From eb819c29e804df02db51f5d80216306f4d5da856 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Tue, 12 Dec 2017 10:39:20 -0500 Subject: [PATCH] Release minimap2-2.6 (r623) --- NEWS.md | 32 ++++++++++++++++++++++++++++++++ README.md | 6 +++--- main.c | 2 +- minimap2.1 | 2 +- python/cmappy.pxd | 1 + setup.py | 4 ++-- 6 files changed, 40 insertions(+), 7 deletions(-) diff --git a/NEWS.md b/NEWS.md index f0a0cce..1de8d1c 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,35 @@ +Release 2.6-r623 (12 December 2017) +----------------------------------- + +This release adds several features and fixes two minor bugs: + + * Optionally build an index without sequences. This helps to reduce the + peak memory for read overlapping and is automatically applied when + base-level alignment is not requested. + + * Approximately estimate per-base sequence divergence (i.e. 1-identity) + without performing base-level alignment, using a MashMap-like method. The + estimate is written to a new dv:f tag. + + * Reduced the number of tiny terminal exons in RNA-seq alignment. The current + setting is conservative. Increase --end-seed-pen to drop more such exons. + + * Reduced the peak memory when aligning long query sequences. + + * Fixed a bug that is caused by HPC minimizers longer than 256bp. This should + have no effect in practice, but it is recommended to rebuild HPC indices if + possible. + + * Fixed a bug when identifying identical hits (#71). This should only affect + artifactual reference consisting of near identical sequences. + +For genomic sequences, minimap2 should give nearly identical alignments to +v2.5, except the new dv:f tag. + +(2.6: 12 December 2017, r623) + + + Release 2.5-r572 (11 November 2017) ----------------------------------- diff --git a/README.md b/README.md index c10a1a5..f12d29b 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -[![GitHub Downloads](https://img.shields.io/github/downloads/lh3/minimap2/total.svg?style=social&logo=github&label=Download%20v2.5)](https://github.com/lh3/minimap2/releases) +[![GitHub Downloads](https://img.shields.io/github/downloads/lh3/minimap2/total.svg?style=social&logo=github&label=Download)](https://github.com/lh3/minimap2/releases) [![BioConda Install](https://img.shields.io/conda/dn/bioconda/minimap2.svg?style=flag&label=BioConda%20install)](https://anaconda.org/bioconda/minimap2) [![PyPI](https://img.shields.io/pypi/v/mappy.svg?style=flat)](https://pypi.python.org/pypi/mappy) [![Build Status](https://travis-ci.org/lh3/minimap2.svg?branch=master)](https://travis-ci.org/lh3/minimap2) @@ -68,9 +68,9 @@ 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 -curl -L https://github.com/lh3/minimap2/releases/download/v2.5/minimap2-2.5_x64-linux.tar.bz2 \ +curl -L https://github.com/lh3/minimap2/releases/download/v2.6/minimap2-2.6_x64-linux.tar.bz2 \ | tar -jxvf - -./minimap2-2.5_x64-linux/minimap2 +./minimap2-2.6_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 7b8ff5a..863116e 100644 --- a/main.c +++ b/main.c @@ -6,7 +6,7 @@ #include "mmpriv.h" #include "getopt.h" -#define MM_VERSION "2.5-r622-dirty" +#define MM_VERSION "2.6-r623" #ifdef __linux__ #include diff --git a/minimap2.1 b/minimap2.1 index b6366fe..49d1de5 100644 --- a/minimap2.1 +++ b/minimap2.1 @@ -1,4 +1,4 @@ -.TH minimap2 1 "8 December 2017" "minimap2-2.5-dirty (r611)" "Bioinformatics tools" +.TH minimap2 1 "12 December 2017" "minimap2-2.6 (r623)" "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 de969a4..b4f965d 100644 --- a/python/cmappy.pxd +++ b/python/cmappy.pxd @@ -30,6 +30,7 @@ cdef extern from "minimap.h": int end_bonus int min_dp_max int min_ksw_len + int anchor_ext_len, anchor_ext_shift int pe_ori, pe_bonus float mid_occ_frac int32_t mid_occ diff --git a/setup.py b/setup.py index cc86c01..d484d0d 100644 --- a/setup.py +++ b/setup.py @@ -23,7 +23,7 @@ def readme(): setup( name = 'mappy', - version = '2.5', + version = '2.6', url = 'https://github.com/lh3/minimap2', description = 'Minimap2 python binding', long_description = readme(), @@ -35,7 +35,7 @@ setup( ext_modules = [Extension('mappy', sources = [module_src, 'align.c', 'bseq.c', 'chain.c', 'format.c', 'hit.c', 'index.c', 'pe.c', 'ksw2_extd2_sse.c', 'ksw2_exts2_sse.c', 'ksw2_extz2_sse.c', 'ksw2_ll_sse.c', - 'kalloc.c', 'kthread.c', 'map.c', 'misc.c', 'sdust.c', 'sketch.c'], + 'kalloc.c', 'kthread.c', 'map.c', 'misc.c', 'sdust.c', 'sketch.c', 'esterr.c'], depends = ['minimap.h', 'bseq.h', 'kalloc.h', 'kdq.h', 'khash.h', 'kseq.h', 'ksort.h', 'ksw2.h', 'kthread.h', 'kvec.h', 'mmpriv.h', 'sdust.h', 'python/cmappy.h', 'python/cmappy.pxd'],