Release 1.22

Author: daviesrob

.appveyor.yml

@@ -7,6 +7,7 @@ version: 'vers.{build}'
 branches:
     except:
       - gh-pages
+      - /.*/ # Appveyor builds are currently disabled.
 
 # Do not build on tags (GitHub and BitBucket)
 skip_tags: true

.ci_helpers/clone

@@ -5,13 +5,25 @@
 # omitted or if there is no branch with that name, checks out origin/HEAD
 # from the samtools/htslib repository.
 
-repository=$1
-localdir=$2
-branch=$3
+echo CLONE: ${@+"$@"}
+
+owner=$1
+repository="https://github.com/$owner/$2"
+localdir=$3
+branch=$4
+htslib_PR=$5
 
 ref=''
 [ -n "$branch" ] && ref=$(git ls-remote --heads "$repository" "$branch" 2>/dev/null)
 [ -z "$ref" ] && repository='https://github.com/samtools/htslib.git'
 
 set -x
-git clone --recurse-submodules --shallow-submodules --depth=1 ${ref:+--branch="$branch"} "$repository" "$localdir"
+git clone --recurse-submodules --shallow-submodules --depth=2 ${ref:+--branch="$branch"} "$repository" "$localdir"
+
+# NB: "samtools" as the owner/organisation, not the repo name
+if [ "x$owner" = "xsamtools" -a -z "$ref" -a "x$htslib_PR" != "x" ]
+then
+    cd "$localdir"
+    git fetch origin "pull/$htslib_PR/head"
+    git checkout FETCH_HEAD
+fi

.cirrus.yml

@@ -21,8 +21,16 @@ timeout_in: 10m
 # clone with our own commands too.
 clone_template: &HTSLIB_CLONE
   htslib_clone_script: |
-    .ci_helpers/clone "https://github.com/${CIRRUS_REPO_OWNER}/htslib" "${HTSDIR}" "${CIRRUS_BRANCH}"
-
+    # Tricky, but when run as a PR Cirrus-CI obscures the branch name and
+    # replaces it by pull/<num>.  This means we can't automatically get PRs
+    # to test whether the user has a similarly named branch to compiler and
+    # test against.
+    #
+    # Instead if we add htslib#NUM into the first line of the commit then
+    # we will use that PR from htslib instead.  This is only needed when
+    # making a PR, so for development prior to the PR being made the
+    # CIRRUS_BRANCH will be used in preference.
+    .ci_helpers/clone ${CIRRUS_REPO_OWNER} htslib "${HTSDIR}" "${CIRRUS_BRANCH}" `printenv CIRRUS_CHANGE_TITLE | sed -n 's/.*htslib#\([0-9]*\).*/\1/p'`
 
 #--------------------------------------------------
 # Template: bcftools compile and test
@@ -34,16 +42,34 @@ compile_template: &COMPILE
     if test "$USE_CONFIG" = "yes"; then
       (cd $HTSDIR && autoreconf -i)
       autoreconf -i
-      ./configure --enable-werror || (cat config.log; /bin/false)
+      ./configure --enable-werror $CONFIG_OPTS \
+           ${CC:+CC="$CC"} \
+           ${CFLAGS:+CFLAGS="$CFLAGS"} \
+           ${CPPFLAGS:+CPPFLAGS="$CPPFLAGS"} \
+           ${LDFLAGS:+LDFLAGS="$LDFLAGS"} \
+         || (cat config.log; /bin/false)
       make -j3
     else
-      make -j3 plugindir=$CIRRUS_WORKING_DIR/plugins -e
+      make -j3 plugindir="$CIRRUS_WORKING_DIR/plugins" \
+           ${HTSDIR:+HTSDIR="$HTSDIR"} \
+           ${CC:+CC="$CC"} \
+           ${CFLAGS:+CFLAGS="$CFLAGS"} \
+           ${CPPFLAGS:+CPPFLAGS="$CPPFLAGS"} \
+           ${LDFLAGS:+LDFLAGS="$LDFLAGS"}
     fi
 
