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r359: identical output to 0.7.2 (without -a)

This commit is contained in:
Heng Li 2013-03-11 23:16:18 -04:00
parent 0f88103d2a
commit 6c665189ad
4 changed files with 5 additions and 3 deletions
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2
bwamem.c
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@ -837,7 +837,7 @@ mem_aln_t mem_reg2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *
}
a.rid = bns_pos2rid(bns, pos);
a.pos = pos - bns->anns[a.rid].offset;
a.score = ar->score; a.sub = ar->sub;
a.score = ar->score; a.sub = ar->sub > ar->csub? ar->sub : ar->csub;
free(query);
return a;
}

2
bwamem_pair.c
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@ -295,6 +295,7 @@ int mem_sam_pe(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, co
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;
mem_aln2sam(bns, &str, &s[0], 1, &h[0], 0, &h[1]); s[0].sam = strdup(str.s); str.l = 0;
mem_aln2sam(bns, &str, &s[1], 1, &h[1], 0, &h[0]); s[1].sam = str.s;
free(h[0].cigar); free(h[1].cigar);
} else goto no_pairing;
return n;
@ -306,5 +307,6 @@ no_pairing:
}
mem_reg2sam_se(opt, bns, pac, &s[0], &a[0], 0x41|extra_flag, &h[1]);
mem_reg2sam_se(opt, bns, pac, &s[1], &a[1], 0x81|extra_flag, &h[0]);
free(h[0].cigar); free(h[1].cigar);
return n;
}

2
example.c
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@ -34,7 +34,7 @@ int main(int argc, char *argv[])
if (ar.a[i].secondary >= 0) continue; // skip secondary alignments
a = mem_reg2aln(opt, idx->bns, idx->pac, ks->seq.l, ks->seq.s, &ar.a[i]); // get forward-strand position and CIGAR
// print alignment
printf("%s\t%c\t%s\t%d\t%d\t", ks->name.s, "+-"[a.is_rev], idx->bns->anns[a.rid].name, a.pos, a.mapq);
printf("%s\t%c\t%s\t%ld\t%d\t", ks->name.s, "+-"[a.is_rev], idx->bns->anns[a.rid].name, (long)a.pos, a.mapq);
for (k = 0; k < a.n_cigar; ++k) // print CIGAR
printf("%d%c", a.cigar[k]>>4, "MIDSH"[a.cigar[k]&0xf]);
printf("\t%d\n", a.NM); // print edit distance

2
main.c
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@ -3,7 +3,7 @@
#include "utils.h"
#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.2-r351"
#define PACKAGE_VERSION "0.7.2-r359-beta"
#endif
int bwa_fa2pac(int argc, char *argv[]);