Release minimap2-2.28 (r1209)

Author: lh3

NEWS.md

@@ -1,3 +1,32 @@
+Release 2.28-r1209 (27 March 2024)
+----------------------------------
+
+Notable changes to minimap2:
+
+ * Bugfix: `--MD` was not working properly due to the addition of `--ds` in the
+   last release (#1181 and #1182).
+
+ * New feature: added an experimental preset `lq:hqae` for aligning accurate
+   long reads back to their assembly. It has been observed that `map-hifi` and
+   `lr:hq` may produce many wrong alignments around centromeres when accurate
+   long reads (PacBio HiFi or Nanopore duplex/Q20+) are mapped to a diploid
+   assembly constructed from them. This new preset produces much more accurate
+   alignment. It is still experimental and may be subjective to changes in
+   future.
+
+ * Change: reduced the default `--cap-kalloc` to 500m to lower the peak
+   memory consumption (#855).
+
+Notable changes to mappy:
+
+ * Bugfix: mappy option struct was out of sync with minimap2 (#1177).
+
+Minimap2 should output identical alignments to v2.27.
+
+(2.28: 27 March 2024, r1209)
+
+
+
 Release 2.27-r1193 (12 March 2024)
 ----------------------------------
 

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/v2.27/minimap2-2.27_x64-linux.tar.bz2 | tar -jxvf -
-./minimap2-2.27_x64-linux/minimap2
+curl -L https://github.com/lh3/minimap2/releases/download/v2.28/minimap2-2.28_x64-linux.tar.bz2 | tar -jxvf -
+./minimap2-2.28_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/v2.27/minimap2-2.27_x64-linux.tar.bz2 | tar jxf -
-cp minimap2-2.27_x64-linux/{minimap2,k8,paftools.js} .  # copy executables
+curl -L https://github.com/lh3/minimap2/releases/download/v2.28/minimap2-2.28_x64-linux.tar.bz2 | tar jxf -
+cp minimap2-2.28_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 -

minimap.h

@@ -5,7 +5,7 @@
 #include <stdio.h>
 #include <sys/types.h>
 
-#define MM_VERSION "2.27-r1208-dirty"
+#define MM_VERSION "2.28-r1209"
 
 #define MM_F_NO_DIAG       (0x001LL) // no exact diagonal hit
 #define MM_F_NO_DUAL       (0x002LL) // skip pairs where query name is lexicographically larger than target name

minimap2.1

@@ -1,4 +1,4 @@
-.TH minimap2 1 "12 March 2024" "minimap2-2.27 (r1193)" "Bioinformatics tools"
+.TH minimap2 1 "12 March 2024" "minimap2-2.28 (r1209)" "Bioinformatics tools"
 .SH NAME
 .PP
 minimap2 - mapping and alignment between collections of DNA sequences
@@ -468,7 +468,7 @@ Set 0 to disable [100m].
 .BI --cap-kalloc \ NUM
 Free thread-local kalloc memory reservoir if after the alignment the size of the reservoir above
 .IR NUM .
-Set 0 to disable [0].
+Set 0 to disable [500m].
 .SS Input/output options
 .TP 10
 .B -a

misc/paftools.js

@@ -1,6 +1,6 @@
 #!/usr/bin/env k8
 
-var paftools_version = '2.27-r1197-dirty';
+var paftools_version = '2.28-r1209';
 
 /*****************************
  ***** Library functions *****

python/mappy.pyx

@@ -3,7 +3,7 @@ from libc.stdlib cimport free
 cimport cmappy
 import sys
 
-__version__ = '2.27'
+__version__ = '2.28'
 
 cmappy.mm_reset_timer()
 
@@ -96,6 +96,7 @@ cdef class Alignment:
 		a = [str(self._q_st), str(self._q_en), strand, self._ctg, str(self._ctg_len), str(self._r_st), str(self._r_en),
 			str(self._mlen), str(self._blen), str(self._mapq), tp, ts, "cg:Z:" + self.cigar_str]
 		if self._cs != "": a.append("cs:Z:" + self._cs)
+		if self._MD != "": a.append("MD:Z:" + self._MD)
 		return "\t".join(a)
 
 cdef class ThreadBuffer:

python/minimap2.py

@@ -5,7 +5,7 @@
 import mappy as mp
 
 def main(argv):
-	opts, args = getopt.getopt(argv[1:], "x:n:m:k:w:r:c")
+	opts, args = getopt.getopt(argv[1:], "x:n:m:k:w:r:cM")
 	if len(args) < 2:
 		print("Usage: minimap2.py [options] <ref.fa>|<ref.mmi> <query.fq>")
 		print("Options:")
@@ -16,10 +16,11 @@ def main(argv):
 		print("  -w INT      minimizer window length")
 		print("  -r INT      band width")
 		print("  -c          output the cs tag")
+		print("  -M          output the MD tag")
 		sys.exit(1)
 
 	preset = min_cnt = min_sc = k = w = bw = None
-	out_cs = False
+	out_cs = out_MD = False
 	for opt, arg in opts:
 		if opt == '-x': preset = arg
 		elif opt == '-n': min_cnt = int(arg)
@@ -28,11 +29,12 @@ def main(argv):
 		elif opt == '-k': k = int(arg)
 		elif opt == '-w': w = int(arg)
 		elif opt == '-c': out_cs = True
+		elif opt == '-M': out_MD = True
 
 	a = mp.Aligner(args[0], preset=preset, min_cnt=min_cnt, min_chain_score=min_sc, k=k, w=w, bw=bw)
 	if not a: raise Exception("ERROR: failed to load/build index file '{}'".format(args[0]))
 	for name, seq, qual in mp.fastx_read(args[1]): # read one sequence
-		for h in a.map(seq, cs=out_cs): # traverse hits
+		for h in a.map(seq, cs=out_cs, MD=out_MD): # traverse hits
 			print('{}\t{}\t{}'.format(name, len(seq), h))
 
 if __name__ == "__main__":

setup.py

@@ -23,7 +23,7 @@ def readme():
 
 setup(
 	name = 'mappy',
-	version = '2.27',
+	version = '2.28',
 	url = 'https://github.com/lh3/minimap2',
 	description = 'Minimap2 python binding',
 	long_description = readme(),