diff --git a/NEWS.md b/NEWS.md index 425545ac..bce33f5f 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,28 @@ +Release 2.22-r1101 (7 August 2021) +---------------------------------- + +When choosing the best alignment, this release uses logarithm gap penalty and +query-specific mismatch penalty. It improves the sensitivity to long INDELs in +repetitive regions. + +Other notable changes: + + * Bugfix: fixed an indirect memory leak that may waste a large amount of + memory given highly repetitive reference such as a 16S RNA database (#749). + All versions of minimap2 have this issue. + + * New feature: added --cap-kalloc to reduce the peak memory. This option is + not enabled by default but may become the default in future releases. + +Known issue: + + * Minimap2 may take a long time to map a read (#771). So far it is not clear + if this happens to v2.18 and earlier versions. + +(2.22: 7 August 2021, r1101) + + + Release 2.21-r1071 (6 July 2021) -------------------------------- @@ -5,7 +30,7 @@ This release fixed a regression in short-read mapping introduced in v2.19 (#776). It also fixed invalid comparisons of uninitialized variables, though these are harmless (#752). Long-read alignment should be identical to v2.20. -(2.21: 6 July 2021) +(2.21: 6 July 2021, r1071) diff --git a/README.md b/README.md index 0bff2e48..90af2829 100644 --- 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/v2.21/minimap2-2.21_x64-linux.tar.bz2 | tar -jxvf - -./minimap2-2.21_x64-linux/minimap2 +curl -L https://github.com/lh3/minimap2/releases/download/v2.22/minimap2-2.22_x64-linux.tar.bz2 | tar -jxvf - +./minimap2-2.22_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 index 8df1e28d..14c4dfac 100644 --- 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/v2.21/minimap2-2.21_x64-linux.tar.bz2 | tar jxf - -cp minimap2-2.21_x64-linux/{minimap2,k8,paftools.js} . # copy executables +curl -L https://github.com/lh3/minimap2/releases/download/v2.22/minimap2-2.22_x64-linux.tar.bz2 | tar jxf - +cp minimap2-2.22_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 index 0c13ab17..3c625760 100644 --- a/main.c +++ b/main.c @@ -7,7 +7,7 @@ #include "mmpriv.h" #include "ketopt.h" -#define MM_VERSION "2.21-dev-r1094-dirty" +#define MM_VERSION "2.22-r1101" #ifdef __linux__ #include diff --git a/minimap2.1 b/minimap2.1 index 96dd4220..86454716 100644 --- a/minimap2.1 +++ b/minimap2.1 @@ -1,4 +1,4 @@ -.TH minimap2 1 "6 July 2021" "minimap2-2.21 (r1071)" "Bioinformatics tools" +.TH minimap2 1 "7 August 2021" "minimap2-2.22 (r1101)" "Bioinformatics tools" .SH NAME .PP minimap2 - mapping and alignment between collections of DNA sequences @@ -423,6 +423,11 @@ alignment. Skip alignment if the DP matrix size is above .IR NUM . Set 0 to disable [100m]. +.TP +.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]. .SS Input/output options .TP 10 .B -a diff --git a/misc/paftools.js b/misc/paftools.js index 11d77222..420cbd60 100755 --- a/misc/paftools.js +++ b/misc/paftools.js @@ -1,6 +1,6 @@ #!/usr/bin/env k8 -var paftools_version = '2.21-r1071'; +var paftools_version = '2.22-r1101'; /***************************** ***** Library functions ***** diff --git a/python/cmappy.pxd b/python/cmappy.pxd index abc3ef7c..b3016746 100644 --- a/python/cmappy.pxd +++ b/python/cmappy.pxd @@ -45,6 +45,9 @@ cdef extern from "minimap.h": int anchor_ext_len, anchor_ext_shift float max_clip_ratio + int rank_min_len + float rank_frac + int pe_ori, pe_bonus float mid_occ_frac @@ -53,6 +56,7 @@ cdef extern from "minimap.h": int32_t max_occ int64_t mini_batch_size int64_t max_sw_mat + int64_t cap_kalloc const char *split_prefix diff --git a/python/mappy.pyx b/python/mappy.pyx index 838b5ad0..8728a3e4 100644 --- a/python/mappy.pyx +++ b/python/mappy.pyx @@ -3,7 +3,7 @@ from libc.stdlib cimport free cimport cmappy import sys -__version__ = '2.21' +__version__ = '2.22' cmappy.mm_reset_timer() diff --git a/setup.py b/setup.py index 1a4d2277..38762a85 100644 --- a/setup.py +++ b/setup.py @@ -23,7 +23,7 @@ def readme(): setup( name = 'mappy', - version = '2.21', + version = '2.22', url = 'https://github.com/lh3/minimap2', description = 'Minimap2 python binding', long_description = readme(),