diff --git a/NEWS.md b/NEWS.md index 078d2447..757da2e1 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,41 @@ +Release 2.4-r555 (6 November 2017) +---------------------------------- + +As is planned, this release focuses on fine tuning the base algorithm. Notable +changes include + + * Changed the mapping quality scale to match the scale of BWA-MEM. This makes + minimap2 and BWA-MEM achieve similar sensitivity-specificity balance on real + short-read data. + + * Improved the accuracy of splice alignment by modeling one additional base + close to the GT-AG signal. This model is used by default with `-x splice`. + For SIRV control data, however, it is recommended to add `--splice-flank=no` + to disable this feature as the SIRV splice signals are slightly different. + + * Tuned the parameters for Nanopore Direct RNA reads. The recommended command + line is `-axsplice -k14 -uf` (#46). + + * Fixed a segmentation fault when aligning PacBio reads (#47 and #48). This + bug is very rare but it affects all versions of minimap2. It is also + recommended to re-index reference genomes created with `map-pb`. For human, + two minimizers in an old index are wrong. + + * Changed option `-L` in sync with the final decision of hts-specs: a fake + CIGAR takes the form of `SN`. Note that `-L` only enables + future tools to recognize long CIGARs. It is not possible for older tools to + work with such alignments in BAM (#43 and #51). + + * Fixed a tiny issue whereby minimap2 may waste 8 bytes per candidate + alignment. + +The minimap2 technical note hosted at arXiv has also been updated to reflect +recent changes. + +(2.4: 6 November 2017, r555) + + + Release 2.3-r531 (22 October 2017) ---------------------------------- @@ -26,7 +64,7 @@ This release come with many improvements and bug fixes: This release has implemented all the major features I planned five months ago, with the addition of spliced long-read alignment. The next couple of releases -will focus on fine tuning of base algorithms. +will focus on fine tuning of the base algorithms. (2.3: 22 October 2017, r531) diff --git a/README.md b/README.md index 82af0754..96a8e2b7 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,10 @@ -[![Release](https://img.shields.io/badge/Release-v2.3-blue.svg?style=flat)](https://github.com/lh3/minimap2/releases) +[![Release](https://img.shields.io/badge/Release-v2.4-blue.svg?style=flat)](https://github.com/lh3/minimap2/releases) [![BioConda](https://img.shields.io/conda/vn/bioconda/minimap2.svg?style=flat)](https://anaconda.org/bioconda/minimap2) [![PyPI](https://img.shields.io/pypi/v/mappy.svg?style=flat)](https://pypi.python.org/pypi/mappy) [![Python Version](https://img.shields.io/pypi/pyversions/mappy.svg?style=flat)](https://pypi.python.org/pypi/mappy) [![License](https://img.shields.io/badge/License-MIT-blue.svg?style=flat)](LICENSE.txt) [![Build Status](https://travis-ci.org/lh3/minimap2.svg?branch=master)](https://travis-ci.org/lh3/minimap2) - +[![Downloads](https://img.shields.io/github/downloads/lh3/minimap2/total.svg?style=flat)](https://github.com/lh3/minimap2/releases) ## Getting Started ```sh git clone https://github.com/lh3/minimap2 @@ -71,9 +71,9 @@ Detailed evaluations are available from the [minimap2 preprint][preprint]. Minimap2 only works on x86-64 CPUs. You can acquire precompiled binaries from the [release page][release] with: ```sh -wget --no-check-certificate -O- https://github.com/lh3/minimap2/releases/download/v2.3/minimap2-2.3_x64-linux.tar.bz2 \ +wget --no-check-certificate -O- https://github.com/lh3/minimap2/releases/download/v2.4/minimap2-2.4_x64-linux.tar.bz2 \ | tar -jxvf - -./minimap2-2.3_x64-linux/minimap2 +./minimap2-2.4_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/main.c b/main.c index 2148b8ff..a6de26b1 100644 --- a/main.c +++ b/main.c @@ -6,7 +6,7 @@ #include "mmpriv.h" #include "getopt.h" -#define MM_VERSION "2.3-r552-dirty" +#define MM_VERSION "2.4-r555" #ifdef __linux__ #include diff --git a/minimap2.1 b/minimap2.1 index 97e1790f..33222cad 100644 --- a/minimap2.1 +++ b/minimap2.1 @@ -1,4 +1,4 @@ -.TH minimap2 1 "27 October 2017" "minimap2-2.3-dirty (r537)" "Bioinformatics tools" +.TH minimap2 1 "6 November 2017" "minimap2-2.4 (r555)" "Bioinformatics tools" .SH NAME .PP minimap2 - mapping and alignment between collections of DNA sequences diff --git a/python/cmappy.pxd b/python/cmappy.pxd index 46004284..e3444a9d 100644 --- a/python/cmappy.pxd +++ b/python/cmappy.pxd @@ -22,7 +22,6 @@ cdef extern from "minimap.h": float mask_level float pri_ratio int best_n - float min_iden int max_join_long, max_join_short int min_join_flank_sc int a, b, q, e, q2, e2 diff --git a/setup.py b/setup.py index e5f6bc35..ea59d5ff 100644 --- a/setup.py +++ b/setup.py @@ -23,7 +23,7 @@ def readme(): setup( name = 'mappy', - version = '2.3', + version = '2.4', url = 'https://github.com/lh3/minimap2', description = 'Minimap2 python binding', long_description = readme(),