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r832: fixed outdated -L. Resolved #231 and #233

This commit is contained in:
Heng Li 2018-09-14 22:21:33 -04:00
parent 98c48a1c45
commit 7d80d6de4a
2 changed files with 6 additions and 4 deletions
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8
format.c
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@ -419,9 +419,11 @@ void mm_write_sam2(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int se
cigar_in_tag = 1;
}
if (cigar_in_tag) {
if (flag & 0x100) mm_sprintf_lite(s, "0S"); // secondary alignment
else if (flag & 0x800) mm_sprintf_lite(s, "%dS", r->re - r->rs); // supplementary alignment
else mm_sprintf_lite(s, "%dS", t->l_seq);
int slen;
if ((flag & 0x900) == 0 || (opt_flag & MM_F_SOFTCLIP)) slen = t->l_seq;
else if (flag & 0x100) slen = 0;
else slen = r->qe - r->qs;
mm_sprintf_lite(s, "%dS%dN", slen, r->re - r->rs);
} else write_sam_cigar(s, flag, 0, t->l_seq, r, opt_flag);
}

2
main.c
View File

@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "ketopt.h"
#define MM_VERSION "2.12-r829-dirty"
#define MM_VERSION "2.12-r832-dirty"
#ifdef __linux__
#include <sys/resource.h>