Release minimap2-2.12 (r827)

NEWS.md

@@ -1,3 +1,27 @@
+Release 2.12-r827 (6 August 2018)
+---------------------------------
+
+Changes to minimap2:
+
+ * Added option --split-prefix to write proper alignments (correct mapping
+   quality and clustered query sequences) given a multi-part index (#141 and
+   #189; mostly by @hasindu2008).
+
+ * Fixed a memory leak when option -y is in use.
+
+Changes to mappy:
+
+ * Support the MD/cs tag (#183 and #203).
+
+ * Allow mappy to index a single sequence, to add extra flags and to change the
+   scoring system.
+
+Minimap2 should produce alignments identical to v2.11.
+
+(2.12: 6 August 2018, r827)
+
+
+
 Release 2.11-r797 (20 June 2018)
 --------------------------------
 

README.md

@@ -70,8 +70,8 @@ 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/v2.11/minimap2-2.11_x64-linux.tar.bz2 | tar -jxvf -
+curl -L https://github.com/lh3/minimap2/releases/download/v2.12/minimap2-2.12_x64-linux.tar.bz2 | tar -jxvf -
-./minimap2-2.11_x64-linux/minimap2
+./minimap2-2.12_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

@@ -24,18 +24,18 @@
 
 This cookbook walks you through a variety of applications of minimap2 and its
 companion script `paftools.js`. All data here are freely available from the
-minimap2 release page at version tag [v2.11][v2.11]. Some examples only work
+minimap2 release page at version tag [v2.12][v2.12]. Some examples only work
-with v2.11 or later.
+with v2.10 or later.
 
 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/v2.11/minimap2-2.11_x64-linux.tar.bz2 | tar jxf -
+curl -L https://github.com/lh3/minimap2/releases/download/v2.12/minimap2-2.12_x64-linux.tar.bz2 | tar jxf -
-cp minimap2-2.11_x64-linux/{minimap2,k8,paftools.js} .  # copy executables
+cp minimap2-2.12_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/v2.11/cookbook-data.tgz | tar zxf -
+curl -L https://github.com/lh3/minimap2/releases/download/v2.10/cookbook-data.tgz | tar zxf -
 ```
 
 ## <a name="map-reads"></a>Mapping Genomic Reads
@@ -240,4 +240,4 @@ with `-x ava-pb` (99% vs 93% with `-x ava-ont`).
 [pbsim]: https://github.com/pfaucon/PBSIM-PacBio-Simulator
 [mason2]: https://github.com/seqan/seqan/tree/master/apps/mason2
 [paf]: https://github.com/lh3/miniasm/blob/master/PAF.md
-[v2.11]: https://github.com/lh3/minimap2/releases/tag/v2.11
+[v2.12]: https://github.com/lh3/minimap2/releases/tag/v2.12

main.c

@@ -10,7 +10,7 @@
 #include "getopt.h"
 #endif
 
-#define MM_VERSION "2.11-r823-dirty"
+#define MM_VERSION "2.12-r827"
 
 #ifdef __linux__
 #include <sys/resource.h>

minimap2.1

@@ -1,4 +1,4 @@
-.TH minimap2 1 "20 June 2018" "minimap2-2.11 (r797)" "Bioinformatics tools"
+.TH minimap2 1 "6 August 2018" "minimap2-2.12 (r827)" "Bioinformatics tools"
 .SH NAME
 .PP
 minimap2 - mapping and alignment between collections of DNA sequences

setup.py

@@ -33,7 +33,7 @@ def readme():
 
 setup(
 	name = 'mappy',
-	version = '2.11',
+	version = '2.12',
 	url = 'https://github.com/lh3/minimap2',
 	description = 'Minimap2 python binding',
 	long_description = readme(),