From 6b391e3373fa9410f2bd30a31914c454353fdfe9 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Thu, 28 Feb 2019 15:49:24 -0500 Subject: [PATCH] Release minimap2-2.16 (r922) --- NEWS.md | 49 ++++++++++++++++++++++++++++++++++++++++++++++++ README.md | 4 ++-- cookbook.md | 4 ++-- main.c | 2 +- minimap2.1 | 2 +- misc/paftools.js | 2 +- python/mappy.pyx | 2 +- setup.py | 2 +- 8 files changed, 58 insertions(+), 9 deletions(-) diff --git a/NEWS.md b/NEWS.md index e540e50..7cb5401 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,52 @@ +Release 2.16-r922 (28 February 2019) +------------------------------------ + +This release is 50% faster for mapping ultra-long nanopore reads at comparable +accuracy. For short-read mapping, long-read overlapping and ordinary long-read +mapping, the performance and accuracy remain similar. This speedup is achieved +with a new heuristic to limit the number of chaining iterations (#324). Users +can disable the heuristic by increasing a new option `--max-chain-iter` to a +huge number. + +Other changes to minimap2: + + * Implemented option `--paf-no-hit` to output unmapped query sequences in PAF. + The strand and reference name columns are both `*` at an unmapped line. The + hidden option is available in earlier minimap2 but had a different 2-column + output format instead of PAF. + + * Fixed a bug that leads to wrongly calculated `de` tags when ambiguous bases + are involved (#309). This bug only affects v2.15. + + * Fixed a bug when parsing command-line option `--splice` (#344). This bug was + introduced in v2.13. + + * Fixed two division-by-zero cases (#326). They don't affect final alignments + because the results of the divisions are not used in both case. + + * Added an option `-o` to output alignments to a specified file. It is still + recommended to use UNIX pipes for on-the-fly conversion or compression. + + * Output a new `rl` tag to give the length of query regions harboring + repetitive seeds. + +Changes to paftool.js: + + * Added a new option to convert the MD tag to the long form of the cs tag. + +Changes to mappy: + + * Added the `mappy.Aligner.seq_names` method to return sequence names (#312). + +For NA12878 ultra-long reads, this release changes the alignments of <0.1% of +reads in comparison to v2.15. All these reads have highly fragmented alignments +and are likely to be problematic anyway. For shorter or well aligned reads, +this release should produce mostly identical alignments to v2.15. + +(2.16: 28 February 2019, r922) + + + Release 2.15-r905 (10 January 2019) ----------------------------------- diff --git a/README.md b/README.md index 5857cdf..11088d9 100644 --- a/README.md +++ b/README.md @@ -71,8 +71,8 @@ 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/v2.15/minimap2-2.15_x64-linux.tar.bz2 | tar -jxvf - -./minimap2-2.15_x64-linux/minimap2 +curl -L https://github.com/lh3/minimap2/releases/download/v2.16/minimap2-2.16_x64-linux.tar.bz2 | tar -jxvf - +./minimap2-2.16_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 6345f0e..ce581bc 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/v2.15/minimap2-2.15_x64-linux.tar.bz2 | tar jxf - -cp minimap2-2.15_x64-linux/{minimap2,k8,paftools.js} . # copy executables +curl -L https://github.com/lh3/minimap2/releases/download/v2.16/minimap2-2.16_x64-linux.tar.bz2 | tar jxf - +cp minimap2-2.16_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/main.c b/main.c index ced4c0b..aa0cf91 100644 --- a/main.c +++ b/main.c @@ -6,7 +6,7 @@ #include "mmpriv.h" #include "ketopt.h" -#define MM_VERSION "2.15-r921-dirty" +#define MM_VERSION "2.16-r922" #ifdef __linux__ #include diff --git a/minimap2.1 b/minimap2.1 index cfcfb1d..c605508 100644 --- a/minimap2.1 +++ b/minimap2.1 @@ -1,4 +1,4 @@ -.TH minimap2 1 "27 Feburary 2019" "minimap2-2.15-dirty (r917)" "Bioinformatics tools" +.TH minimap2 1 "28 Feburary 2019" "minimap2-2.16-dirty (r922)" "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 4fe692e..459eebd 100755 --- a/misc/paftools.js +++ b/misc/paftools.js @@ -1,6 +1,6 @@ #!/usr/bin/env k8 -var paftools_version = '2.15-r921-dirty'; +var paftools_version = '2.16-r922'; /***************************** ***** Library functions ***** diff --git a/python/mappy.pyx b/python/mappy.pyx index 7b0667f..2528d9d 100644 --- a/python/mappy.pyx +++ b/python/mappy.pyx @@ -3,7 +3,7 @@ from libc.stdlib cimport free cimport cmappy import sys -__version__ = '2.15' +__version__ = '2.16' cmappy.mm_reset_timer() diff --git a/setup.py b/setup.py index bf689f4..b61a5e2 100644 --- a/setup.py +++ b/setup.py @@ -33,7 +33,7 @@ def readme(): setup( name = 'mappy', - version = '2.15', + version = '2.16', url = 'https://github.com/lh3/minimap2', description = 'Minimap2 python binding', long_description = readme(),