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r655: options to map to one strand of the ref #91

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Heng Li
2018-01-16 10:34:30 -05:00
parent eecc06086f
commit 33f8157961
5 changed files with 29 additions and 3 deletions
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align.c
+1 -1
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@@ -696,7 +696,7 @@ mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *m
regs[i].p->trans_strand = opt->flag&MM_F_SPLICE_FOR? 1 : 2;
}
if (r2.cnt > 0) regs = mm_insert_reg(&r2, i, &n_regs, regs);
if (!(opt->flag&MM_F_SPLICE) && !(opt->flag&MM_F_SR) && i > 0) { // don't try inversion alignment for -xsplice or -xsr
if (!(opt->flag&(MM_F_SPLICE|MM_F_SR)) && !(opt->flag&(MM_F_FOR_ONLY|MM_F_REV_ONLY)) && i > 0) { // don't try inversion alignment for -xsplice or -xsr, or --for-only/rev-only
if (mm_align1_inv(km, opt, mi, qlen, qseq0, &regs[i-1], &regs[i], &r2, &ez)) {
regs = mm_insert_reg(&r2, i, &n_regs, regs);
++i; // skip the inserted INV alignment