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r736: improved in low-complexity regions 

Example: GGAGGGGAAGGGTGGGCTGGAGGGGACGGGTGGGCTGGAGGGGAAGGGTGTGCTGGAGGGAAAAGGTGGACTGGAGGGGAAGGGTGGGCTGGAGGGGAAGG

This read has 5 chains, two of which are:

weight=80  26;26;0,4591439948(10:-3095894)  23;23;27,4591439957(10:-3095888)  31;31;70,4591439964(10:-3095873)
weight=50  45;45;51,4591440017(10:-3095806) 50;50;51,4591440017(10:-3095801)  31;31;70,4591440090(10:-3095747)

Extension from the 26bp seed in the 1st chain gives an alignment [0,101) <=> [4591439948,4591440067), which
contains the 50bp seed in the second chain. However, if we extend the 50bp seed, it yields a better alignment
[0,101) <=> [4591439966,4591440067) with a different starting position. The 26bp seed is wrong. This commit
adds a heuristic to fix this issue.
This commit is contained in:
Heng Li 2014-04-30 14:14:20 -04:00
parent 11698fc4e5
commit 88f89be60e
3 changed files with 8 additions and 2 deletions
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7
bwamem.c
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@ -417,6 +417,8 @@ int mem_sort_dedup_patch(const mem_opt_t *opt, const bntseq_t *bns, const uint8_
} else if (q->rb < p->rb && (score = mem_patch_reg(opt, bns, pac, query, q, p, &w)) > 0) { // then merge q into p
p->n_comp += q->n_comp + 1;
p->seedcov = p->seedcov > q->seedcov? p->seedcov : q->seedcov;
p->sub = p->sub > q->sub? p->sub : q->sub;
p->csub = p->csub > q->csub? p->csub : q->csub;
p->qb = q->qb, p->rb = q->rb;
p->truesc = p->score = score;
p->w = w;
@ -650,6 +652,7 @@ void mem_chain2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac
int64_t rd;
int qd, w, max_gap;
if (s->rbeg < p->rb || s->rbeg + s->len > p->re || s->qbeg < p->qb || s->qbeg + s->len > p->qe) continue; // not fully contained
if (s->len - p->seedlen0 > .1 * l_query) continue; // this seed may give a better alignment
// 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
@ -663,7 +666,8 @@ void mem_chain2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac
}
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
if (bwa_verbose >= 4)
printf("** Seed(%d) [%ld;%ld,%ld] is almost contained in an existing alignment. Confirming whether extension is needed...\n", k, (long)s->len, (long)s->qbeg, (long)s->rbeg);
printf("** Seed(%d) [%ld;%ld,%ld] is almost contained in an existing alignment [%d,%d) <=> [%ld,%ld)\n",
k, (long)s->len, (long)s->qbeg, (long)s->rbeg, av->a[i].qb, av->a[i].qe, (long)av->a[i].rb, (long)av->a[i].re);
for (i = k + 1; i < c->n; ++i) { // check overlapping seeds in the same chain
const mem_seed_t *t;
if (srt[i] == 0) continue;
@ -753,6 +757,7 @@ void mem_chain2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac
a->seedcov += t->len; // this is not very accurate, but for approx. mapQ, this is good enough
}
a->w = aw[0] > aw[1]? aw[0] : aw[1];
a->seedlen0 = s->len;
}
free(srt); free(rseq);
}

1
bwamem.h
View File

@ -62,6 +62,7 @@ typedef struct {
int w; // actual band width used in extension
int seedcov; // length of regions coverged by seeds
int secondary; // index of the parent hit shadowing the current hit; <0 if primary
int seedlen0; // length of the starting seed
int n_comp; // number of sub-alignments chained together
uint64_t hash;
} mem_alnreg_t;

2
main.c
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@ -4,7 +4,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.8-r735-dirty"
#define PACKAGE_VERSION "0.7.8-r736-dirty"
#endif
int bwa_fa2pac(int argc, char *argv[]);