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r824: ALT mapping seems working

This commit is contained in:
Heng Li 2014-09-15 00:29:05 -04:00
parent 015ab3f6c3
commit aee53f1334
3 changed files with 8 additions and 7 deletions
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9
bwamem.c
View File

@ -157,7 +157,7 @@ typedef struct {
typedef struct {
int n, m, first, rid;
uint32_t w:30, kept:2;
uint32_t w:29, kept:2, is_alt:1;
float frac_rep;
int64_t pos;
mem_seed_t *seeds;
@ -278,6 +278,7 @@ mem_chain_v mem_chain(const mem_opt_t *opt, const bwt_t *bwt, const bntseq_t *bn
tmp.seeds = calloc(tmp.m, sizeof(mem_seed_t));
tmp.seeds[0] = s;
tmp.rid = rid;
tmp.is_alt = !!bns->anns[rid].is_alt;
kb_putp(chn, tree, &tmp);
}
}
@ -331,7 +332,7 @@ int mem_chain_flt(const mem_opt_t *opt, int n_chn, mem_chain_t *a)
int j = chains.a[k];
int b_max = chn_beg(a[j]) > chn_beg(a[i])? chn_beg(a[j]) : chn_beg(a[i]);
int e_min = chn_end(a[j]) < chn_end(a[i])? chn_end(a[j]) : chn_end(a[i]);
if (e_min > b_max) { // have overlap
if (e_min > b_max && (!a[j].is_alt || a[i].is_alt)) { // have overlap; don't consider ovlp where the kept chain is ALT while the current chain is primary
int li = chn_end(a[i]) - chn_beg(a[i]);
int lj = chn_end(a[j]) - chn_beg(a[j]);
int min_l = li < lj? li : lj;
@ -518,7 +519,7 @@ int mem_mark_primary_se(const mem_opt_t *opt, int n, mem_alnreg_t *a, int64_t id
}
ks_introsort(mem_ars_hash, n, a);
mem_mark_primary_se_core(opt, n, a, &z);
for (i = 0; i < n; ++i) // this block is used to trigger potential bugs; if no bugs, it has no effects
for (i = 0; i < n; ++i) // don't track the "parent" hit of ALT secondary hits
if (a[i].is_alt && a[i].secondary >= 0)
a[i].secondary = INT_MAX;
if (n_pri > 0 || n_pri != n) {
@ -957,7 +958,7 @@ void mem_reg2sam(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac,
mem_aln_t *q;
if (p->score < opt->T) continue;
if (p->secondary >= 0 && (p->is_alt || !(opt->flag&MEM_F_ALL))) continue;
if (p->secondary >= 0 && p->score < a->a[p->secondary].score * opt->drop_ratio) continue;
if (p->secondary >= 0 && p->secondary < INT_MAX && p->score < a->a[p->secondary].score * opt->drop_ratio) continue;
q = kv_pushp(mem_aln_t, aa);
*q = mem_reg2aln(opt, bns, pac, s->l_seq, s->seq, p);
assert(q->rid >= 0); // this should not happen with the new code

4
bwamem_extra.c
View File

@ -128,7 +128,7 @@ char **mem_gen_alt(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac
cnt = calloc(a->n, sizeof(int));
for (i = 0, tot = 0; i < a->n; ++i) {
int j = a->a[i].secondary;
if (j >= 0 && a->a[i].score >= a->a[j].score * opt->XA_drop_ratio)
if (j >= 0 && j < INT_MAX && a->a[i].score >= a->a[j].score * opt->XA_drop_ratio)
++cnt[j], ++tot;
}
if (tot == 0) goto end_gen_alt;
@ -136,7 +136,7 @@ char **mem_gen_alt(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac
for (i = 0; i < a->n; ++i) {
mem_aln_t t;
int j = a->a[i].secondary;
if (j < 0 || a->a[i].score < a->a[j].score * opt->XA_drop_ratio) continue; // we don't process the primary alignments as they will be converted to SAM later
if (j < 0 || j == INT_MAX || a->a[i].score < a->a[j].score * opt->XA_drop_ratio) continue; // we don't process the primary alignments as they will be converted to SAM later
if (cnt[j] > opt->max_hits) continue;
t = mem_reg2aln(opt, bns, pac, l_query, query, &a->a[i]);
kputs(bns->anns[t.rid].name, &aln[j]);

2
main.c
View File

@ -4,7 +4,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.10-r823-dirty"
#define PACKAGE_VERSION "0.7.10-r824-dirty"
#endif
int bwa_fa2pac(int argc, char *argv[]);