Release minimap2-2.22 (r1101)
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Heng Li
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NEWS.md
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NEWS.md
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@ -1,3 +1,28 @@
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Release 2.22-r1101 (7 August 2021)
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----------------------------------
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When choosing the best alignment, this release uses logarithm gap penalty and
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query-specific mismatch penalty. It improves the sensitivity to long INDELs in
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repetitive regions.
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Other notable changes:
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* Bugfix: fixed an indirect memory leak that may waste a large amount of
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memory given highly repetitive reference such as a 16S RNA database (#749).
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All versions of minimap2 have this issue.
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* New feature: added --cap-kalloc to reduce the peak memory. This option is
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not enabled by default but may become the default in future releases.
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Known issue:
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* Minimap2 may take a long time to map a read (#771). So far it is not clear
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if this happens to v2.18 and earlier versions.
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(2.22: 7 August 2021, r1101)
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Release 2.21-r1071 (6 July 2021)
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--------------------------------
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@ -5,7 +30,7 @@ This release fixed a regression in short-read mapping introduced in v2.19
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(#776). It also fixed invalid comparisons of uninitialized variables, though
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these are harmless (#752). Long-read alignment should be identical to v2.20.
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(2.21: 6 July 2021)
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(2.21: 6 July 2021, r1071)
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@ -74,8 +74,8 @@ Detailed evaluations are available from the [minimap2 paper][doi] or the
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Minimap2 is optimized for x86-64 CPUs. You can acquire precompiled binaries from
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the [release page][release] with:
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```sh
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curl -L https://github.com/lh3/minimap2/releases/download/v2.21/minimap2-2.21_x64-linux.tar.bz2 | tar -jxvf -
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./minimap2-2.21_x64-linux/minimap2
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curl -L https://github.com/lh3/minimap2/releases/download/v2.22/minimap2-2.22_x64-linux.tar.bz2 | tar -jxvf -
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./minimap2-2.22_x64-linux/minimap2
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```
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If you want to compile from the source, you need to have a C compiler, GNU make
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and zlib development files installed. Then type `make` in the source code
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@ -31,8 +31,8 @@ To acquire the data used in this cookbook and to install minimap2 and paftools,
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please follow the command lines below:
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```sh
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# install minimap2 executables
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curl -L https://github.com/lh3/minimap2/releases/download/v2.21/minimap2-2.21_x64-linux.tar.bz2 | tar jxf -
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cp minimap2-2.21_x64-linux/{minimap2,k8,paftools.js} . # copy executables
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curl -L https://github.com/lh3/minimap2/releases/download/v2.22/minimap2-2.22_x64-linux.tar.bz2 | tar jxf -
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cp minimap2-2.22_x64-linux/{minimap2,k8,paftools.js} . # copy executables
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export PATH="$PATH:"`pwd` # put the current directory on PATH
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# download example datasets
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curl -L https://github.com/lh3/minimap2/releases/download/v2.10/cookbook-data.tgz | tar zxf -
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2
main.c
2
main.c
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@ -7,7 +7,7 @@
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#include "mmpriv.h"
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#include "ketopt.h"
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#define MM_VERSION "2.21-dev-r1094-dirty"
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#define MM_VERSION "2.22-r1101"
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#ifdef __linux__
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#include <sys/resource.h>
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@ -1,4 +1,4 @@
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.TH minimap2 1 "6 July 2021" "minimap2-2.21 (r1071)" "Bioinformatics tools"
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.TH minimap2 1 "7 August 2021" "minimap2-2.22 (r1101)" "Bioinformatics tools"
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.SH NAME
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.PP
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minimap2 - mapping and alignment between collections of DNA sequences
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@ -423,6 +423,11 @@ alignment.
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Skip alignment if the DP matrix size is above
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.IR NUM .
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Set 0 to disable [100m].
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.TP
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.BI --cap-kalloc \ NUM
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Free thread-local kalloc memory reservoir if after the alignment the size of the reservoir above
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.IR NUM .
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Set 0 to disable [0].
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.SS Input/output options
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.TP 10
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.B -a
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@ -1,6 +1,6 @@
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#!/usr/bin/env k8
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var paftools_version = '2.21-r1071';
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var paftools_version = '2.22-r1101';
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/*****************************
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***** Library functions *****
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@ -45,6 +45,9 @@ cdef extern from "minimap.h":
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int anchor_ext_len, anchor_ext_shift
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float max_clip_ratio
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int rank_min_len
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float rank_frac
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int pe_ori, pe_bonus
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float mid_occ_frac
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@ -53,6 +56,7 @@ cdef extern from "minimap.h":
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int32_t max_occ
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int64_t mini_batch_size
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int64_t max_sw_mat
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int64_t cap_kalloc
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const char *split_prefix
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@ -3,7 +3,7 @@ from libc.stdlib cimport free
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cimport cmappy
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import sys
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__version__ = '2.21'
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__version__ = '2.22'
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cmappy.mm_reset_timer()
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