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r742: further control the max bandwidth 

I am looking at 6kb bandwidth...
This commit is contained in:
Heng Li 2014-05-01 14:27:38 -04:00
parent 7954e77a1b
commit fa20c71920
3 changed files with 5 additions and 3 deletions
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4
bwamem.c
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@ -381,6 +381,7 @@ int mem_patch_reg(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac,
} else if (w > opt->w<<2 || r >= PATCH_MAX_R_BW*2) return 0; // more permissive if overlapping on both ref and query
// global alignment
w += a->w + b->w;
w = w < opt->w<<2? w : opt->w<<2;
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
@ -1044,9 +1045,10 @@ mem_aln_t mem_reg2aln2(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t
i = 0; a.cigar = 0;
do {
free(a.cigar);
w2 = w2 < opt->w<<2? w2 : opt->w<<2;
a.cigar = bwa_gen_cigar2(opt->mat, opt->o_del, opt->e_del, opt->o_ins, opt->e_ins, w2, bns->l_pac, pac, qe - qb, (uint8_t*)&query[qb], rb, re, &score, &a.n_cigar, &NM);
if (bwa_verbose >= 4) printf("* Final alignment: w2=%d, global_sc=%d, local_sc=%d\n", w2, score, ar->truesc);
if (score == last_sc) break; // it is possible that global alignment and local alignment give different scores
if (score == last_sc || w2 == opt->w<<2) break; // it is possible that global alignment and local alignment give different scores
last_sc = score;
w2 <<= 1;
} while (++i < 3 && score < ar->truesc - opt->a);

2
ksw.c
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@ -510,7 +510,7 @@ int ksw_global2(int qlen, const uint8_t *query, int tlen, const uint8_t *target,
if (n_cigar_) *n_cigar_ = 0;
// allocate memory
n_col = qlen < 2*w+1? qlen : 2*w+1; // maximum #columns of the backtrack matrix
z = n_cigar_ && cigar_? malloc(n_col * tlen) : 0;
z = n_cigar_ && cigar_? malloc((long)n_col * tlen) : 0;
qp = malloc(qlen * m);
eh = calloc(qlen + 1, 8);
// generate the query profile

2
main.c
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@ -4,7 +4,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.8-r741-dirty"
#define PACKAGE_VERSION "0.7.8-r742-dirty"
#endif
int bwa_fa2pac(int argc, char *argv[]);