 test_template: &TEST
   test_script: |
-    make -e test
-
+    if test "$USE_CONFIG" = "yes"; then
+        make test
+    else
+        make test  \
+           ${HTSDIR:+HTSDIR="$HTSDIR"} \
+           ${CC:+CC="$CC"} \
+           ${CFLAGS:+CFLAGS="$CFLAGS"} \
+           ${CPPFLAGS:+CPPFLAGS="$CPPFLAGS"} \
+           ${LDFLAGS:+LDFLAGS="$LDFLAGS"}
+    fi
 
 #--------------------------------------------------
 # Task: linux builds.
@@ -60,15 +86,23 @@ gcc_task:
     LC_ALL: C
     CIRRUS_CLONE_DEPTH: 1
     HTSDIR: ./htslib
-    CFLAGS:  -fsanitize=address
-    LDFLAGS: -fsanitize=address
 
   matrix:
     - environment:
        USE_CONFIG: no
+       CFLAGS:  -g -Og -Wall -Werror -fsanitize=address
+       LDFLAGS: -fsanitize=address
     - environment:
        USE_CONFIG: yes
-       CFLAGS: -std=gnu99 -O0
+       CONFIG_OPTS: --enable-libgsl --enable-perl-filters 
+       CFLAGS: -std=gnu99 -g -Og -Wall -fsanitize=address
+       LDFLAGS: -fsanitize=address
+
+  install_script: |
+    apt-get update
+    apt-get install -y --no-install-suggests --no-install-recommends \
+        libdeflate-dev libperl-dev libgsl0-dev libio-pty-perl
+
 
   << : *COMPILE
   << : *TEST
@@ -84,18 +118,19 @@ ubuntu_task:
 
   environment:
     CC: clang
-    CFLAGS: -g -O2 -Werror -Wall -Wformat -Wformat=2
     LC_ALL: C
     CIRRUS_CLONE_DEPTH: 1
     HTSDIR: ./htslib
 
   matrix:
     - environment:
        USE_CONFIG: no
+       CFLAGS: -g -O2 -Werror -Wall -Wformat -Wformat=2
     - container:
        memory: 2G
       environment:
        USE_CONFIG: yes
+       CONFIG_OPTS: --enable-libgsl --enable-perl-filters
        CFLAGS: -g -Wall -O3
        LDFLAGS: -Wl,-rpath,`pwd`/inst/lib
 
@@ -106,7 +141,7 @@ ubuntu_task:
     apt-get install -y --no-install-suggests --no-install-recommends \
         ca-certificates clang git autoconf automake  \
         make zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev   \
-        libssl-dev libdeflate-dev
+        libssl-dev libdeflate-dev libperl-dev libgsl0-dev libio-pty-perl
 
   << : *COMPILE
   << : *TEST
@@ -125,13 +160,14 @@ rockylinux_task:
     CIRRUS_CLONE_DEPTH: 1
     HTSDIR: ./htslib
     USE_CONFIG: yes
+    CONFIG_OPTS: --enable-libgsl --enable-perl-filters
 
   # NB: we could consider building a docker image with these
   # preinstalled and specifying that instead, to speed up testing.
   install_script: |
     yum install -y autoconf automake make gcc perl-Data-Dumper perl-FindBin \
         zlib-devel bzip2 bzip2-devel xz-devel curl-devel openssl-devel \
-        git diffutils
+        git diffutils gsl-devel perl-ExtUtils-Embed
 
   << : *COMPILE
   << : *TEST
@@ -143,7 +179,7 @@ rockylinux_task:
 macosx_task:
   name: macosx + clang
   macos_instance:
-    image: ghcr.io/cirruslabs/macos-ventura-base:latest
+    image: ghcr.io/cirruslabs/macos-runner:sonoma
 
   environment:
     CC: clang

.gitattributes

@@ -10,3 +10,9 @@
 .git*           export-ignore
 .ci_helpers     export-ignore
 README.md       export-ignore
+
+# Prevent Windows cr-lf endings.
+test/**        -text
+test/**.c       text
+test/**.h       text
+test/**.pl      text

