updatehtslib against intel_mods

.appveyor.yml

@@ -18,19 +18,23 @@ skip_tags: true
 #    - docs/*
 #    - '**/*.html'
 
+# Appveyor Windows images are based on Visual studio version
+image: Visual Studio 2019
+
 # We use Mingw/Msys, so use pacman for installs
 install:
   - set HOME=.
   - set MSYSTEM=MINGW64
   - set PATH=C:/msys64/usr/bin;C:/msys64/mingw64/bin;%PATH%
   - set MINGWPREFIX=x86_64-w64-mingw32
-  - "sh -lc \"pacman -S --noconfirm --needed base-devel mingw-w64-x86_64-toolchain mingw-w64-x86_64-zlib mingw-w64-x86_64-bzip2 mingw-w64-x86_64-xz mingw-w64-x86_64-curl\""
+  - "sh -lc \"pacman -S --noconfirm --needed base-devel mingw-w64-x86_64-toolchain mingw-w64-x86_64-autotools mingw-w64-x86_64-zlib mingw-w64-x86_64-bzip2 mingw-w64-x86_64-xz mingw-w64-x86_64-curl mingw-w64-x86_64-tools-git\""
 
 build_script:
   - set HOME=.
   - set MSYSTEM=MINGW64
   - set PATH=C:/msys64/usr/bin;C:/msys64/mingw64/bin;%PATH%
-  - "sh -lc \"autoheader && autoconf && ./configure --enable-werror CFLAGS='-g -O3' && make -j2\""
+  - git submodule update --init --recursive
+  - "sh -lc \"autoreconf -i && ./configure --enable-werror CFLAGS='-g -O3' && make -j2\""
 
 #build_script:
 #  - make

.cirrus.yml

@@ -0,0 +1,209 @@
+# Note we have a maximum of 16 CPUs available, so adjust our
+# builds so we can start all concurrently without needing to schedule.
+
+# Sadly though there is still a finite limit to macOS of one instance.
+# Can we cull our Mac test to just one instance?
+
+timeout_in: 20m
+
+#--------------------------------------------------
+# Template: build libdeflate dependency
+
+libdeflate_template: &LIBDEFLATE
+  libdeflate_script: |
+    if test "x$USE_LIBDEFLATE" == "xyes"; then
+      pushd "$HOME"
+      git clone --depth 1 https://github.com/ebiggers/libdeflate.git
+      pushd libdeflate
+      cmake -B build -DLIBDEFLATE_BUILD_SHARED_LIB=OFF -DLIBDEFLATE_BUILD_GZIP=OFF -DCMAKE_C_FLAGS="-g -O3 -fPIC $LIBDEFLATE_CFLAGS"
+      cmake --build build --verbose
+      popd
+      popd
+    fi
+
+#--------------------------------------------------
+# Template: compile and test
+
+compile_template: &COMPILE
+  compile_script: |
+    git submodule update --init --recursive
+    if test "x$USE_LIBDEFLATE" = "xyes"; then
+      CONFIG_OPTS='CPPFLAGS="-I$HOME/libdeflate" LDFLAGS="$LDFLAGS -L$HOME/libdeflate/build" --with-libdeflate'
+    else
+      CONFIG_OPTS='--without-libdeflate'
+    fi
+    if test "$USE_CONFIG" = "yes"; then
+      MAKE_OPTS=
+      autoreconf -i
+      eval ./configure --enable-plugins --enable-werror $CONFIG_OPTS CFLAGS=\"-g -O3 $CFLAGS\" || \
+        ( cat config.log; false )
+    else
+      MAKE_OPTS=-e
+    fi
+    if test "x$DO_MAINTAINER_CHECKS" = "xyes"; then
+      make maintainer-check
+    fi
+    make -j 4 $MAKE_OPTS
+
+test_template: &TEST
+  test_script: |
+    make test-shlib-exports
+    make test
+    if test "x$DO_UNTRACKED_FILE_CHECK" = "xyes"; then make check-untracked ; fi
+
+#--------------------------------------------------
+# Task: linux builds.
+
+# Debian + latest GCC
+gcc_task:
+  name: debian-gcc
+  container:
+    image: gcc:latest
+    cpu: 2
+    memory: 1G
+
+  environment:
+    LC_ALL: C
+    CIRRUS_CLONE_DEPTH: 1
+
+  matrix:
+    - environment:
+       DO_MAINTAINER_CHECKS: yes
+       DO_UNTRACKED_FILE_CHECK: yes
+       USE_CONFIG: no
+    - environment:
+       USE_CONFIG: yes
+       CFLAGS: -std=c99 -pedantic -Wformat=2
+       USE_LIBDEFLATE: yes
+
+  install_script: |
+    apt-get update
+    apt-get install -y --no-install-suggests --no-install-recommends     \
+        ca-certificates libc-dev make git autoconf automake              \
+        zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev libssl-dev \
+        cmake
+
+  << : *LIBDEFLATE
+  << : *COMPILE
+  << : *TEST
+
+
+# Ubuntu + Clang
+ubuntu_task:
+  name: ubuntu-clang
+  container:
+    image: ubuntu:latest
+    # image: ubuntu:devel
+    cpu: 2
+    memory: 1G
+
+  environment:
+    CC: clang
+    LC_ALL: C
+    CIRRUS_CLONE_DEPTH: 1
+
+  matrix:
+    - environment:
+       USE_CONFIG: yes
+       DO_UNTRACKED_FILE_CHECK: yes
+    - environment:
+       USE_CONFIG: yes
+       CFLAGS: -g -Wall -O3 -fsanitize=address
+       LDFLAGS: -fsanitize=address
+       USE_LIBDEFLATE: yes
+
+  # NB: we could consider building a docker image with these
+  # preinstalled and specifying that instead, to speed up testing.
+  install_script: |
+    apt-get update
+    apt-get install -y --no-install-suggests --no-install-recommends     \
+        ca-certificates clang libc-dev make git autoconf automake        \
+        zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev libssl-dev \
+        libdeflate-dev
+
+  << : *COMPILE
+  << : *TEST
+
+
+# Rocky Linux
+rocky_task:
+  name: rockylinux-gcc
+  container:
+    image: rockylinux:9
+    cpu: 2
+    memory: 1G
+
+  environment:
+    LC_ALL: C
+    CIRRUS_CLONE_DEPTH: 1
+    USE_CONFIG: yes
+    CFLAGS: -std=gnu90
+
+  # 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 \
+        ncurses-devel diffutils git
+
+  << : *COMPILE
+  << : *TEST
+
+# Arm Linux
+arm_ubuntu_task:
+  name: ubuntu-arm
+  arm_container:
+    image: ubuntu:latest
+    cpu: 2
+    memory: 1G
+
+  environment:
+    LC_ALL: C
+    CIRRUS_CLONE_DEPTH: 1
+    DO_UNTRACKED_FILE_CHECK: yes
+    USE_CONFIG: yes
+    CFLAGS: -g -Wall -O3 -std=c99 -pedantic
+
+  # NB: we could consider building a docker image with these
+  # preinstalled and specifying that instead, to speed up testing.
+  install_script: |
+    apt-get update
+    apt-get install -y --no-install-suggests --no-install-recommends     \
+        ca-certificates clang libc-dev make git autoconf automake        \
+        zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev libssl-dev \
+        libdeflate-dev
+
+  << : *COMPILE
+  << : *TEST
+
+#--------------------------------------------------
+# Task: macOS builds
+
+macosx_task:
+  name: macosx + clang
+  macos_instance:
+    image: ghcr.io/cirruslabs/macos-ventura-base:latest
+
+  environment:
+    CC: clang
+    CFLAGS: "-Wall -arch arm64 -arch x86_64"
+    LDFLAGS: "-arch arm64 -arch x86_64"
+    LIBDEFLATE_CFLAGS: "-arch arm64 -arch x86_64"
+    LC_ALL: C
+    CIRRUS_CLONE_DEPTH: 1
+
+  matrix:
+    - environment:
+       USE_CONFIG: no
+    - environment:
+       USE_CONFIG: yes
+       USE_LIBDEFLATE: yes
+
+  package_install_script: |
+    HOMEBREW_NO_AUTO_UPDATE=1 brew install autoconf automake libtool xz git \
+        cmake
+
+  << : *LIBDEFLATE
+  << : *COMPILE
+  << : *TEST
+

