diff --git a/NEWS.md b/NEWS.md index 6fc45098..d72e8ba1 100644 --- a/NEWS.md +++ b/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) diff --git a/README.md b/README.md index e000bb85..056dd5d7 100644 --- a/README.md +++ b/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 diff --git a/cookbook.md b/cookbook.md index 428f1179..c337d050 100644 --- a/cookbook.md +++ b/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 - diff --git a/minimap.h b/minimap.h index 42f48675..b944199a 100644 --- a/minimap.h +++ b/minimap.h @@ -5,7 +5,7 @@ #include #include -#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 diff --git a/minimap2.1 b/minimap2.1 index c2e68d94..aa674d19 100644 --- a/minimap2.1 +++ b/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 diff --git a/misc/paftools.js b/misc/paftools.js index 89152ae9..67819e9b 100755 --- a/misc/paftools.js +++ b/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 ***** diff --git a/python/mappy.pyx b/python/mappy.pyx index e73c4f54..c51f0646 100644 --- a/python/mappy.pyx +++ b/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() diff --git a/setup.py b/setup.py index fa6d0860..04db5b18 100644 --- a/setup.py +++ b/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(),