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r739: output suboptimal hits in the PE mode 

However, PE information is not used for suboptimal hits
This commit is contained in:
Heng Li 2014-04-30 23:23:54 -04:00
parent c6c943f9d7
commit 5aedc978d1
2 changed files with 29 additions and 5 deletions
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32
bwamem_pair.c
View File

@ -248,6 +248,7 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
extern int mem_approx_mapq_se(const mem_opt_t *opt, const mem_alnreg_t *a);
extern void mem_reg2sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, mem_alnreg_v *a, int extra_flag, const mem_aln_t *m);
extern void mem_aln2sam(const bntseq_t *bns, kstring_t *str, bseq1_t *s, int n, const mem_aln_t *list, int which, const mem_aln_t *m, int softclip_all);
extern char **mem_gen_alt(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, const mem_alnreg_v *a, int l_query, const char *query);
int n = 0, i, j, z[2], o, subo, n_sub, extra_flag = 1;
kstring_t str;
@ -272,6 +273,7 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
// pairing single-end hits
if (a[0].n && a[1].n && (o = mem_pair(opt, bns, pac, pes, s, a, id, &subo, &n_sub, z)) > 0) {
int is_multi[2], q_pe, score_un, q_se[2];
char **XA[2];
// check if an end has multiple hits even after mate-SW
for (i = 0; i < 2; ++i) {
for (j = 1; j < a[i].n; ++j)
@ -307,14 +309,36 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
q_se[0] = mem_approx_mapq_se(opt, &a[0].a[0]);
q_se[1] = mem_approx_mapq_se(opt, &a[1].a[0]);
}
// suboptimal hits
if (!(opt->flag & MEM_F_ALL)) {
for (i = 0; i < 2; ++i) {
int k = a[i].a[z[i]].secondary;
if (k >= 0) { // switch secondary and primary
assert(a[i].a[k].secondary < 0);
for (j = 0; j < a[i].n; ++j)
if (a[i].a[j].secondary == k || j == k)
a[i].a[j].secondary = z[i];
a[i].a[z[i]].secondary = -1;
}
XA[i] = mem_gen_alt(opt, bns, pac, &a[i], s[i].l_seq, s[i].seq);
}
} else XA[0] = XA[1] = 0;
// write SAM
h[0] = mem_reg2aln(opt, bns, pac, s[0].l_seq, s[0].seq, &a[0].a[z[0]]); h[0].mapq = q_se[0]; h[0].flag |= 0x40 | extra_flag;
h[1] = mem_reg2aln(opt, bns, pac, s[1].l_seq, s[1].seq, &a[1].a[z[1]]); h[1].mapq = q_se[1]; h[1].flag |= 0x80 | extra_flag;
h[0] = mem_reg2aln(opt, bns, pac, s[0].l_seq, s[0].seq, &a[0].a[z[0]]); h[0].mapq = q_se[0]; h[0].flag |= 0x40 | extra_flag; h[0].XA = XA[0]? XA[0][z[0]] : 0;
h[1] = mem_reg2aln(opt, bns, pac, s[1].l_seq, s[1].seq, &a[1].a[z[1]]); h[1].mapq = q_se[1]; h[1].flag |= 0x80 | extra_flag; h[1].XA = XA[1]? XA[1][z[1]] : 0;
mem_aln2sam(bns, &str, &s[0], 1, &h[0], 0, &h[1], opt->flag&MEM_F_SOFTCLIP); s[0].sam = strdup(str.s); str.l = 0;
mem_aln2sam(bns, &str, &s[1], 1, &h[1], 0, &h[0], opt->flag&MEM_F_SOFTCLIP); s[1].sam = str.s;
if (strcmp(s[0].name, s[1].name) != 0) err_fatal(__func__, "paired reads have different names: \"%s\", \"%s\"\n", s[0].name, s[1].name);
free(h[0].cigar); free(h[0].XA);
free(h[1].cigar); free(h[1].XA);
free(h[0].cigar); // h[0].XA will be freed in the following block
free(h[1].cigar);
// free XA
for (i = 0; i < 2; ++i) {
if (XA[i]) {
for (j = 0; j < a[i].n; ++j)
free(XA[i][j]);
free(XA[i]);
}
}
} else goto no_pairing;
return n;

2
main.c
View File

@ -4,7 +4,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.8-r738-dirty"
#define PACKAGE_VERSION "0.7.8-r739-dirty"
#endif
int bwa_fa2pac(int argc, char *argv[]);