From f536b69b81083cae2ecdd75e1b82076507194daf Mon Sep 17 00:00:00 2001 From: Heng Li Date: Sun, 30 Mar 2025 21:47:47 -0400 Subject: [PATCH] r1237: documented -x splice:sr --- main.c | 3 +++ minimap.h | 2 +- minimap2.1 | 12 +++++++++++- 3 files changed, 15 insertions(+), 2 deletions(-) diff --git a/main.c b/main.c index 02b36bf..b4d3ce4 100644 --- a/main.c +++ b/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"); diff --git a/minimap.h b/minimap.h index 5efa6d0..e2faade 100644 --- a/minimap.h +++ b/minimap.h @@ -5,7 +5,7 @@ #include #include -#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 diff --git a/minimap2.1 b/minimap2.1 index 352396e..b1bdf10 100644 --- a/minimap2.1 +++ b/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