From 01ccedd5a0206b6e6d6e74c2ab6d1c9cd454dbca Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Sun, 13 Apr 2025 17:07:39 -0400
Subject: [PATCH] r1275: renamed --jump-pass1 to --pass1

Also documented 2-pass
---
 main.c     |  2 +-
 minimap.h  |  2 +-
 minimap2.1 | 27 +++++++++++++++++++++++----
 3 files changed, 25 insertions(+), 6 deletions(-)

diff --git a/main.c b/main.c
index 0d725bd..8d44ac6 100644
--- a/main.c
+++ b/main.c
@@ -84,7 +84,7 @@ static ko_longopt_t long_options[] = {
 	{ "pairing",        ko_required_argument, 359 },
 	{ "jump-min-match", ko_required_argument, 360 },
 	{ "write-junc",     ko_no_argument,       361 },
-	{ "jump-pass1",     ko_required_argument, 362 },
+	{ "pass1",          ko_required_argument, 362 },
 	{ "dbg-seed-occ",   ko_no_argument,       501 },
 	{ "help",           ko_no_argument,       'h' },
 	{ "max-intron-len", ko_required_argument, 'G' },
diff --git a/minimap.h b/minimap.h
index ab70d75..7618250 100644
--- a/minimap.h
+++ b/minimap.h
@@ -5,7 +5,7 @@
 #include <stdio.h>
 #include <sys/types.h>
 
-#define MM_VERSION "2.28-r1274-dirty"
+#define MM_VERSION "2.28-r1275-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 58b626f..b852c88 100644
--- a/minimap2.1
+++ b/minimap2.1
@@ -1,4 +1,4 @@
-.TH minimap2 1 "6 April 2025" "minimap2-2.28-dirty (r1264)" "Bioinformatics tools"
+.TH minimap2 1 "13 April 2025" "minimap2-2.28-dirty (r1274)" "Bioinformatics tools"
 .SH NAME
 .PP
 minimap2 - mapping and alignment between collections of DNA sequences
@@ -361,9 +361,9 @@ has no effect with the default
 Junctions used to extend alignment towards ends of reads [].
 .I FILE
 can be gene annotations in the BED12 format (aka 12-column BED), or intron
-positions in 5-column BED. BED12 file can be converted from GTF/GFF3 with
-`paftools.js gff2bed anno.gtf'.
-This option is intended for short RNA-seq reads, while
+positions in 5-column BED with the strand column required. BED12 file can be
+converted from GTF/GFF3 with `paftools.js gff2bed anno.gtf'. This option is
+intended for short RNA-seq reads, while
 .B --junc-bed
 for long noisy RNA-seq reads.
 .TP
@@ -547,6 +547,25 @@ In SAM output, use soft clipping for supplementary alignments.
 .B --secondary-seq
 In SAM output, show query sequences for secondary alignments.
 .TP
+.B --write-junc
+Output splice junctions in 6-column BED: contig name, start, end,
+read name, score and strand. Score is the sum of donor and acceptor scores,
+where GT gets 3, GC gets 2 and AT gets 1 at donor sites,
+while AG gets 3 and AC gets 1 at acceptor sites.
+.TP
+.BI --pass1 \ FILE
+Junctions BED file outputted by
+.B --write-junc
+[]. Rows with scores lower than 5 are ignored. When both
+.B -j
+and
+.B --pass1
+are present, junctions in
+.B -j
+are preferred over in
+.BR --pass1
+when there is ambiguity.
+.TP
 .BI --seed \ INT
 Integer seed for randomizing equally best hits. Minimap2 hashes
 .I INT