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r1237: documented -x splice:sr

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Heng Li
2025-03-30 21:47:47 -04:00
parent 4b8b4418df
commit f536b69b81
3 changed files with 15 additions and 2 deletions
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3
main.c
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@@ -81,6 +81,7 @@ static ko_longopt_t long_options[] = {
{ "rmq-inner", ko_required_argument, 356 },
{ "spsc", ko_required_argument, 357 },
{ "junc-pen", ko_required_argument, 358 },
{ "pe-ind-chain", ko_no_argument, 359 },
{ "dbg-seed-occ", ko_no_argument, 501 },
{ "help", ko_no_argument, 'h' },
{ "max-intron-len", ko_required_argument, 'G' },
@@ -252,6 +253,7 @@ int main(int argc, char *argv[])
else if (c == 355) opt.flag |= MM_F_OUT_DS; // --ds
else if (c == 356) opt.rmq_inner_dist = mm_parse_num(o.arg); // --rmq-inner
else if (c == 357) fn_spsc = o.arg; // --spsc
else if (c == 359) opt.flag |= MM_F_PE_IND; // --pe-ind-chain
else if (c == 501) mm_dbg_flag |= MM_DBG_SEED_FREQ; // --dbg-seed-occ
else if (c == 330) {
fprintf(stderr, "[WARNING] \033[1;31m --lj-min-ratio has been deprecated.\033[0m\n");
@@ -378,6 +380,7 @@ int main(int argc, char *argv[])
fprintf(fp_help, " -x STR preset (always applied before other options; see minimap2.1 for details) []\n");
fprintf(fp_help, " - lr:hq - accurate long reads (error rate <1%%) against a reference genome\n");
fprintf(fp_help, " - splice/splice:hq - spliced alignment for long reads/accurate long reads\n");
fprintf(fp_help, " - splice:sr - spliced alignment for short RNA-seq reads\n");
fprintf(fp_help, " - asm5/asm10/asm20 - asm-to-ref mapping, for ~0.1/1/5%% sequence divergence\n");
fprintf(fp_help, " - sr - short reads against a reference\n");
fprintf(fp_help, " - map-pb/map-hifi/map-ont/map-iclr - CLR/HiFi/Nanopore/ICLR vs reference mapping\n");

2
minimap.h
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@@ -5,7 +5,7 @@
#include <stdio.h>
#include <sys/types.h>
#define MM_VERSION "2.28-r1236-dirty"
#define MM_VERSION "2.28-r1237-dirty"
#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

12
minimap2.1
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@@ -1,4 +1,4 @@
.TH minimap2 1 "12 March 2024" "minimap2-2.28 (r1209)" "Bioinformatics tools"
.TH minimap2 1 "30 March 2025" "minimap2-2.28-dirty (r1237)" "Bioinformatics tools"
.SH NAME
.PP
minimap2 - mapping and alignment between collections of DNA sequences
@@ -416,6 +416,10 @@ Score bonus when alignment extends to the end of the query sequence [0].
.BI --score-N \ INT
Score of a mismatch involving ambiguous bases [1].
.TP
.BI --pe-ind-chain
For paired-end short reads, perform chaining for each end independently.
By default, minimap2 chains the two ends together.
.TP
.BR --splice-flank = yes | no
Assume the next base to a
.B GT
@@ -682,6 +686,12 @@ Spliced alignment for accurate long RNA-seq reads such as PacBio iso-seq
.B -C5 -O6,24
.BR -B4 ).
.TP
.B splice:sr
Spliced alignment for short RNA-seq reads
.RB ( -xsplice:hq
.B --frag=yes --end-bonus=10 -2K50m --heap-sort=yes --pe-ind-chain
.BR --secondary=no ).
.TP
.B sr
Short-read alignment without splicing
.RB ( -k21