Release minimap2-2.20 (r1061)

lh3 · May 27, 2021 · 15471bd · 15471bd
1 parent ca19463
commit 15471bd
Show file tree

Hide file tree

Showing 10 changed files with 25 additions and 13 deletions.
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,15 @@
+Release 2.20-r1061 (27 May 2021)
+--------------------------------
+
+This release fixed a bug in the Python module and improves the command-line
+compatibiliity with v2.18. In v2.19, if `-r` is specified with an `asm*` preset,
+users would get alignments more fragmented than v2.18. This could be an issue
+for existing pipelines specifying `-r`. This release resolves this issue.
+
+(2.20: 27 May 2021, r1061)
+
+
+
 Release 2.19-r1057 (26 May 2021)
 --------------------------------
 
@@ -33,7 +45,7 @@ unimap for contig alignment. Unimap will remain an experimental project and is
 no longer recommended over minimap2. Sorry for reverting the recommendation in
 short time.
 
-(2.20: 26 May 2021, r1057)
+(2.19: 26 May 2021, r1057)
 
 
 

diff --git a/README.md b/README.md
@@ -74,8 +74,8 @@ 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/v2.19/minimap2-2.19_x64-linux.tar.bz2 | tar -jxvf -
-./minimap2-2.19_x64-linux/minimap2
+curl -L https://github.com/lh3/minimap2/releases/download/v2.20/minimap2-2.20_x64-linux.tar.bz2 | tar -jxvf -
+./minimap2-2.20_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/v2.19/minimap2-2.19_x64-linux.tar.bz2 | tar jxf -
-cp minimap2-2.19_x64-linux/{minimap2,k8,paftools.js} .  # copy executables
+curl -L https://github.com/lh3/minimap2/releases/download/v2.20/minimap2-2.20_x64-linux.tar.bz2 | tar jxf -
+cp minimap2-2.20_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
@@ -7,7 +7,7 @@
 #include "mmpriv.h"
 #include "ketopt.h"
 
-#define MM_VERSION "2.19-r1060-dirty"
+#define MM_VERSION "2.20-r1061"
 
 #ifdef __linux__
 #include <sys/resource.h>

diff --git a/map.c b/map.c
@@ -277,7 +277,7 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
 						 opt->chain_gap_scale * 0.01 * mi->k, 0.0f, is_splice, n_segs, n_a, a, &n_regs0, &u, b->km);
 	}
 
-	if (opt->bw_long > opt->bw && (opt->flag & MM_F_NO_LJOIN) == 0 && n_segs == 1 && n_regs0 > 1) { // re-chain/long-join for long sequences
+	if (opt->bw_long > opt->bw && (opt->flag & (MM_F_SPLICE|MM_F_SR|MM_F_NO_LJOIN)) == 0 && n_segs == 1 && n_regs0 > 1) { // re-chain/long-join for long sequences
 		int32_t st = (int32_t)a[0].y, en = (int32_t)a[(int32_t)u[0] - 1].y;
 		if (qlen_sum - (en - st) > opt->rmq_rescue_size || en - st > qlen_sum * opt->rmq_rescue_ratio) {
 			int32_t i;

diff --git a/minimap2.1 b/minimap2.1
@@ -1,4 +1,4 @@
-.TH minimap2 1 "26 May 2021" "minimap2-2.19 (r1057)" "Bioinformatics tools"
+.TH minimap2 1 "27 May 2021" "minimap2-2.20 (r1061)" "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 = '2.19-r1057';
+var paftools_version = '2.20-r1061';
 
 /*****************************
  ***** Library functions *****

diff --git a/options.c b/options.c
@@ -75,7 +75,7 @@ void mm_mapopt_update(mm_mapopt_t *opt, const mm_idx_t *mi)
 void mm_mapopt_max_intron_len(mm_mapopt_t *opt, int max_intron_len)
 {
 	if ((opt->flag & MM_F_SPLICE) && max_intron_len > 0)
-		opt->max_gap_ref = opt->bw = max_intron_len;
+		opt->max_gap_ref = opt->bw = opt->bw_long = max_intron_len;
 }
 
 int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
@@ -109,7 +109,7 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
 		io->flag = 0, io->k = 19, io->w = 19;
 		mo->bw = mo->bw_long = 100000;
 		mo->max_gap = 10000;
-		mo->flag |= MM_F_RMQ | MM_F_NO_LJOIN;
+		mo->flag |= MM_F_RMQ;
 		mo->min_mid_occ = 50, mo->max_mid_occ = 500;
 		mo->min_dp_max = 200;
 		mo->best_n = 50;

diff --git a/python/mappy.pyx b/python/mappy.pyx
@@ -3,7 +3,7 @@ from libc.stdlib cimport free
 cimport cmappy
 import sys
 
-__version__ = '2.19'
+__version__ = '2.20'
 
 cmappy.mm_reset_timer()
 

diff --git a/setup.py b/setup.py
@@ -23,7 +23,7 @@ def readme():
 
 setup(
 	name = 'mappy',
-	version = '2.19',
+	version = '2.20',
 	url = 'https://github.com/lh3/minimap2',
 	description = 'Minimap2 python binding',
 	long_description = readme(),