Release 1.10

Author: daviesrob

.appveyor.yml

@@ -30,10 +30,10 @@ build_script:
   - set HOME=.
   - set MSYSTEM=MINGW64
   - set PATH=C:/msys64/usr/bin;C:/msys64/mingw64/bin;%PATH%
-  - "sh -lc \"aclocal && autoheader && autoconf && ./configure && make -j2\""
+  - "sh -lc \"aclocal && autoheader && autoconf && ./configure --enable-werror CFLAGS='-g -O3' && make -j2\""
 
 #build_script:
 #  - make
 
 test_script:
-  - "sh -lc \"make test\""
+  - "sh -lc \"make test-shlib-exports && make test\""

.gitignore

@@ -4,6 +4,7 @@
 *.dSYM
 *.exe
 *.dll
+*.dll.a
 *.pc.tmp
 *-uninstalled.pc
 /version.h
@@ -22,6 +23,7 @@ hfile_*.cygdll
 hfile_*.dll
 hfile_*.so
 
+hts-object-files
 htslib_static.mk
 
 cyg*.dll
@@ -31,24 +33,33 @@ lib*.dylib
 lib*.so
 lib*.so.*
 
+header-exports.txt
+shlib-exports-*.txt
+
 /bgzip
 /htsfile
 /tabix
 /test/fieldarith
 /test/hfile
 /test/hts_endian
+/test/longrefs/*.tmp.*
+/test/pileup
 /test/sam
 /test/tabix/*.tmp.*
 /test/tabix/FAIL*
 /test/test-bcf-sr
 /test/test-bcf-translate
 /test/test_bgzf
+/test/test_index
+/test/test_kstring
+/test/test-parse-reg
 /test/test_realn
 /test/test-regidx
+/test/test_str2int
 /test/test-vcf-api
 /test/test-vcf-sweep
 /test/test_view
-/test/thrash_threads[1-6]
+/test/thrash_threads[1-7]
 /test/*.tmp
 /test/*.tmp.*
 

.travis.yml

@@ -1,41 +1,96 @@
 # Control file for continuous integration testing at http://travis-ci.org/
 
 language: c
-compiler:
-  - clang
-  - gcc
-
-os:
-  - linux
-  - osx
-
-env:
-  - USE_CONFIG=no
-  - USE_CONFIG=yes
 
 matrix:
   include:
   - compiler: gcc
     os: linux
-    env: USE_CONFIG=yes USE_LIBDEFLATE=yes
+    env: DO_MAINTAINER_CHECKS=yes USE_CONFIG=no
+
+  - compiler: gcc-8
+    os: linux
+    env: USE_CONFIG=yes CC=gcc-8 AR=gcc-ar-8
+    addons:
+      apt:
+        sources:
+          - ubuntu-toolchain-r-test
+        packages:
+          - gcc-8
+
+  # An optimised build with address and leak checking, also using libdeflate
+  - compiler: gcc-8
+    os: linux
+    dist: xenial
+    env: USE_CONFIG=yes USE_LIBDEFLATE=yes CC=gcc-8 AR=gcc-ar-8 CFLAGS="-g -Wall -O3 -fsanitize=address" LDFLAGS="-fsanitize=address"
+    addons:
+      apt:
+        sources:
+          - ubuntu-toolchain-r-test
+        packages:
+          - gcc-8
+
+  - compiler: clang
+    os: osx
+    env: USE_CONFIG=no
+
+  - compiler: clang
+    os: osx
+    env: USE_CONFIG=yes
+
   - compiler: clang
     os: osx
     env: USE_CONFIG=yes USE_LIBDEFLATE=yes
 
-# For linux systems
-addons:
-  apt:
-    packages:
-    - liblzma-dev
-    - libbz2-dev
+  - compiler: gcc
+    os: linux
+    env: USE_CONFIG=yes
+
+  - compiler: clang
+    os: linux
+    env: USE_CONFIG=yes
+
+  - compiler: gcc
+    os: linux
+    env: CFLAGS="-std=c99 -pedantic" USE_CONFIG=yes
 
 # For MacOSX systems
 before_install:
-  - if [[ "$TRAVIS_OS_NAME" == "osx" && "$USE_CONFIG" == "no" ]]; then HOMEBREW_NO_AUTO_UPDATE=1 brew install xz || ( brew update && brew install xz ); fi
+  - |
+    if [[ "$TRAVIS_OS_NAME" == "osx" && "$USE_CONFIG" == "no" ]]; then
+      HOMEBREW_NO_AUTO_UPDATE=1 brew install xz || ( brew update && brew install xz )
+    fi
 
 before_script:
-  - if test "x$USE_LIBDEFLATE" == "xyes" ; then ( cd "$HOME" && git clone --depth 1 https://github.com/ebiggers/libdeflate.git && cd libdeflate && make -j 2 CFLAGS='-fPIC -O3' libdeflate.a ); fi
+  - |
+    if test "x$USE_LIBDEFLATE" == "xyes"; then
+      pushd "$HOME" && \
+        git clone --depth 1 https://github.com/ebiggers/libdeflate.git && \
+        pushd libdeflate && \
+        make -j 2 CFLAGS='-fPIC -O3' libdeflate.a && \
+        popd && \
+        popd
+    fi
 
 script:
-  - if test "x$USE_LIBDEFLATE" = "xyes" ; then CONFIG_OPTS='CPPFLAGS="-I$HOME/libdeflate" LDFLAGS="-L$HOME/libdeflate" --with-libdeflate' ; else CONFIG_OPTS='--without-libdeflate' ; fi
-  - if test "$USE_CONFIG" = "yes" ; then autoreconf && eval ./configure $CONFIG_OPTS || { cat config.log ; false ; } ; fi && make -j 2 -e && make test
+  - |
+    if test "x$USE_LIBDEFLATE" = "xyes"; then
+      CONFIG_OPTS='CPPFLAGS="-I$HOME/libdeflate" LDFLAGS="$LDFLAGS -L$HOME/libdeflate" --with-libdeflate'
+    else
+      CONFIG_OPTS='--without-libdeflate'
+    fi
+  - |
+    if test "$USE_CONFIG" = "yes"; then
+      MAKE_OPTS= ;
+      autoreconf && \
+        eval ./configure --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 2 $MAKE_OPTS && \
+    make test-shlib-exports && \
+    make test

LICENSE

@@ -3,7 +3,7 @@ according to the terms of the following MIT/Expat license.]
 
 The MIT/Expat License
 
-Copyright (C) 2012-2018 Genome Research Ltd.
+Copyright (C) 2012-2019 Genome Research Ltd.
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -29,7 +29,7 @@ according to the terms of the following Modified 3-Clause BSD license.]
 
 The Modified-BSD License
 
-Copyright (C) 2012-2018 Genome Research Ltd.
+Copyright (C) 2012-2019 Genome Research Ltd.
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met: