samtools · pd3 · Jul 23, 2026 · Jul 22, 2026 · Jul 22, 2026 · Jul 22, 2026
diff --git a/.github/workflows/container-build.yml b/.github/workflows/container-build.yml
@@ -0,0 +1,79 @@
+name: Containers
+on: [push, pull_request]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  Containers:
+    # comment out if we're using the cache
+    runs-on: ubuntu-latest
+    container: ${{ matrix.image }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os:      ['alpine', 'archlinux', 'centos', 'rockylinux', 'opensuse']
+        include:
+          - os:          alpine
+            image:       alpine:3.23
+            cflags:      -Wno-sign-conversion
+          - os:          archlinux
+            image:       archlinux:base-devel
+            #-Wno-discarded-qualified needed?
+            cflags:      -Wno-sign-conversion -Wno-discarded-qualifiers
+          - os:          centos
+            image:       quay.io/centos/centos:10
+          - os:          rockylinux
+            image:       quay.io/rockylinux/rockylinux:10
+          - os:          opensuse
+            image:       opensuse/tumbleweed
+            #needed?
+            cflags:      -Wno-discarded-qualifiers
+
+    steps:
+      - name: Install dependencies
+        run: |
+          case ${{ matrix.os }} in
+          *alpine*)
+            apk update
+            apk add git autoconf automake make gcc musl-dev perl bash zlib-dev bzip2-dev xz-dev curl-dev openssl-dev ncurses-dev
+            ;;
+          *archlinux*)
+            pacman -Syyu --noconfirm
+            pacman -Sy --noconfirm base-devel git libdeflate
+            ;;
+          *centos*)
+            yum install -y autoconf automake make gcc perl-Data-Dumper zlib-devel bzip2 bzip2-devel xz-devel curl-devel openssl-devel git perl-FindBin ncurses-devel
+            ;;
+          *rockylinux*)
+            yum install -y autoconf automake make gcc perl-Data-Dumper zlib-devel bzip2 bzip2-devel xz-devel curl-devel openssl-devel git perl-FindBin diffutils ncurses-devel
+            ;;
+          *opensuse*)
+            zypper --non-interactive install --allow-downgrade --force-resolution git autoconf automake make gcc perl zlib-devel libbz2-devel xz-devel libcurl-devel libopenssl-devel diffutils llvm-clang ncurses-devel bzip2
+            ;;
+          esac
+
+      - name: Checkout
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
+        with:
+          persist-credentials: false
+
+      - name: Clone htslib
+        run: |
+          git config --global --add safe.directory `pwd`
+          htslib_pr=`git log -2 --format='%s' | sed -n 's/.*htslib#\([0-9]*\).*/\1/p'`
+          .ci_helpers/clone ${GITHUB_REPOSITORY_OWNER} htslib htslib ${GITHUB_HEAD_REF:-$GITHUB_REF_NAME} $htslib_pr
+
+      - name: Configure bcftools
+        run: |
+          autoreconf -i
+          ./configure --enable-werror CFLAGS="-g -O3 -std=gnu99 ${{ matrix.cflags }}"
+
+      - name: Build htslib and bcftools
+        run: |
+          make -j5
+
+      - name: Test
+        run: |
+          make check
diff --git a/.github/workflows/linux-build.yml b/.github/workflows/linux-build.yml
@@ -1,6 +1,10 @@
 name: Linux CI
 on: [push, pull_request]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build-linux:
     runs-on: ${{ matrix.os }}

diff --git a/.github/workflows/macos-build.yml b/.github/workflows/macos-build.yml
@@ -1,6 +1,10 @@
 name: Mac OS CI
 on: [push, pull_request]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build-macos:
     runs-on: macos-latest

