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no effective changes

This commit is contained in:
Heng Li 2017-09-20 10:11:05 -04:00
parent 5caadc28b4
commit fd14618e61
1 changed files with 10 additions and 5 deletions
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15
map.c
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@ -271,12 +271,17 @@ mm_reg1_t *mm_map_seg(const mm_idx_t *mi, int n_segs, int *qlens, const char *se
if (!(opt->flag & MM_F_SPLICE))
mm_join_long(b->km, opt, qlen_sum, n_regs, regs, a); // TODO: this can be applied to all-vs-all in principle
}
if (opt->flag & MM_F_CIGAR) {
regs = mm_align_skeleton(b->km, opt, mi, qlen_sum, seqs, n_regs, regs, a); // this calls mm_filter_regs()
if (!(opt->flag & MM_F_AVA)) {
mm_set_parent(b->km, opt->mask_level, *n_regs, regs, opt->a * 2 + opt->b);
mm_select_sub(b->km, opt->mask_level, opt->pri_ratio, mi->k*2, opt->best_n, n_regs, regs);
mm_set_sam_pri(*n_regs, regs);
if (n_segs == 1) {
regs = mm_align_skeleton(b->km, opt, mi, qlen_sum, seqs, n_regs, regs, a); // this calls mm_filter_regs()
if (!(opt->flag & MM_F_AVA)) {
mm_set_parent(b->km, opt->mask_level, *n_regs, regs, opt->a * 2 + opt->b);
mm_select_sub(b->km, opt->mask_level, opt->pri_ratio, mi->k*2, opt->best_n, n_regs, regs);
mm_set_sam_pri(*n_regs, regs);
}
} else {
abort();
}
}
mm_set_mapq(*n_regs, regs, opt->min_chain_score, opt->a, rep_len);