal_max_gap(opt, qd < rd? qd : rd); // the maximal gap allowed in regions ahead of the seed
w = max_gap < opt->w? max_gap : opt->w; // bounded by the band width
w = max_gap < p->w? max_gap : p->w; // bounded by the band width
if (qd - rd < w && rd - qd < w) break; // the seed is "around" a previous hit
// similar to the previous four lines, but this time we look at the region behind
qd = p->qe - (s->qbeg + s->len); rd = p->re - (s->rbeg + s->len);
max_gap = cal_max_gap(opt, qd < rd? qd : rd);
w = max_gap < opt->w? max_gap : opt->w;
w = max_gap < p->w? max_gap : p->w;
if (qd - rd < w && rd - qd < w) break;
}
if (i < av->n) { // the seed is (almost) contained in an existing alignment; further testing is needed to confirm it is not leading to a different aln

2
main.c
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@ -4,7 +4,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.10-r819-dirty"
#define PACKAGE_VERSION "0.7.10-r821-dirty"
#endif
int bwa_fa2pac(int argc, char *argv[]);