diff --git a/.github/workflows/vm-build.yml b/.github/workflows/vm-build.yml
@@ -0,0 +1,165 @@
+name: VMs
+on: [push, pull_request]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  # ----------
+  FreeBSD:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      #matrix:
+      #  arch:    ['x86_64', 'aarch64']
+
+    steps:
+      - name: Checkout
+        # This is actions/checkout@v6.0.2
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
+        with:
+          submodules: true
+          fetch-depth: 1
+
+      - name: Clone htslib
+        run: |
+          git config --global --add safe.directory `pwd`
+          htslib_pr=`git log -2 --format='%s' | sed -n 's/.*htslib#\([0-9]*\).*/\1/p'`
+          .ci_helpers/clone ${GITHUB_REPOSITORY_OWNER} htslib htslib ${GITHUB_HEAD_REF:-$GITHUB_REF_NAME} $htslib_pr
+
+      - name: Setup VM
+        # This is vmactions/freebsd-vm@@v1.5.2
+        uses: vmactions/freebsd-vm@77ed28d336d03fe19a3f4f7266c1d2c4714dd79d
+        with:
+          #debug-on-error: true
+          #vnc-password: ${{ secrets.VNC_PASSWORD }}
+          #arch: ${{ matrix.arch }}
+          usesh: true
+          cpu: 4
+          prepare: |
+            pkg update
+            pkg install -y autoconf automake bash curl bzip2 gmake libdeflate perl5 git
+
+      # Inside VM
+      - name: Configure
+        shell: freebsd {0}
+        run: |
+          (cd htslib; autoreconf -i)
+          autoreconf -i
+          ./configure --enable-werror CFLAGS="-g -O3 -fsanitize=address,undefined -DHTS_ALLOW_UNALIGNED=0 -Wno-format-truncation -Wno-format-overflow" CPPFLAGS="-I/usr/local/include" LDFLAGS="-fsanitize=address,undefined -L/usr/local/lib -Wl,-R/usr/local/lib"
+
+      - name: Build
+        shell: freebsd {0}
+        run: |
+          gmake -j5
+
+      - name: Test
+        shell: freebsd {0}
+        run: |
+          gmake check
+
+  # ----------
+  OpenBSD:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+
+    steps:
+      - name: Checkout
+        # This is actions/checkout@v6.0.2
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
+        with:
+          submodules: true
+          fetch-depth: 1
+
+      - name: Clone htslib
+        run: |
+          git config --global --add safe.directory `pwd`
+          mkdir -p htslib
+          htslib_pr=`git log -2 --format='%s' | sed -n 's/.*htslib#\([0-9]*\).*/\1/p'`
+          .ci_helpers/clone ${GITHUB_REPOSITORY_OWNER} htslib htslib ${GITHUB_HEAD_REF:-$GITHUB_REF_NAME} $htslib_pr
+
+      - name: Setup VM
+        # This is vmactions/openbsd-vm@v1.4.5
+        uses: vmactions/openbsd-vm@c941015845c0f0c429676840963dc63b226d4f69
+        with:
+          usesh: true
+          cpu: 4
+          prepare: |
+            pkg_add autoconf-2.71p0 automake-1.18.1 bash bzip2 curl gmake libdeflate xz git
+
+      # Inside VM
+      - name: Configure
+        shell: openbsd {0}
+        run: |
+          export AUTOCONF_VERSION=2.71
+          export AUTOMAKE_VERSION=1.18
+          (cd htslib; autoreconf -i)
+          autoreconf -i
+          ./configure --enable-werror CPPFLAGS="-I/usr/local/include" LDFLAGS="-L/usr/local/lib -Wl,-R/usr/local/lib"
+
+      - name: Build
+        shell: openbsd {0}
+        run: |
+          gmake -j5
+
+      - name: Test
+        shell: openbsd {0}
+        run: |
+          gmake check
+
+
+  # ----------
+  Solaris:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+
+    steps:
+      - name: Checkout
+        # This is actions/checkout@v6.0.2
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
+        with:
+          submodules: true
+          fetch-depth: 1
+
+      - name: Clone htslib
+        run: |
+          git config --global --add safe.directory `pwd`
+          mkdir -p htslib
+          htslib_pr=`git log -2 --format='%s' | sed -n 's/.*htslib#\([0-9]*\).*/\1/p'`
+          .ci_helpers/clone ${GITHUB_REPOSITORY_OWNER} htslib htslib ${GITHUB_HEAD_REF:-$GITHUB_REF_NAME} $htslib_pr
+
+      - name: Setup VM
+        # This is vmactions/solaris-vm@v1.3.8
+        uses: vmactions/solaris-vm@315163f088b66e55bbcc45928bd224d4973b2312
+        with:
+          release: "11.4-clang-19"
+          usesh: true
+          cpu: 4
+          prepare: |
+            pkg install autoconf automake bash curl bzip2 git
+
+      # Inside VM
+      - name: Configure
+        shell: solaris {0}
+        run: |
+          (cd htslib; autoreconf -i)
+          autoreconf -i
+          # -Wno-char-subscripts turns off errors such as phase.c:460, which are
+          # false alarms anyway.
+          ./configure --enable-werror CFLAGS="-g -O3 -Wno-char-subscripts"
+
+      - name: Build
+        shell: solaris {0}
+        run: |
+          gmake -j5
+
+      - name: Test
+        shell: solaris {0}
+        run: |
+          # We need more compliant versions of tr and grep.
+          PATH=/usr/xpg4/bin:$PATH
+          export PATH
+          gmake check
diff --git a/.github/workflows/windows-build.yml b/.github/workflows/windows-build.yml
@@ -1,6 +1,10 @@
 name: Windows/MinGW-W64 CI
 on: [push, pull_request]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build-windows:
     runs-on: windows-latest