.github/workflows/windows-build.yml

@@ -0,0 +1,52 @@
+name: Windows/MinGW-W64 CI
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: windows-latest
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+      with:
+        ref: ${{ github.event.pull_request.head.sha }}
+    - name: Set up MSYS2 MinGW-W64
+      uses: msys2/setup-msys2@v2
+      with:
+        msystem: mingw64
+        update: false
+        install: >-
+          mingw-w64-x86_64-toolchain
+          mingw-w64-x86_64-autotools
+          mingw-w64-x86_64-curl
+          mingw-w64-x86_64-libdeflate
+          mingw-w64-x86_64-tools-git
+          mingw-w64-x86_64-zlib
+          mingw-w64-x86_64-bzip2
+          mingw-w64-x86_64-xz
+    - name: Clone htslib
+      shell: msys2 {0}
+      run: |
+        export PATH="$PATH:/mingw64/bin:/c/Program Files/Git/bin"
+        export MSYSTEM=MINGW64
+        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} $htslib_pr
+        pushd .
+        cd htslib
+        autoreconf -i
+        popd
+    - name: Compile bcftools
+      shell: msys2 {0}
+      run: |
+        export PATH="$PATH:/mingw64/bin:/c/Program Files/Git/bin"
+        export MSYSTEM=MINGW64
+        autoheader
+        autoconf -Wno-syntax
+        ./configure --enable-werror
+        make -j4
+    - name: Check bcftools
+      shell: msys2 {0}
+      run: |
+        export PATH="$PATH:/mingw64/bin:/c/Program Files/Git/bin"
+        export MSYSTEM=MINGW64
+        make check
+

AUTHORS

@@ -9,6 +9,7 @@ Alphabetical list of people who have made contributions:
     Javier Herrero
     Warren Kretzschmar <[email protected]>
     Heng Li
+    Pierre Lindenbaum
     Shane McCarthy <[email protected]>
     John Marshall <[email protected]>
     Joel Martin

Makefile

@@ -41,9 +41,10 @@ OBJS     = main.o vcfindex.o tabix.o \
            vcfcnv.o vcfhead.o HMM.o consensus.o ploidy.o bin.o hclust.o version.o \
            regidx.o smpl_ilist.o csq.o vcfbuf.o \
            mpileup.o bam2bcf.o bam2bcf_indel.o bam2bcf_iaux.o bam2bcf_edlib.o \
-           read_consensus.o bam_sample.o \
+	       read_consensus.o bam_sample.o \
            vcfsort.o cols.o extsort.o dist.o abuf.o \
-           ccall.o em.o prob1.o kmin.o str_finder.o gff.o edlib.o
+           ccall.o em.o prob1.o kmin.o str_finder.o gff.o edlib.o \
+           mpileup2/mpileup.o
 PLUGIN_OBJS = vcfplugin.o
 
 prefix      = /usr/local
@@ -105,7 +106,7 @@ endif
 
 include config.mk
 
-PACKAGE_VERSION = 1.21
+PACKAGE_VERSION = 1.22
 
 # If building from a Git repository, replace $(PACKAGE_VERSION) with the Git
 # description of the working tree: either a release tag with the same value
@@ -195,7 +196,10 @@ libbcftools.a: $(OBJS)
 
 vcfplugin.o: EXTRA_CPPFLAGS += -DPLUGINPATH='"$(pluginpath)"'
 