.gitattributes

@@ -9,10 +9,18 @@
 # Omit these files from release tarballs.
 /.appveyor.yml  export-ignore
 .git*           export-ignore
-/.travis.yml    export-ignore
+/.cirrus.yml    export-ignore
 README.md       export-ignore
 
 # Remove the text attribute from reference files, so that git doesn't convert
 # line separators on Windows machines. It causes the index files to become out
 # of sync with the fasta files.
 *.fa* -text
+
+# Remove the text attribute from index_dos.sam, so that the line separators
+# for the test file don't get converted into Unix format.
+test/index_dos.sam -text
+
+# Remove the text attribute from various faidx test files
+test/faidx/faidx*.fa* -text
+test/faidx/fastqs*.fq* -text

.gitignore

@@ -7,16 +7,20 @@
 *.dll.a
 *.pc.tmp
 *-uninstalled.pc
+config_vars.h
 /version.h
 
 autom4te.cache
 config.cache
+config.guess
 config.h
 config.h.in
 config.log
 config.mk
 config.status
+config.sub
 configure
+install-sh
 
 hfile_*.bundle
 hfile_*.cygdll
@@ -25,6 +29,7 @@ hfile_*.so
 
 hts-object-files
 htslib_static.mk
+htscodecs.mk
 
 cyg*.dll
 lib*.a
@@ -39,25 +44,34 @@ shlib-exports-*.txt
 /bgzip
 /htsfile
 /tabix
+/test/faidx/*.tmp*
+/test/faidx/FAIL*
 /test/fieldarith
 /test/hfile
 /test/hts_endian
 /test/longrefs/*.tmp.*
 /test/pileup
+/test/pileup_mod
 /test/plugins-dlhts
 /test/sam
 /test/tabix/*.tmp.*
 /test/tabix/FAIL*
 /test/test-bcf-sr
 /test/test-bcf-translate
+/test/test-bcf_set_variant_type
 /test/test_bgzf
+/test/test_expr
+/test/test_faidx
 /test/test_index
+/test/test_introspection
 /test/test_kfunc
 /test/test_kstring
+/test/test_mod
 /test/test-parse-reg
 /test/test_realn
 /test/test-regidx
 /test/test_str2int
+/test/test_time_funcs
 /test/test-vcf-api
 /test/test-vcf-sweep
 /test/test_view

.gitmodules

@@ -0,0 +1,4 @@
+[submodule "htscodecs"]
+	path = htscodecs
+	url = https://github.com/samtools/htscodecs.git
+	fetchRecurseSubmodules = true