Release minimap2-2.6 (r623)

Author: lh3

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)
 -----------------------------------
 

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

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 <sys/resource.h>

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

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

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 @@ def readme():
     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'],