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r1275: renamed --jump-pass1 to --pass1

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Also documented 2-pass
This commit is contained in:
Heng Li
2025-04-13 17:07:39 -04:00
parent 819b3bf017
commit 01ccedd5a0
3 changed files with 25 additions and 6 deletions
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main.c
+1 -1
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@@ -84,7 +84,7 @@ static ko_longopt_t long_options[] = {
{ "pairing", ko_required_argument, 359 }, { "pairing", ko_required_argument, 359 },
{ "jump-min-match", ko_required_argument, 360 }, { "jump-min-match", ko_required_argument, 360 },
{ "write-junc", ko_no_argument, 361 }, { "write-junc", ko_no_argument, 361 },
{ "jump-pass1", ko_required_argument, 362 }, { "pass1", ko_required_argument, 362 },
{ "dbg-seed-occ", ko_no_argument, 501 }, { "dbg-seed-occ", ko_no_argument, 501 },
{ "help", ko_no_argument, 'h' }, { "help", ko_no_argument, 'h' },
{ "max-intron-len", ko_required_argument, 'G' }, { "max-intron-len", ko_required_argument, 'G' },
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-r1274-dirty" #define MM_VERSION "2.28-r1275-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
+23 -4
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@@ -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 .SH NAME
.PP .PP
minimap2 - mapping and alignment between collections of DNA sequences 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 []. Junctions used to extend alignment towards ends of reads [].
.I FILE .I FILE
can be gene annotations in the BED12 format (aka 12-column BED), or intron 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 positions in 5-column BED with the strand column required. BED12 file can be
`paftools.js gff2bed anno.gtf'. converted from GTF/GFF3 with `paftools.js gff2bed anno.gtf'. This option is
This option is intended for short RNA-seq reads, while intended for short RNA-seq reads, while
.B --junc-bed .B --junc-bed
for long noisy RNA-seq reads. for long noisy RNA-seq reads.
.TP .TP
@@ -547,6 +547,25 @@ In SAM output, use soft clipping for supplementary alignments.
.B --secondary-seq .B --secondary-seq
In SAM output, show query sequences for secondary alignments. In SAM output, show query sequences for secondary alignments.
.TP .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 .BI --seed \ INT
Integer seed for randomizing equally best hits. Minimap2 hashes Integer seed for randomizing equally best hits. Minimap2 hashes
.I INT .I INT