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r1208: reverted RMQ gap coefficient

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Such that minimap2 can give the same alignment in other modes
This commit is contained in:
Heng Li
2024-03-27 08:48:10 -04:00
parent 119bdc6029
commit e3d8c708ac
4 changed files with 8 additions and 3 deletions
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format.c
+1 -1
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@@ -393,7 +393,7 @@ void mm_write_paf3(kstring_t *s, const mm_idx_t *mi, const mm_bseq1_t *t, const
mm_sprintf_lite(s, "%d%c", r->p->cigar[k]>>4, MM_CIGAR_STR[r->p->cigar[k]&0xf]); mm_sprintf_lite(s, "%d%c", r->p->cigar[k]>>4, MM_CIGAR_STR[r->p->cigar[k]&0xf]);
} }
if (r->p && (opt_flag & (MM_F_OUT_CS|MM_F_OUT_DS|MM_F_OUT_MD))) if (r->p && (opt_flag & (MM_F_OUT_CS|MM_F_OUT_DS|MM_F_OUT_MD)))
write_cs_ds_or_MD(km, s, mi, t, r, !(opt_flag&MM_F_OUT_CS_LONG), opt_flag&MM_F_OUT_MD, !!(opt_flag&MM_F_OUT_DS), 1, !!(opt_flag&MM_F_QSTRAND)); write_cs_ds_or_MD(km, s, mi, t, r, !(opt_flag&MM_F_OUT_CS_LONG), !!(opt_flag&MM_F_OUT_MD), !!(opt_flag&MM_F_OUT_DS), 1, !!(opt_flag&MM_F_QSTRAND));
if ((opt_flag & MM_F_COPY_COMMENT) && t->comment) if ((opt_flag & MM_F_COPY_COMMENT) && t->comment)
mm_sprintf_lite(s, "\t%s", t->comment); mm_sprintf_lite(s, "\t%s", t->comment);
} }
lchain.c
+1 -1
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@@ -282,7 +282,7 @@ mm128_t *mg_lchain_rmq(int max_dist, int max_dist_inner, int bw, int max_chn_ski
int64_t j; int64_t j;
for (j = i0; j < i; ++j) { for (j = i0; j < i; ++j) {
q = kmp_alloc_rmq(mp); q = kmp_alloc_rmq(mp);
q->y = (int32_t)a[j].y, q->i = j, q->pri = -(f[j] + 0.25 * chn_pen_gap * ((int32_t)a[j].x + (int32_t)a[j].y)); q->y = (int32_t)a[j].y, q->i = j, q->pri = -(f[j] + 0.5 * chn_pen_gap * ((int32_t)a[j].x + (int32_t)a[j].y));
krmq_insert(lc_elem, &root, q, 0); krmq_insert(lc_elem, &root, q, 0);
if (max_dist_inner > 0) { if (max_dist_inner > 0) {
r = kmp_alloc_rmq(mp); r = kmp_alloc_rmq(mp);
minimap.h
+1 -1
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@@ -5,7 +5,7 @@
#include <stdio.h> #include <stdio.h>
#include <sys/types.h> #include <sys/types.h>
#define MM_VERSION "2.27-r1207-dirty" #define MM_VERSION "2.27-r1208-dirty"
#define MM_F_NO_DIAG (0x001LL) // no exact diagonal hit #define MM_F_NO_DIAG (0x001LL) // no exact diagonal hit
#define MM_F_NO_DUAL (0x002LL) // skip pairs where query name is lexicographically larger than target name #define MM_F_NO_DUAL (0x002LL) // skip pairs where query name is lexicographically larger than target name
minimap2.1
+5
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@@ -268,6 +268,11 @@ or more of the shorter chain [0.5]
Use the minigraph chaining algorithm [no]. The minigraph algorithm is better Use the minigraph chaining algorithm [no]. The minigraph algorithm is better
for aligning contigs through long INDELs. for aligning contigs through long INDELs.
.TP .TP
.BI --rmq-inner \ NUM
Apply full dynamic programming for anchors within distance
.I NUM
[1000].
.TP
.B --hard-mask-level .B --hard-mask-level
Honor option Honor option
.B -M .B -M