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Release bwa-0.7.19 (r1273)
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‎.github/workflows/ci.yaml‎

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- name: Compile with ${{ matrix.compiler }}
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run: make CC=${{ matrix.compiler }}
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# build-aarch64:
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# runs-on: ubuntu-latest
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# strategy:
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# matrix:
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# compiler: [gcc, clang]
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#
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# steps:
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# - name: Checkout bwa
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# uses: actions/checkout@v3
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#
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# - name: Compile with ${{ matrix.compiler }}
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# uses: uraimo/run-on-arch-action@v2
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# with:
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# arch: aarch64
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# distro: ubuntu20.04
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# githubToken: ${{ github.token }}
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# dockerRunArgs: |
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# --volume "${PWD}:/bwa"
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# install: |
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# apt-get update -q -y
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# apt-get install -q -y make ${{ matrix.compiler }} zlib1g-dev
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# run: |
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# cd /bwa
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# make CC=${{ matrix.compiler }}
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build-aarch64:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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compiler: [gcc, clang]
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steps:
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- name: Checkout bwa
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uses: actions/checkout@v3
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- name: Compile with ${{ matrix.compiler }}
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uses: uraimo/run-on-arch-action@v2
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with:
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arch: aarch64
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distro: ubuntu20.04
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githubToken: ${{ github.token }}
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dockerRunArgs: |
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--volume "${PWD}:/bwa"
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install: |
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apt-get update -q -y
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apt-get install -q -y make ${{ matrix.compiler }} zlib1g-dev
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run: |
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cd /bwa
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make CC=${{ matrix.compiler }}

‎Makefile‎

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CC= gcc
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#CC= clang --analyze
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CFLAGS= -g -Wall -Wno-unused-function -O2
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CFLAGS= -g -Wall -Wno-unused-function -O3
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WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
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AR= ar
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DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC)

‎NEWS.md‎

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Release 0.7.19 (22 March 2025)
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------------------------------
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Notable changes:
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* Bugfix: internal `@HD` lines. The bug was introduced in 0.7.18.
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* Merged #414, #391, #346, #312, #311, #308, #291, #288, #286 and #212
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BWA produces alignments identical to v0.7.17 and v0.7.18.
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(0.7.19: 22 March 2025, r1273)
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Release 0.7.18 (14 April 2024)
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------------------------------
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‎README.md‎

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5. [How can a BWA-backtrack alignment stands out of the end of a chromosome?](#endref)
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6. [Does BWA work with ALT contigs in the GRCh38 release?](#altctg)
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7. [Can I just run BWA-MEM against GRCh38+ALT without post-processing?](#postalt)
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8. [Why does BWA use a lot of memory?](#largemem)
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#### <a name="type"></a>1. What types of data does BWA work with?
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diverged part of ALT contigs and also enables HLA typing. It is recommended to
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run the post-processing script.
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### <a name="largemem"></a>8. Why does BWA use a lot of memory?
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This is typically caused by FASTQ generated from a coordinate-sorted BAM.
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BWA uses a lot more memory for centromeric reads than for unique reads.
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In a FASTQ file generated from a sequencing run, centromeric reads are rare in each batch and rarely cause troubles.
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However, in a coordinate-sorted FASTQ file, a whole batch could consist of centromeric reads.
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Such a batch will take a lot more memory and time to map; the insert size estimate will be distorted as well.
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General rule: ***NEVER*** use Picard SamToFastq on coordiate-sorted BAM;
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use samtools [collate+fastq][remap] instead.
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[remap]: https://lh3.github.io/2021/07/06/remapping-an-aligned-bam
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[1]: http://en.wikipedia.org/wiki/GNU_General_Public_License
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[2]: https://github.com/lh3/bwa
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[3]: http://sourceforge.net/projects/bio-bwa/files/

‎bwa.1‎

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.TH bwa 1 "14 April 2023" "bwa-0.7.18-r1243" "Bioinformatics tools"
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.TH bwa 1 "22 March 2025" "bwa-0.7.19-r1273" "Bioinformatics tools"
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.SH NAME
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.PP
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bwa - Burrows-Wheeler Alignment Tool

‎main.c‎

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#include "utils.h"
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#ifndef PACKAGE_VERSION
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#define PACKAGE_VERSION "0.7.18-r1272-dirty"
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#define PACKAGE_VERSION "0.7.19-r1273"
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#endif
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int bwa_fa2pac(int argc, char *argv[]);

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