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r550: fixed -L issues with secondary and supp aln

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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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format.c
+5 -2
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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