Release minimap2-2.27 (r1193)

Author: lh3

NEWS.md

@@ -1,4 +1,4 @@
-Release 2.27-rXXXX (XX March 2024)
+Release 2.27-r1193 (12 March 2024)
 ----------------------------------
 
 Notable changes to minimap2:
@@ -8,14 +8,17 @@ Notable changes to minimap2:
    clear if this preset also works well for PacBio HiFi reads.
 
  * New feature: added the `map-iclr` preset for Illumina Complete Long Reads
-   (#1069), provided by Illumina developers. This change also added option `-b`
-   to specify mismatch penalty for transition mutations.
+   (#1069), provided by Illumina developers.
 
- * New feature: added option `--ds` to generate a new `ds:Z` tag. `ds`
+ * New feature: added option `-b` to specify mismatch penalty for base
+   transitions (i.e. A-to-G or C-to-T changes).
+
+ * New feature: added option `--ds` to generate a new `ds:Z` tag that
    indicates uncertainty in INDEL positions. It is an extension to `cs`. The
    `mgutils-es6.js` script in minigraph parses `ds`.
 
- * Bugfix: avoided a NULL pointer dereference (#1154).
+ * Bugfix: avoided a NULL pointer dereference (#1154). This would not have an
+   effect on most systems but would still be good to fix.
 
  * Bugfix: reverted the value of `ms:i` to pre-2.22 versions (#1146). This was
    an oversight. See fcd4df2 for details.
@@ -27,7 +30,9 @@ Notable changes to paftools.js and mappy:
  * Bugfix: fixed several compatibility issues with k8 v1.0 (#1161 and #1166).
    Subcommands "call", "pbsim2fq" and "mason2fq" were not working with v1.0.
 
-(2.27: XX March 2024, rXXXX)
+Minimap2 should output identical alignments to v2.26, except the ms tag.
+
+(2.27: 12 March 2024, r1193)
 
 
 

README.md

@@ -15,7 +15,7 @@ cd minimap2 && make
 ./minimap2 -ax map-pb ref.fa pacbio.fq.gz > aln.sam       # PacBio CLR genomic reads
 ./minimap2 -ax map-ont ref.fa ont.fq.gz > aln.sam         # Oxford Nanopore genomic reads
 ./minimap2 -ax map-hifi ref.fa pacbio-ccs.fq.gz > aln.sam # PacBio HiFi/CCS genomic reads (v2.19 or later)
-./minimap2 -ax asm20 ref.fa pacbio-ccs.fq.gz > aln.sam    # PacBio HiFi/CCS genomic reads (v2.18 or earlier)
+./minimap2 -ax lr:hq ref.fa ont-Q20.fq.gz > aln.sam       # Nanopore Q20 genomic reads (v2.27 or later)
 ./minimap2 -ax sr ref.fa read1.fa read2.fa > aln.sam      # short genomic paired-end reads
 ./minimap2 -ax splice ref.fa rna-reads.fa > aln.sam       # spliced long reads (strand unknown)
 ./minimap2 -ax splice -uf -k14 ref.fa reads.fa > aln.sam  # noisy Nanopore Direct RNA-seq
@@ -74,8 +74,8 @@ 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/v2.26/minimap2-2.26_x64-linux.tar.bz2 | tar -jxvf -
-./minimap2-2.26_x64-linux/minimap2
+curl -L https://github.com/lh3/minimap2/releases/download/v2.27/minimap2-2.27_x64-linux.tar.bz2 | tar -jxvf -
+./minimap2-2.27_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

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/v2.26/minimap2-2.26_x64-linux.tar.bz2 | tar jxf -
-cp minimap2-2.26_x64-linux/{minimap2,k8,paftools.js} .  # copy executables
+curl -L https://github.com/lh3/minimap2/releases/download/v2.27/minimap2-2.27_x64-linux.tar.bz2 | tar jxf -
+cp minimap2-2.27_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 "2.26-r1190-dirty"
+#define MM_VERSION "2.27-r1193"
 
 #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 "29 April 2023" "minimap2-2.26 (r1175)" "Bioinformatics tools"
+.TH minimap2 1 "12 March 2024" "minimap2-2.27 (r1193)" "Bioinformatics tools"
 .SH NAME
 .PP
 minimap2 - mapping and alignment between collections of DNA sequences

misc/paftools.js

@@ -1,6 +1,6 @@
 #!/usr/bin/env k8
 
-var paftools_version = '2.26-r1191-dirty';
+var paftools_version = '2.27-r1193';
 
 /*****************************
  ***** Library functions *****

python/mappy.pyx

@@ -3,7 +3,7 @@ from libc.stdlib cimport free
 cimport cmappy
 import sys
 
-__version__ = '2.26'
+__version__ = '2.27'
 
 cmappy.mm_reset_timer()
 

setup.py

@@ -23,7 +23,7 @@ def readme():
 
 setup(
 	name = 'mappy',
-	version = '2.26',
+	version = '2.27',
 	url = 'https://github.com/lh3/minimap2',
 	description = 'Minimap2 python binding',
 	long_description = readme(),