Release minimap2-2.29 (r1283)

Author: lh3

NEWS.md

@@ -1,11 +1,11 @@
 Release 2.29-r1283 (18 April 2025)
 ----------------------------------
 
-Notable changes:
+Notable changes to minimap2:
 
  * New feature: added the `splice:sr` preset for short RNA-seq read alignment.
    Users may use `-j` to specify known gene annotation to improve spliced
-   alignment close to the ends of reads. Also added `--write-junc` and
+   alignment close to the ends of short reads. Also added `--write-junc` and
    `--pass1` for 2-pass short-read RNA-seq alignment.
 
  * Experimental feature: read splice scores from a file specified by `--spsc`
@@ -14,10 +14,24 @@ Notable changes:
 
  * Change: adjusted the mapping quality calculation for spliced alignment.
 
-This release produces identical genomic long-read alignment to v2.27. Short
-genomic read alignment and the mapping quality of long RNA-seq read alignment
-may slightly differ in very rare cases. Minimap2 now supports short/long
-genomic/RNA-seq read alignment.
+ * Bugfixes: a) missing overlap alignment when base alignment is requested
+   (#969); b) incorrect summary information for long genomes (#1192); c)
+   missing parameter check for `--score-N` (#1226).
+
+ * Improvement: a) warn about absent junction files (#1229); b) report an error
+   if a wrong preset prefixed with "splice" is specified (#589).
+
+Notable changes to mappy:
+
+ * Improvement: allow passing read name (#1260)
+
+ * Improvement: exposed score for ambiguous bases (#1240)
+
+Minimap2 now supports short/long genomic/RNA-seq read alignment along with
+contig alignment and all-vs-all read overlapping. It produces identical genomic
+long-read or contig alignment to v2.27. Short genomic read alignment and the
+mapping quality of long RNA-seq read alignment may slightly differ in very rare
+cases.
 
 (2.29: 18 April 2025, r1283)
 

README.md

@@ -21,7 +21,7 @@ cd minimap2 && make
 ./minimap2 -ax splice -uf -k14 ref.fa reads.fa > aln.sam  # noisy Nanopore direct RNA-seq
 ./minimap2 -ax splice:hq -uf ref.fa query.fa > aln.sam    # PacBio Kinnex/Iso-seq (RNA-seq)
 ./minimap2 -ax splice --junc-bed=anno.bed12 ref.fa query.fa > aln.sam  # use annotated junctions
-./minimap2 -ax splice:sr ref.fa r1.fq r2.fq > aln.sam     # short-read RNA-seq (r1236+; experimental)
+./minimap2 -ax splice:sr ref.fa r1.fq r2.fq > aln.sam     # short-read RNA-seq (v2.29+)
 ./minimap2 -ax splice:sr -j anno.bed12 ref.fa r1.fq r2.fq > aln.sam
 ./minimap2 -cx asm5 asm1.fa asm2.fa > aln.paf             # intra-species asm-to-asm alignment
 ./minimap2 -x ava-pb reads.fa reads.fa > overlaps.paf     # PacBio read overlap
@@ -41,7 +41,7 @@ man ./minimap2.1
     - [Map long mRNA/cDNA reads](#map-long-splice)
     - [Find overlaps between long reads](#long-overlap)
     - [Map short genomic reads](#short-genomic)
-    - [Map short RNA-seq reads (experimental & evolving)](#short-rna-seq)
+    - [Map short RNA-seq reads](#short-rna-seq)
     - [Full genome/assembly alignment](#full-genome)
   - [Advanced features](#advanced)
     - [Working with >65535 CIGAR operations](#long-cigar)
@@ -77,8 +77,8 @@ Detailed evaluations are available from the [minimap2 paper][doi] or the
 Minimap2 is optimized for x86-64 CPUs. You can acquire precompiled binaries from
 the [release page][release] with:
 ```sh
-curl -L https://github.com/lh3/minimap2/releases/download/v2.28/minimap2-2.28_x64-linux.tar.bz2 | tar -jxvf -
-./minimap2-2.28_x64-linux/minimap2
+curl -L https://github.com/lh3/minimap2/releases/download/v2.29/minimap2-2.29_x64-linux.tar.bz2 | tar -jxvf -
+./minimap2-2.29_x64-linux/minimap2
 ```
 If you want to compile from the source, you need to have a C compiler, GNU make
 and zlib development files installed. Then type `make` in the source code
@@ -235,7 +235,7 @@ be paired if they are adjacent in the input stream and have the same name (with
 the `/[0-9]` suffix trimmed if present). Single- and paired-end reads can be
 mixed.
 
-#### <a name="short-rna-seq"></a>Map short RNA-seq reads (experimental & evolving)
+#### <a name="short-rna-seq"></a>Map short RNA-seq reads
 
 ```sh
 minimap2 -ax splice:sr ref.fa reads-se.fq.gz > aln.sam           # single-end
@@ -245,10 +245,8 @@ minimap2 -ax splice:sr -j anno.bed ref.fa r1.fq r2.fq > aln.sam  # use annotatio
 minimap2 -x splice:sr -j anno.bed --write-junc ref.fa r1.fq r2.fq > junc.bed
 minimap2 -ax splice:sr -j anno.bed --pass1=junc.bed ref.fa r1.fq r2.fq > aln.sam
 ```
-The new preset `splice:sr` was added between v2.28 and v2.29. It functions
-similarly to `sr` except that it performs spliced alignment. Note that this
-functionality is ***experiemental*** and evolving. It is better not to use it
-for production.
+The new preset `splice:sr` was added in v2.29. It functions similarly to `sr`
+except that it performs spliced alignment.
 
 #### <a name="full-genome"></a>Full genome/assembly alignment
 

cookbook.md

@@ -31,8 +31,8 @@ To acquire the data used in this cookbook and to install minimap2 and paftools,
 please follow the command lines below:
 ```sh
 # install minimap2 executables
-curl -L https://github.com/lh3/minimap2/releases/download/v2.28/minimap2-2.28_x64-linux.tar.bz2 | tar jxf -
-cp minimap2-2.28_x64-linux/{minimap2,k8,paftools.js} .  # copy executables
+curl -L https://github.com/lh3/minimap2/releases/download/v2.29/minimap2-2.29_x64-linux.tar.bz2 | tar jxf -
+cp minimap2-2.29_x64-linux/{minimap2,k8,paftools.js} .  # copy executables
 export PATH="$PATH:"`pwd`                               # put the current directory on PATH
 # download example datasets
 curl -L https://github.com/lh3/minimap2/releases/download/v2.10/cookbook-data.tgz | tar zxf -

minimap.h

@@ -5,7 +5,7 @@
 #include <stdio.h>
 #include <sys/types.h>
 
-#define MM_VERSION "2.28-r1281-dirty"
+#define MM_VERSION "2.29-r1283"
 
 #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

misc/paftools.js

@@ -1,6 +1,6 @@
 #!/usr/bin/env k8
 
-var paftools_version = '2.28-r1230-dirty';
+var paftools_version = '2.29-r1283';
 
 /*****************************
  ***** Library functions *****

python/mappy.pyx

@@ -3,7 +3,7 @@ from libc.stdlib cimport free
 cimport cmappy
 import sys
 
-__version__ = '2.28'
+__version__ = '2.29'
 
 cmappy.mm_reset_timer()
 

setup.py

@@ -23,7 +23,7 @@ def readme():
 
 setup(
 	name = 'mappy',
-	version = '2.28',
+	version = '2.29',
 	url = 'https://github.com/lh3/minimap2',
 	description = 'Minimap2 python binding',
 	long_description = readme(),