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optionally mark multi-part hits as secondary

This commit is contained in:
Heng Li 2011-11-23 23:39:59 -05:00
parent 9f84384ed2
commit 196b50dde3
2 changed files with 2 additions and 2 deletions
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2
bwtsw2_aux.c
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@ -489,7 +489,7 @@ static void print_hits(const bntseq_t *bns, const bsw2opt_t *opt, bsw2seq1_t *ks
bsw2aux_t *q = b->aux + i; bsw2aux_t *q = b->aux + i;
int j, beg, end, type = 0; int j, beg, end, type = 0;
// print mandatory fields before SEQ // print mandatory fields before SEQ
ksprintf(&str, "%s\t%d", ks->name, q->flag); ksprintf(&str, "%s\t%d", ks->name, q->flag | (opt->multi_2nd && i? 0x100 : 0));
ksprintf(&str, "\t%s\t%ld", q->chr>=0? bns->anns[q->chr].name : "*", (long)q->pos + 1); ksprintf(&str, "\t%s\t%ld", q->chr>=0? bns->anns[q->chr].name : "*", (long)q->pos + 1);
if (p->l == 0) { // not a repetitive hit if (p->l == 0) { // not a repetitive hit
ksprintf(&str, "\t%d\t", q->pqual); ksprintf(&str, "\t%d\t", q->pqual);

2
main.c
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@ -4,7 +4,7 @@
#include "utils.h" #include "utils.h"
#ifndef PACKAGE_VERSION #ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.6.0-r91-dev" #define PACKAGE_VERSION "0.6.0-r97-dev"
#endif #endif
static int usage() static int usage()