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r1278: reduced --min-dp-len to 20 for splice:sr

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30% reduced time at 0.01% more junction errors
This commit is contained in:
Heng Li
2025-04-16 21:55:59 -04:00
parent c19e3ccb86
commit 7a540c37ca
4 changed files with 5 additions and 4 deletions
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align.c
+2 -2
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@@ -753,14 +753,14 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
re1 = rs, qe1 = qs; re1 = rs, qe1 = qs;
assert(qs1 >= 0 && rs1 >= 0); assert(qs1 >= 0 && rs1 >= 0);
for (i = is_sr? cnt1 - 1 : 1; i < cnt1; ++i) { // gap filling for (i = is_sr? cnt1 - 1 : 1; i < cnt1; ++i) { // gap filling; for short genomic reads, fill from the first seed to the last
if ((a[as1+i].y & (MM_SEED_IGNORE|MM_SEED_TANDEM)) && i != cnt1 - 1) continue; if ((a[as1+i].y & (MM_SEED_IGNORE|MM_SEED_TANDEM)) && i != cnt1 - 1) continue;
if (is_sr && !(mi->flag & MM_I_HPC)) { if (is_sr && !(mi->flag & MM_I_HPC)) {
re = (int32_t)a[as1 + i].x + 1; re = (int32_t)a[as1 + i].x + 1;
qe = (int32_t)a[as1 + i].y + 1; qe = (int32_t)a[as1 + i].y + 1;
} else mm_adjust_minier(mi, qseq0, &a[as1 + i], &re, &qe); } else mm_adjust_minier(mi, qseq0, &a[as1 + i], &re, &qe);
re1 = re, qe1 = qe; re1 = re, qe1 = qe;
if (i == cnt1 - 1 || (a[as1+i].y&MM_SEED_LONG_JOIN) || (qe - qs >= opt->min_ksw_len && re - rs >= opt->min_ksw_len)) { if (i == cnt1 - 1 || (a[as1+i].y&MM_SEED_LONG_JOIN) || (qe - qs >= opt->min_ksw_len && re - rs >= opt->min_ksw_len)) { // gap filling
int j, bw1 = bw_long, zdrop_code; int j, bw1 = bw_long, zdrop_code;
if (a[as1+i].y & MM_SEED_LONG_JOIN) if (a[as1+i].y & MM_SEED_LONG_JOIN)
bw1 = qe - qs > re - rs? qe - qs : re - rs; bw1 = qe - qs > re - rs? qe - qs : re - rs;
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 "2.28-r1277-dirty" #define MM_VERSION "2.28-r1278-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
+1 -1
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@@ -708,7 +708,7 @@ Spliced alignment for accurate long RNA-seq reads such as PacBio iso-seq
.B splice:sr .B splice:sr
Spliced alignment for short RNA-seq reads Spliced alignment for short RNA-seq reads
.RB ( -xsplice:hq .RB ( -xsplice:hq
.B --frag=yes -m25 -s40 -2K100m --heap-sort=yes --pairing=weak --sr=rna .B --frag=yes -m25 -s40 -2K100m --heap-sort=yes --pairing=weak --sr=rna --min-dp-len=20
.BR --secondary=no ). .BR --secondary=no ).
.TP .TP
.B sr .B sr
options.c
+1
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@@ -183,6 +183,7 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
mo->noncan = 5, mo->b = 4, mo->q = 6, mo->q2 = 24; mo->noncan = 5, mo->b = 4, mo->q = 6, mo->q2 = 24;
mo->min_chain_score = 25; mo->min_chain_score = 25;
mo->min_dp_max = 40; mo->min_dp_max = 40;
mo->min_ksw_len = 20;
mo->pe_ori = 0<<1|1; // FR mo->pe_ori = 0<<1|1; // FR
mo->best_n = 10; mo->best_n = 10;
mo->mini_batch_size = 100000000; mo->mini_batch_size = 100000000;