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r550: fixed -L issues with secondary and supp aln

This commit is contained in:
Heng Li 2017-11-04 12:13:38 -04:00
parent 52ffbc9e0c
commit a3f0aa1d5b
3 changed files with 8 additions and 7 deletions
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6
README.md
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@ -212,10 +212,8 @@ To avoid this issue, you can add option `-L` at the minimap2 command line.
This option moves a long CIGAR to the `CG` tag and leaves a fully clipped CIGAR
at the SAM CIGAR column. Current tools that don't read CIGAR (e.g. merging and
sorting) still work with such BAM records; tools that read CIGAR will
effectively ignore these records. I have pull requests to the SAM spec, htslib,
htsjdk, bedtools2, Rsamtools and igv.js. If they are accepted, future versions
of these tools will seamlessly recognize long-cigar records generated by option
`-L`.
effectively ignore these records. It has been decided that future tools will
will seamlessly recognize long-cigar records generated by option `-L`.
**TD;DR**: if you work with ultra-long reads and use tools that only process
BAM files, please add option `-L`.

7
format.c
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@ -346,8 +346,11 @@ void mm_write_sam2(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, int se
if (n_cigar > max_bam_cigar_op)
cigar_in_tag = 1;
}
if (cigar_in_tag) mm_sprintf_lite(s, "%dS", t->l_seq);
else write_sam_cigar(s, flag, 0, t->l_seq, r);
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);
} else write_sam_cigar(s, flag, 0, t->l_seq, r);
}
// write mate positions

2
main.c
View File

@ -6,7 +6,7 @@
#include "mmpriv.h"
#include "getopt.h"
#define MM_VERSION "2.3-r546-dirty"
#define MM_VERSION "2.3-r550-dirty"
#ifdef __linux__
#include <sys/resource.h>