Release bwa-0.7.19 (r1273)

Author: lh3

.github/workflows/ci.yaml

@@ -20,27 +20,27 @@ jobs:
     - name: Compile with ${{ matrix.compiler }}
       run:  make CC=${{ matrix.compiler }}
 
-#  build-aarch64:
-#    runs-on: ubuntu-latest
-#    strategy:
-#      matrix:
-#        compiler: [gcc, clang]
-#
-#    steps:
-#    - name: Checkout bwa
-#      uses: actions/checkout@v3
-#
-#    - name: Compile with ${{ matrix.compiler }}
-#      uses: uraimo/run-on-arch-action@v2
-#      with:
-#        arch: aarch64
-#        distro: ubuntu20.04
-#        githubToken: ${{ github.token }}
-#        dockerRunArgs: |
-#          --volume "${PWD}:/bwa"
-#        install: |
-#          apt-get update -q -y
-#          apt-get install -q -y make ${{ matrix.compiler }} zlib1g-dev
-#        run: |
-#          cd /bwa
-#          make CC=${{ matrix.compiler }}
+  build-aarch64:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        compiler: [gcc, clang]
+
+    steps:
+    - name: Checkout bwa
+      uses: actions/checkout@v3
+
+    - name: Compile with ${{ matrix.compiler }}
+      uses: uraimo/run-on-arch-action@v2
+      with:
+        arch: aarch64
+        distro: ubuntu20.04
+        githubToken: ${{ github.token }}
+        dockerRunArgs: |
+          --volume "${PWD}:/bwa"
+        install: |
+          apt-get update -q -y
+          apt-get install -q -y make ${{ matrix.compiler }} zlib1g-dev
+        run: |
+          cd /bwa
+          make CC=${{ matrix.compiler }}

Makefile

@@ -1,6 +1,6 @@
 CC=			gcc
 #CC=			clang --analyze
-CFLAGS=		-g -Wall -Wno-unused-function -O2
+CFLAGS=		-g -Wall -Wno-unused-function -O3
 WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
 AR=			ar
 DFLAGS=		-DHAVE_PTHREAD $(WRAP_MALLOC)

NEWS.md

@@ -1,3 +1,17 @@
+Release 0.7.19 (22 March 2025)
+------------------------------
+
+Notable changes:
+
+ * Bugfix: internal `@HD` lines. The bug was introduced in 0.7.18.
+ * Merged #414, #391, #346, #312, #311, #308, #291, #288, #286 and #212
+
+BWA produces alignments identical to v0.7.17 and v0.7.18.
+
+(0.7.19: 22 March 2025, r1273)
+
+
+
 Release 0.7.18 (14 April 2024)
 ------------------------------
 

README.md

@@ -83,6 +83,7 @@ do not have plan to submit it to a peer-reviewed journal in the near future.
 5. [How can a BWA-backtrack alignment stands out of the end of a chromosome?](#endref)
 6. [Does BWA work with ALT contigs in the GRCh38 release?](#altctg)
 7. [Can I just run BWA-MEM against GRCh38+ALT without post-processing?](#postalt)
+8. [Why does BWA use a lot of memory?](#largemem)
 
 #### <a name="type"></a>1. What types of data does BWA work with?
 
@@ -163,8 +164,17 @@ post-processing helps to reduce false mappings caused by reads from the
 diverged part of ALT contigs and also enables HLA typing. It is recommended to
 run the post-processing script.
 
+### <a name="largemem"></a>8. Why does BWA use a lot of memory?
 
+This is typically caused by FASTQ generated from a coordinate-sorted BAM.
+BWA uses a lot more memory for centromeric reads than for unique reads.
+In a FASTQ file generated from a sequencing run, centromeric reads are rare in each batch and rarely cause troubles.
+However, in a coordinate-sorted FASTQ file, a whole batch could consist of centromeric reads.
+Such a batch will take a lot more memory and time to map; the insert size estimate will be distorted as well.
+General rule: ***NEVER*** use Picard SamToFastq on coordiate-sorted BAM;
+use samtools [collate+fastq][remap] instead.
 
+[remap]: https://lh3.github.io/2021/07/06/remapping-an-aligned-bam
 [1]: http://en.wikipedia.org/wiki/GNU_General_Public_License
 [2]: https://github.com/lh3/bwa
 [3]: http://sourceforge.net/projects/bio-bwa/files/

bwa.1

@@ -1,4 +1,4 @@
-.TH bwa 1 "14 April 2023" "bwa-0.7.18-r1243" "Bioinformatics tools"
+.TH bwa 1 "22 March 2025" "bwa-0.7.19-r1273" "Bioinformatics tools"
 .SH NAME
 .PP
 bwa - Burrows-Wheeler Alignment Tool

main.c

@@ -30,7 +30,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.18-r1272-dirty"
+#define PACKAGE_VERSION "0.7.19-r1273"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);