-%.dll %.cygdll: %.c version.h version.c libbcftools.a $(HTSLIB_DLL)
+%.dll: %.c version.h version.c libbcftools.a $(HTSLIB_DLL)
+	$(CC) $(PLUGIN_FLAGS) $(CFLAGS) $(ALL_CPPFLAGS) $(EXTRA_CPPFLAGS) $(LDFLAGS) -o $@ version.c $< $(PLUGIN_LIBS)
+
+%.cygdll: %.c version.h version.c libbcftools.a $(HTSLIB_DLL)
 	$(CC) $(PLUGIN_FLAGS) $(CFLAGS) $(ALL_CPPFLAGS) $(EXTRA_CPPFLAGS) $(LDFLAGS) -o $@ version.c $< $(PLUGIN_LIBS)
 
 %.so: %.c version.h version.c
@@ -239,6 +243,7 @@ bam_sample_h = bam_sample.h $(htslib_sam_h)
 cigar_state_h = cigar_state.h $(htslib_hts_h) $(htslib_sam_h)
 read_consensus_h = read_consensus.h $(htslib_hts_h) $(htslib_sam_h)
 str_finder_h = str_finder.h utlist.h
+mpileup2_mpileup_h = mpileup2/mpileup.h $(htslib_sam_h)
 
 str_finder.o: str_finder.c $(str_finder_h) utlist.h
 main.o: main.c $(htslib_hts_h) config.h version.h $(bcftools_h)
@@ -283,13 +288,14 @@ cols.o: cols.c cols.h
 regidx.o: regidx.c $(htslib_hts_h) $(htslib_kstring_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) regidx.h
 consensus.o: consensus.c $(htslib_vcf_h) $(htslib_kstring_h) $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_bgzf_h) regidx.h $(bcftools_h) rbuf.h $(filter_h) $(smpl_ilist_h)
 mpileup.o: mpileup.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) $(htslib_hts_os_h) regidx.h $(bcftools_h) $(bam2bcf_h) $(bam_sample_h) $(gvcf_h)
+mpileup2/mpileup.o: mpileup2/mpileup.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) regidx.h $(mpileup2_mpileup_h) $(bam_sample_h)
 bam2bcf.o: bam2bcf.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_h) mw.h
 bam2bcf_indel.o: bam2bcf_indel.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_str2int_h) $(bam2bcf_h) $(htslib_ksort_h) $(str_finder_h)
 bam2bcf_iaux.o: bam2bcf_iaux.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_str2int_h) $(bcftools_h) $(bam2bcf_h) $(htslib_ksort_h) $(read_consensus_h) $(cigar_state_h)
 bam2bcf_edlib.o: bam2bcf_edlib.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_str2int_h) $(bam2bcf_h) $(str_finder_h) $(htslib_ksort_h) edlib.h
 read_consensus.o: read_consensus.c $(read_consensus_h) $(cigar_state_h) $(bcftools_h) kheap.h
 bam_sample.o: bam_sample.c $(htslib_hts_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) $(khash_str2str_h) $(bam_sample_h) $(bcftools_h)
-version.o: version.h version.c
+version.o: version.c $(htslib_hts_h) $(bcftools_h) version.h
 hclust.o: hclust.c $(htslib_hts_h) $(htslib_kstring_h) $(bcftools_h) hclust.h
 HMM.o: HMM.c $(htslib_hts_h) HMM.h
 vcfbuf.o: vcfbuf.c $(htslib_vcf_h) $(htslib_vcfutils_h) $(htslib_hts_os_h) $(htslib_kbitset_h) $(bcftools_h) $(vcfbuf_h) rbuf.h
@@ -354,7 +360,7 @@ install: $(PROGRAMS) $(PLUGINS)
 	$(INSTALL_PROGRAM) plugins/*$(PLUGIN_EXT) $(DESTDIR)$(plugindir)
 
 clean: testclean clean-plugins
-	-rm -f gmon.out *.o *.a *~ $(PROGRAMS) version.h
+	-rm -f gmon.out *.o mpileup2/*.o *.a *~ $(PROGRAMS) version.h
 	-rm -rf *.dSYM test/*.dSYM
 
 clean-plugins: