Release minimap2-2.4 (r555)
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Heng Li
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NEWS.md
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NEWS.md
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Release 2.4-r555 (6 November 2017)
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----------------------------------
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As is planned, this release focuses on fine tuning the base algorithm. Notable
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changes include
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* Changed the mapping quality scale to match the scale of BWA-MEM. This makes
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minimap2 and BWA-MEM achieve similar sensitivity-specificity balance on real
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short-read data.
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* Improved the accuracy of splice alignment by modeling one additional base
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close to the GT-AG signal. This model is used by default with `-x splice`.
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For SIRV control data, however, it is recommended to add `--splice-flank=no`
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to disable this feature as the SIRV splice signals are slightly different.
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* Tuned the parameters for Nanopore Direct RNA reads. The recommended command
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line is `-axsplice -k14 -uf` (#46).
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* Fixed a segmentation fault when aligning PacBio reads (#47 and #48). This
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bug is very rare but it affects all versions of minimap2. It is also
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recommended to re-index reference genomes created with `map-pb`. For human,
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two minimizers in an old index are wrong.
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* Changed option `-L` in sync with the final decision of hts-specs: a fake
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CIGAR takes the form of `<readLen>S<refLen>N`. Note that `-L` only enables
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future tools to recognize long CIGARs. It is not possible for older tools to
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work with such alignments in BAM (#43 and #51).
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* Fixed a tiny issue whereby minimap2 may waste 8 bytes per candidate
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alignment.
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The minimap2 technical note hosted at arXiv has also been updated to reflect
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recent changes.
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(2.4: 6 November 2017, r555)
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Release 2.3-r531 (22 October 2017)
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----------------------------------
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@ -26,7 +64,7 @@ This release come with many improvements and bug fixes:
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This release has implemented all the major features I planned five months ago,
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with the addition of spliced long-read alignment. The next couple of releases
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will focus on fine tuning of base algorithms.
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will focus on fine tuning of the base algorithms.
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(2.3: 22 October 2017, r531)
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[](https://github.com/lh3/minimap2/releases)
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[](https://github.com/lh3/minimap2/releases)
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[](https://anaconda.org/bioconda/minimap2)
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[](https://pypi.python.org/pypi/mappy)
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[](https://pypi.python.org/pypi/mappy)
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[](LICENSE.txt)
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[](https://travis-ci.org/lh3/minimap2)
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<!-- [](https://github.com/lh3/minimap2/releases) -->
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[](https://github.com/lh3/minimap2/releases)
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## <a name="started"></a>Getting Started
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```sh
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git clone https://github.com/lh3/minimap2
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@ -71,9 +71,9 @@ Detailed evaluations are available from the [minimap2 preprint][preprint].
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Minimap2 only works on 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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wget --no-check-certificate -O- https://github.com/lh3/minimap2/releases/download/v2.3/minimap2-2.3_x64-linux.tar.bz2 \
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wget --no-check-certificate -O- https://github.com/lh3/minimap2/releases/download/v2.4/minimap2-2.4_x64-linux.tar.bz2 \
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| tar -jxvf -
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./minimap2-2.3_x64-linux/minimap2
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./minimap2-2.4_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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2
main.c
2
main.c
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#include "mmpriv.h"
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#include "getopt.h"
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#define MM_VERSION "2.3-r552-dirty"
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#define MM_VERSION "2.4-r555"
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#ifdef __linux__
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#include <sys/resource.h>
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.TH minimap2 1 "27 October 2017" "minimap2-2.3-dirty (r537)" "Bioinformatics tools"
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.TH minimap2 1 "6 November 2017" "minimap2-2.4 (r555)" "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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@ -22,7 +22,6 @@ cdef extern from "minimap.h":
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float mask_level
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float pri_ratio
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int best_n
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float min_iden
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int max_join_long, max_join_short
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int min_join_flank_sc
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int a, b, q, e, q2, e2
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