r1237: documented -x splice:sr

Author: lh3

main.c

@@ -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");

minimap.h

@@ -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

minimap2.1

@@ -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