diff --git a/Makefile b/Makefile
@@ -117,8 +117,8 @@ PACKAGE_VERSION = 1.24
 # $(shell), :=, etc are GNU Make-specific.  If you don't have GNU Make,
 # comment out this conditional.
 ifneq "$(wildcard .git)" ""
-PACKAGE_VERSION := $(shell git describe --always --dirty)
-DOC_VERSION :=  $(shell git describe --always)+
+PACKAGE_VERSION := $(shell git -c safe.directory=`pwd` describe --always --dirty)
+DOC_VERSION :=  $(shell git -c safe.directory=`pwd` describe --always)+
 DOC_DATE := $(shell date +'%Y-%m-%d %R %Z')
 
 # Force version.h to be remade if $(PACKAGE_VERSION) has changed.

diff --git a/misc/plot-vcfstats b/misc/plot-vcfstats
@@ -644,7 +644,7 @@ sub parse_vcfstats1
     my ($opts,$i) = @_;
     my $file = $$opts{vcfstats}[$i];
     print STDERR "Parsing bcftools stats output: $file\n" unless !$$opts{verbose};
-    open(my $fh,"gunzip -cfq $file |") or error("gunzip -cfq $file: $!");
+    open(my $fh,"gunzip -cq $file || cat $file |") or error("gunzip -cfq $file: $!");
     my $line = <$fh>;
     if ( !$line or !($line=~/^# This file was produced by \S*/) ) { error("Sanity check failed: was this file generated by bcftools stats?"); }
     my %dat;

diff --git a/test/trio-dnm3/test.sh b/test/trio-dnm3/test.sh
@@ -7,5 +7,5 @@ export LC_ALL=C
 
 for x in *.vcf; do
     "$BCFTOOLS" +trio-dnm3 -p 1X:child,dad,mom $x | "$BCFTOOLS" query -uf$x'\t%CHROM:%POS\t%EXP\t[ %DNM]\t[ %VAF]\t[ %AD]\t%REF,%ALT\t[ %VA]\t[ %SP]';
-done | sort | sed 's,fp,-, ; s,tp,o,'
+done | sort | sed 's/fp/-/;s/tp/o/'
 
diff --git a/version.sh b/version.sh
@@ -27,7 +27,7 @@
 VERSION=1.24
 
 # If we have a git clone, then check against the current tag
-if [ -e .git ]
+if [ -e .git -a "x`which git`" != "x" ]
 then
     # If we ever get to 10.x this will need to be more liberal
     VERSION=`git describe --match '[0-9].[0-9]*' --dirty --always`