Release minimap2-2.14 (r883)

lh3 · Nov 6, 2018 · 59f23f7 · 59f23f7
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diff --git a/NEWS.md b/NEWS.md
@@ -1,22 +1,26 @@
-Release 2.14-r8xx (yy November 2018)
-------------------------------------
+Release 2.14-r883 (5 November 2018)
+-----------------------------------
 
-Changes to minimap2:
+Notable changes:
 
  * Fixed two minor bugs caused by typos (#254 and #266).
 
- * Fixed a bug that made minimap2 abort when -L was used with --MD/--cs (#257).
+ * Fixed a bug that made minimap2 abort when --eqx was used together with --MD
+   or --cs (#257).
 
  * Added --cap-sw-mem to cap the size of DP matrices (#259). Base alignment may
    take a lot of memory in the splicing mode. This may lead to issues when we
    run minimap2 on a cluster with a hard memory limit. The new option avoids
    unlimited memory usage at the cost of missing a few long introns.
 
- * Conforming to C99 and C11 if possible (#261).
+ * Conforming to C99 and C11 when possible (#261).
 
  * Warn about malformatted FASTA or FASTQ (#252 and #255).
 
-(2.14: yy November 2018, r8xx)
+This release occasionally produces base alignments different from v2.13. The
+overall alignment accuracy remain similar.
+
+(2.14: 5 November 2018, r883)
 
 
 

diff --git a/README.md b/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/v2.13/minimap2-2.13_x64-linux.tar.bz2 | tar -jxvf -
-./minimap2-2.13_x64-linux/minimap2
+curl -L https://github.com/lh3/minimap2/releases/download/v2.14/minimap2-2.14_x64-linux.tar.bz2 | tar -jxvf -
+./minimap2-2.14_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/cookbook.md b/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/v2.13/minimap2-2.13_x64-linux.tar.bz2 | tar jxf -
-cp minimap2-2.13_x64-linux/{minimap2,k8,paftools.js} .  # copy executables
+curl -L https://github.com/lh3/minimap2/releases/download/v2.14/minimap2-2.14_x64-linux.tar.bz2 | tar jxf -
+cp minimap2-2.14_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 -

diff --git a/main.c b/main.c
@@ -6,7 +6,7 @@
 #include "mmpriv.h"
 #include "ketopt.h"
 
-#define MM_VERSION "2.13-r882-dirty"
+#define MM_VERSION "2.14-r883"
 
 #ifdef __linux__
 #include <sys/resource.h>

diff --git a/minimap2.1 b/minimap2.1
@@ -1,4 +1,4 @@
-.TH minimap2 1 "11 October 2018" "minimap2-2.13 (r850)" "Bioinformatics tools"
+.TH minimap2 1 "5 November 2018" "minimap2-2.14 (r883)" "Bioinformatics tools"
 .SH NAME
 .PP
 minimap2 - mapping and alignment between collections of DNA sequences

diff --git a/misc/paftools.js b/misc/paftools.js
@@ -1,6 +1,6 @@
 #!/usr/bin/env k8
 
-var paftools_version = '2.13-r872-dirty';
+var paftools_version = '2.14-r883';
 
 /*****************************
  ***** Library functions *****
@@ -781,6 +781,10 @@ function paf_asmgene(args)
 	var n_fn = args.length - getopt.ind;
 	if (n_fn < 2) {
 		print("Usage: paftools.js asmgene [options] <ref-splice.paf> <asm-splice.paf> [...]");
+		print("Options:");
+		print("  -i FLOAT     min identity [" + opt.min_iden + "]");
+		print("  -c FLOAT     min coverage [" + opt.min_cov + "]");
+		print("  -e           print fragmented/missing genes");
 		exit(1);
 	}
 
@@ -2339,6 +2343,7 @@ function main(args)
 		print("");
 		print("  stat       collect basic mapping information in PAF/SAM");
 		print("  asmstat    collect basic assembly information");
+		print("  asmgene    evaluate gene completeness (EXPERIMENTAL)");
 		print("  liftover   simplistic liftOver");
 		print("  call       call variants from asm-to-ref alignment with the cs tag");
 		print("  bedcov     compute the number of bases covered");

diff --git a/python/mappy.pyx b/python/mappy.pyx
@@ -3,7 +3,7 @@ from libc.stdlib cimport free
 cimport cmappy
 import sys
 
-__version__ = '2.13'
+__version__ = '2.14'
 
 cmappy.mm_reset_timer()
 

diff --git a/setup.py b/setup.py
@@ -33,7 +33,7 @@ def readme():
 
 setup(
 	name = 'mappy',
-	version = '2.13',
+	version = '2.14',
 	url = 'https://github.com/lh3/minimap2',
 	description = 'Minimap2 python binding',
 	long_description = readme(),