Release minimap2-2.17 (r941)

NEWS.md

@@ -1,3 +1,31 @@
+Release 2.17-r941 (4 May 2019)
+------------------------------
+
+Changes since the last release:
+
+ * Fixed flawed CIGARs like `5I6D7I` (#392).
+
+ * Bugfix: TLEN should be 0 when either end is unmapped (#373 and #365).
+
+ * Bugfix: mappy is unable to write index (#372).
+
+ * Added option `--junc-bed` to load known gene annotations in the BED12
+   format. Minimap2 prefers annotated junctions over novel junctions (#197 and
+   #348). GTF can be converted to BED12 with `paftools.js gff2bed`.
+
+ * Added option `--sam-hit-only` to suppress unmapped hits in SAM (#377).
+
+ * Added preset `splice:hq` for high-quality CCS or mRNA sequences. It applies
+   better scoring and improves the sensitivity to small exons. This preset may
+   introduce false small introns, but the overall accuracy should be higher.
+
+This version produces nearly identical alignments to v2.16, except for CIGARs
+affected by the bug mentioned above.
+
+(2.17: 5 May 2019, r941)
+
+
+
 Release 2.16-r922 (28 February 2019)
 ------------------------------------
 

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/v2.16/minimap2-2.16_x64-linux.tar.bz2 | tar -jxvf -
+curl -L https://github.com/lh3/minimap2/releases/download/v2.17/minimap2-2.17_x64-linux.tar.bz2 | tar -jxvf -
-./minimap2-2.16_x64-linux/minimap2
+./minimap2-2.17_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

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/v2.16/minimap2-2.16_x64-linux.tar.bz2 | tar jxf -
+curl -L https://github.com/lh3/minimap2/releases/download/v2.17/minimap2-2.17_x64-linux.tar.bz2 | tar jxf -
-cp minimap2-2.16_x64-linux/{minimap2,k8,paftools.js} .  # copy executables
+cp minimap2-2.17_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 -

main.c

@@ -6,7 +6,7 @@
 #include "mmpriv.h"
 #include "ketopt.h"
 
-#define MM_VERSION "2.16-r940-dirty"
+#define MM_VERSION "2.17-r941"
 
 #ifdef __linux__
 #include <sys/resource.h>

minimap2.1

@@ -1,4 +1,4 @@
-.TH minimap2 1 "4 May 2019" "minimap2-2.16-dirty (r940)" "Bioinformatics tools"
+.TH minimap2 1 "4 May 2019" "minimap2-2.17 (r941)" "Bioinformatics tools"
 .SH NAME
 .PP
 minimap2 - mapping and alignment between collections of DNA sequences

misc/paftools.js

@@ -1,6 +1,6 @@
 #!/usr/bin/env k8
 
-var paftools_version = '2.16-r933-dirty';
+var paftools_version = '2.17-r941';
 
 /*****************************
  ***** Library functions *****

python/mappy.pyx

@@ -3,7 +3,7 @@ from libc.stdlib cimport free
 cimport cmappy
 import sys
 
-__version__ = '2.16'
+__version__ = '2.17'
 
 cmappy.mm_reset_timer()
 

setup.py

@@ -33,7 +33,7 @@ def readme():
 
 setup(
 	name = 'mappy',
-	version = '2.16',
+	version = '2.17',
 	url = 'https://github.com/lh3/minimap2',
 	description = 'Minimap2 python binding',
 	long_description = readme(),