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r1261: code clean up; renamed --jump-bed to -j

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Also added --pairing to replace --no-pairing and --pe-ind-chain
This commit is contained in:
Heng Li
2025-04-06 18:32:58 -04:00
parent 3d351267a0
commit 38acd6617f
7 changed files with 53 additions and 50 deletions
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map.c
+1 -1
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@@ -379,7 +379,7 @@ void mm_map_frag_core(const mm_idx_t *mi, int n_segs, const int *qlens, const ch
void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **seqs, int *n_regs, mm_reg1_t **regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *qname)
{
if ((opt->flag & MM_F_PE_IND) && n_segs == 2 && opt->pe_ori >= 0 && (opt->flag&MM_F_CIGAR)) {
if ((opt->flag & MM_F_WEAK_PAIRING) && n_segs == 2 && opt->pe_ori >= 0 && (opt->flag&MM_F_CIGAR)) {
int i;
for (i = 0; i < n_segs; ++i)
mm_map_frag_core(mi, 1, &qlens[i], &seqs[i], &n_regs[i], &regs[i], b, opt, qname);