From 59f23f7579b6c6abab044db68c4907ffc8af692e Mon Sep 17 00:00:00 2001 From: Heng Li Date: Tue, 6 Nov 2018 00:03:16 -0500 Subject: [PATCH] Release minimap2-2.14 (r883) --- NEWS.md | 16 ++++++++++------ README.md | 4 ++-- cookbook.md | 4 ++-- main.c | 2 +- minimap2.1 | 2 +- misc/paftools.js | 7 ++++++- python/mappy.pyx | 2 +- setup.py | 2 +- 8 files changed, 24 insertions(+), 15 deletions(-) diff --git a/NEWS.md b/NEWS.md index f38789f7..e5060bc9 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,22 +1,26 @@ -Release 2.14-r8xx (yy November 2018) ------------------------------------- +Release 2.14-r883 (5 November 2018) +----------------------------------- -Changes to minimap2: +Notable changes: * Fixed two minor bugs caused by typos (#254 and #266). - * Fixed a bug that made minimap2 abort when -L was used with --MD/--cs (#257). + * Fixed a bug that made minimap2 abort when --eqx was used together with --MD + or --cs (#257). * Added --cap-sw-mem to cap the size of DP matrices (#259). Base alignment may take a lot of memory in the splicing mode. This may lead to issues when we run minimap2 on a cluster with a hard memory limit. The new option avoids unlimited memory usage at the cost of missing a few long introns. - * Conforming to C99 and C11 if possible (#261). + * Conforming to C99 and C11 when possible (#261). * Warn about malformatted FASTA or FASTQ (#252 and #255). -(2.14: yy November 2018, r8xx) +This release occasionally produces base alignments different from v2.13. The +overall alignment accuracy remain similar. + +(2.14: 5 November 2018, r883) diff --git a/README.md b/README.md index 6f7ed644..d3ba33fc 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/v2.13/minimap2-2.13_x64-linux.tar.bz2 | tar -jxvf - -./minimap2-2.13_x64-linux/minimap2 +curl -L https://github.com/lh3/minimap2/releases/download/v2.14/minimap2-2.14_x64-linux.tar.bz2 | tar -jxvf - +./minimap2-2.14_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 ea77817d..d43d190d 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/v2.13/minimap2-2.13_x64-linux.tar.bz2 | tar jxf - -cp minimap2-2.13_x64-linux/{minimap2,k8,paftools.js} . # copy executables +curl -L https://github.com/lh3/minimap2/releases/download/v2.14/minimap2-2.14_x64-linux.tar.bz2 | tar jxf - +cp minimap2-2.14_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 cb6f6dc6..504c2525 100644 --- a/main.c +++ b/main.c @@ -6,7 +6,7 @@ #include "mmpriv.h" #include "ketopt.h" -#define MM_VERSION "2.13-r882-dirty" +#define MM_VERSION "2.14-r883" #ifdef __linux__ #include diff --git a/minimap2.1 b/minimap2.1 index d8936770..8fddac98 100644 --- a/minimap2.1 +++ b/minimap2.1 @@ -1,4 +1,4 @@ -.TH minimap2 1 "11 October 2018" "minimap2-2.13 (r850)" "Bioinformatics tools" +.TH minimap2 1 "5 November 2018" "minimap2-2.14 (r883)" "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 21268612..e6339572 100755 --- a/misc/paftools.js +++ b/misc/paftools.js @@ -1,6 +1,6 @@ #!/usr/bin/env k8 -var paftools_version = '2.13-r872-dirty'; +var paftools_version = '2.14-r883'; /***************************** ***** Library functions ***** @@ -781,6 +781,10 @@ function paf_asmgene(args) var n_fn = args.length - getopt.ind; if (n_fn < 2) { print("Usage: paftools.js asmgene [options] [...]"); + print("Options:"); + print(" -i FLOAT min identity [" + opt.min_iden + "]"); + print(" -c FLOAT min coverage [" + opt.min_cov + "]"); + print(" -e print fragmented/missing genes"); exit(1); } @@ -2339,6 +2343,7 @@ function main(args) print(""); print(" stat collect basic mapping information in PAF/SAM"); print(" asmstat collect basic assembly information"); + print(" asmgene evaluate gene completeness (EXPERIMENTAL)"); print(" liftover simplistic liftOver"); print(" call call variants from asm-to-ref alignment with the cs tag"); print(" bedcov compute the number of bases covered"); diff --git a/python/mappy.pyx b/python/mappy.pyx index 8083187e..b9e703f5 100644 --- a/python/mappy.pyx +++ b/python/mappy.pyx @@ -3,7 +3,7 @@ from libc.stdlib cimport free cimport cmappy import sys -__version__ = '2.13' +__version__ = '2.14' cmappy.mm_reset_timer() diff --git a/setup.py b/setup.py index 66145719..1760057d 100644 --- a/setup.py +++ b/setup.py @@ -33,7 +33,7 @@ def readme(): setup( name = 'mappy', - version = '2.13', + version = '2.14', url = 'https://github.com/lh3/minimap2', description = 'Minimap2 python binding', long_description = readme(),