Release minimap2-2.11 (r797)

NEWS.md

@@ -1,3 +1,58 @@
+Release 2.11-r797 (20 June 2018)
+--------------------------------
+
+Changes to minimap2:
+
+ * Improved alignment accuracy in low-complexity regions for SV calling. Thank
+   @armintoepfer for multiple offline examples.
+
+ * Added option --eqx to encode sequence match/mismatch with the =/X CIGAR
+   operators (#156, #157 and #175).
+
+ * When compiled with VC++, minimap2 generated wrong alignments due to a
+   comparison between a signed integer and an unsigned integer (#184). Also
+   fixed warnings reported by "clang -Wextra".
+
+ * Fixed incorrect anchor filtering due to a missing 64- to 32-bit cast.
+
+ * Fixed incorrect mapping quality for inversions (#148).
+
+ * Fixed incorrect alignment involving ambiguous bases (#155).
+
+ * Fixed incorrect presets: option `-r 2000` is intended to be used with
+   ava-ont, not ava-pb. The bug was introduced in 2.10.
+
+ * Fixed a bug when --for-only/--rev-only is used together with --sr or
+   --heap-sort=yes (#166).
+
+ * Fixed option -Y that was not working in the previous releases.
+
+ * Added option --lj-min-ratio to fine control the alignment of long gaps
+   found by the "long-join" heuristic (#128).
+
+ * Exposed `mm_idx_is_idx`, `mm_idx_load` and `mm_idx_dump` C APIs (#177).
+   Also fixed a bug when indexing without reference names (this feature is not
+   exposed to the command line).
+
+Changes to mappy:
+
+ * Added `__version__` (#165).
+
+ * Exposed the maximum fragment length parameter to mappy (#174).
+
+Changes to paftools:
+
+ * Don't crash when there is no "cg" tag (#153).
+
+ * Fixed wrong coverage report by "paftools.js call" (#145).
+
+This version may produce slightly different base-level alignment. The overall
+alignment statistics should remain similar.
+
+(2.11: 20 June 2018, r797)
+
+
+
 Release 2.10-r761 (27 March 2018)
 ---------------------------------
 

README.md

@@ -69,8 +69,8 @@ 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/v2.10/minimap2-2.10_x64-linux.tar.bz2 | tar -jxvf -
+curl -L https://github.com/lh3/minimap2/releases/download/v2.11/minimap2-2.11_x64-linux.tar.bz2 | tar -jxvf -
-./minimap2-2.10_x64-linux/minimap2
+./minimap2-2.11_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 [v2.10][v2.10]. Some examples only work
+minimap2 release page at version tag [v2.11][v2.11]. Some examples only work
-with v2.10 or later.
+with v2.11 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/v2.10/minimap2-2.10_x64-linux.tar.bz2 | tar jxf -
+curl -L https://github.com/lh3/minimap2/releases/download/v2.11/minimap2-2.11_x64-linux.tar.bz2 | tar jxf -
-cp minimap2-2.10_x64-linux/{minimap2,k8,paftools.js} .  # copy executables
+cp minimap2-2.11_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 -
+curl -L https://github.com/lh3/minimap2/releases/download/v2.11/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
-[v2.10]: https://github.com/lh3/minimap2/releases/tag/v2.10
+[v2.11]: https://github.com/lh3/minimap2/releases/tag/v2.11

main.c

@@ -10,7 +10,7 @@
 #include "getopt.h"
 #endif
 
-#define MM_VERSION "2.10-r796-dirty"
+#define MM_VERSION "2.11-r797"
 
 #ifdef __linux__
 #include <sys/resource.h>

minimap.h

@@ -222,24 +222,27 @@ int mm_idx_reader_eof(const mm_idx_reader_t *r);
 /**
  * Check whether the file contains a minimap2 index
  *
- * @param fn         index file name
+ * @param fn         file name
- * @return 1 if file can be opened and is a minimap2 index; 0 otherwise
+ *
+ * @return the file size if fn is an index file; 0 if fn is not.
  */
 int64_t mm_idx_is_idx(const char *fn);
 
 /**
- * Load an index
+ * Load a part of an index
  *
- * Unlike mm_idx_reader_read this function specifically loads an existing
+ * Given a uni-part index, this function loads the entire index into memory.
- * index.
+ * Given a multi-part index, it loads one part only and places the file pointer
+ * at the end of that part.
  *
  * @param fp         pointer to FILE object
+ *
  * @return minimap2 index read from fp
  */
 mm_idx_t *mm_idx_load(FILE *fp);
 
 /**
- * Save an index
+ * Append an index (or one part of a full index) to file
  *
  * @param fp         pointer to FILE object
  * @param mi         minimap2 index

minimap2.1

@@ -1,4 +1,4 @@
-.TH minimap2 1 "30 April 2018" "minimap2-2.10-dirty (r770)" "Bioinformatics tools"
+.TH minimap2 1 "20 June 2018" "minimap2-2.11 (r797)" "Bioinformatics tools"
 .SH NAME
 .PP
 minimap2 - mapping and alignment between collections of DNA sequences
@@ -239,6 +239,10 @@ Disable the long gap patching heuristic. When this option is applied, the
 maximum alignment gap is mostly controlled by
 .BR -r .
 .TP
+.B --lj-min-ratio \ FLOAT
+Fraction of query sequence length required to bridge a long gap [0.5]. A
+smaller value helps to recover longer gaps, at the cost of more false gaps.
+.TP
 .B --splice
 Enable the splice alignment mode.
 .TP

python/mappy.pyx

@@ -3,7 +3,7 @@ from libc.stdlib cimport free
 cimport cmappy
 import sys
 
-__version__ = '2.10'
+__version__ = '2.11'
 
 cmappy.mm_reset_timer()
 

setup.py

@@ -23,7 +23,7 @@ def readme():
 
 setup(
 	name = 'mappy',
-	version = '2.10',
+	version = '2.11',
 	url = 'https://github.com/lh3/minimap2',
 	description = 'Minimap2 python binding',
 	long_description = readme(),