Skip to content

Commit

Permalink
r1036: PE ALT mapping incorrect
Browse files Browse the repository at this point in the history 
No SA/XA tags!
  • Loading branch information
@lh3
lh3 committed Dec 24, 2014
1 parent 408fd5e commit b9bbf2d
Show file tree
Hide file tree
Showing 2 changed files with 39 additions and 38 deletions.
75 changes: 38 additions & 37 deletions bwamem_pair.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -244,17 +244,6 @@ int mem_pair(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, cons

void mem_aln2sam(const mem_opt_t *opt, const bntseq_t *bns, kstring_t *str, bseq1_t *s, int n, const mem_aln_t *list, int which, const mem_aln_t *m);

static inline void mem_reg2sam_alt(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, kstring_t *str, bseq1_t *s, mem_alnreg_t *p, int extra_flag, const mem_aln_t *m)
{ // a simplified version of mem_reg2sam()
mem_aln_t t;
if (p->score < opt->T || p->secondary >= 0 || !p->is_alt) return;
t = mem_reg2aln(opt, bns, pac, s->l_seq, s->seq, p);
t.flag |= extra_flag;
t.flag |= (opt->flag&MEM_F_NO_MULTI)? 0x10000 : 0x800;
mem_aln2sam(opt, bns, str, s, 1, &t, 0, m);
free(t.cigar);
}

#define raw_mapq(diff, a) ((int)(6.02 * (diff) / (a) + .499))

int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, const mem_pestat_t pes[4], uint64_t id, bseq1_t s[2], mem_alnreg_v a[2])
Expand All @@ -264,11 +253,14 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
extern void mem_reg2sam(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 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, n_pri[2];
int n = 0, i, j, z[2], o, subo, n_sub, extra_flag = 1, n_pri[2], n_aa[2];
kstring_t str;
mem_aln_t h[2];
mem_aln_t h[2], g[2], aa[2][2];

str.l = str.m = 0; str.s = 0;
memset(h, 0, sizeof(mem_aln_t) * 2);
memset(g, 0, sizeof(mem_aln_t) * 2);
n_aa[0] = n_aa[1] = 0;
if (!(opt->flag & MEM_F_NO_RESCUE)) { // then perform SW for the best alignment
mem_alnreg_v b[2];
kv_init(b[0]); kv_init(b[1]);
Expand Down Expand Up @@ -324,38 +316,47 @@ 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
for (i = 0; i < 2; ++i) {
int k = a[i].a[z[i]].secondary_all;
if (k >= 0 && k < n_pri[i]) { // switch secondary and primary if both of them are non-ALT
assert(a[i].a[k].secondary_all < 0);
for (j = 0; j < a[i].n; ++j)
if (a[i].a[j].secondary_all == k || j == k)
a[i].a[j].secondary_all = z[i];
a[i].a[z[i]].secondary_all = -1;
}
}
if (!(opt->flag & MEM_F_ALL)) {
for (i = 0; i < 2; ++i) {
int k = a[i].a[z[i]].secondary_all;
if (k >= 0 && k < n_pri[i]) { // switch secondary and primary if both of them are non-ALT
assert(a[i].a[k].secondary_all < 0);
for (j = 0; j < a[i].n; ++j)
if (a[i].a[j].secondary_all == k || j == k)
a[i].a[j].secondary_all = z[i];
a[i].a[z[i]].secondary_all = -1;
}
for (i = 0; i < 2; ++i)
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[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(opt, bns, &str, &s[0], 1, &h[0], 0, &h[1]); // write the primary hit for read1
if (n_pri[0] < a[0].n) mem_reg2sam_alt(opt, bns, pac, &str, &s[0], &a[0].a[n_pri[0]], 0x41|extra_flag, &h[1]);
for (i = 0; i < 2; ++i) {
h[i] = mem_reg2aln(opt, bns, pac, s[i].l_seq, s[i].seq, &a[i].a[z[i]]);
h[i].mapq = q_se[i];
h[i].flag |= 0x40 | extra_flag;
h[i].XA = XA[i]? XA[i][z[i]] : 0;
aa[i][n_aa[i]++] = h[i];
if (n_pri[i] < a[i].n) { // the read has ALT hits
g[i] = mem_reg2aln(opt, bns, pac, s[i].l_seq, s[i].seq, &a[i].a[n_pri[i]]);
g[i].flag |= 0x40 | extra_flag;
g[i].XA = XA[i]? XA[i][n_pri[i]] : 0;
aa[i][n_aa[i]++] = g[i];
}
}
for (i = 0; i < n_aa[0]; ++i)
mem_aln2sam(opt, bns, &str, &s[0], n_aa[0], aa[0], i, &h[1]); // write read1 hits
s[0].sam = strdup(str.s); str.l = 0;
mem_aln2sam(opt, bns, &str, &s[1], 1, &h[1], 0, &h[0]); // write the primary hit for read2
if (n_pri[1] < a[1].n) mem_reg2sam_alt(opt, bns, pac, &str, &s[1], &a[1].a[n_pri[1]], 0x81|extra_flag, &h[0]);
for (i = 0; i < n_aa[1]; ++i)
mem_aln2sam(opt, bns, &str, &s[1], n_aa[1], aa[1], i, &h[0]); // write read2 hits
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); // h[0].XA will be freed in the following block
free(h[1].cigar);
// free XA
// free
for (i = 0; i < 2; ++i) {
if (XA[i]) {
for (j = 0; j < a[i].n; ++j) free(XA[i][j]);
free(XA[i]);
}
free(h[i].cigar); free(g[i].cigar);
if (XA[i] == 0) continue;
for (j = 0; j < a[i].n; ++j) free(XA[i][j]);
free(XA[i]);
}
} else goto no_pairing;
return n;
Expand Down
2 changes: 1 addition & 1 deletion main.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
#include "utils.h"

#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.11-r1034"
#define PACKAGE_VERSION "0.7.11-r1036-dirty"
#endif

int bwa_fa2pac(int argc, char *argv[]);
Expand Down

0 comments on commit b9bbf2d

Please sign in to comment.