Release 1.17

Author: daviesrob

.cirrus.yml

@@ -15,7 +15,8 @@ libdeflate_template: &LIBDEFLATE
       pushd "$HOME"
       git clone --depth 1 https://github.com/ebiggers/libdeflate.git
       pushd libdeflate
-      make -j 4 CFLAGS='-fPIC -O3' libdeflate.a
+      cmake -B build -DLIBDEFLATE_BUILD_SHARED_LIB=OFF -DLIBDEFLATE_BUILD_GZIP=OFF -DCMAKE_C_FLAGS='-g -O3 -fPIC'
+      cmake --build build --verbose
       popd
       popd
     fi
@@ -27,7 +28,7 @@ compile_template: &COMPILE
   compile_script: |
     git submodule update --init --recursive
     if test "x$USE_LIBDEFLATE" = "xyes"; then
-      CONFIG_OPTS='CPPFLAGS="-I$HOME/libdeflate" LDFLAGS="$LDFLAGS -L$HOME/libdeflate" --with-libdeflate'
+      CONFIG_OPTS='CPPFLAGS="-I$HOME/libdeflate" LDFLAGS="$LDFLAGS -L$HOME/libdeflate/build" --with-libdeflate'
     else
       CONFIG_OPTS='--without-libdeflate'
     fi
@@ -75,6 +76,13 @@ gcc_task:
        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
@@ -129,6 +137,7 @@ rocky_task:
     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.
@@ -172,8 +181,8 @@ arm_ubuntu_task:
 
 macosx_task:
   name: macosx + clang
-  osx_instance:
-    image: monterey-base
+  macos_instance:
+    image: ghcr.io/cirruslabs/macos-ventura-base:latest
 
   environment:
     CC: clang
@@ -187,8 +196,9 @@ macosx_task:
        USE_CONFIG: yes
        USE_LIBDEFLATE: yes
 
-  package_install_script:
-    - HOMEBREW_NO_AUTO_UPDATE=1 brew install autoconf automake libtool xz git
+  package_install_script: |
+    HOMEBREW_NO_AUTO_UPDATE=1 brew install autoconf automake libtool xz git \
+        cmake
 
   << : *LIBDEFLATE
   << : *COMPILE

.gitattributes

@@ -20,3 +20,7 @@ README.md       export-ignore
 # 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

@@ -44,6 +44,8 @@ shlib-exports-*.txt
 /bgzip
 /htsfile
 /tabix
+/test/faidx/*.tmp*
+/test/faidx/FAIL*
 /test/fieldarith
 /test/hfile
 /test/hts_endian
@@ -59,6 +61,7 @@ shlib-exports-*.txt
 /test/test-bcf_set_variant_type
 /test/test_bgzf
 /test/test_expr
+/test/test_faidx
 /test/test_index
 /test/test_introspection
 /test/test_kfunc

INSTALL

@@ -110,6 +110,7 @@ The 'make install' command installs the libraries, library header files,
 utilities, several manual pages, and a pkgconfig file to /usr/local.
 The installation location can be changed by configuring with --prefix=DIR
 or via 'make prefix=DIR install' (see Installation Locations below).
+Shared library permissions can be set via e.g. 'make install LIB_PERM=755'.
 
 
 Configuration
@@ -291,3 +292,13 @@ mingw-w64-x86_64-xz mingw-w64-x86_64-curl mingw-w64-x86_64-autotools
 mingw-w64-x86_64-tools-git
 
 (The last is only needed for building libraries compatible with MSVC.)
+
+HP-UX
+-----
+
+HP-UX requires that shared libraries have execute permission.  The
+default for HTSlib is to install with permission 644 (read-write for
+owner and read-only for group / other). This can be overridden by
+setting the LIB_PERM variable at install time with:
+
+    make install LIB_PERM=755

LICENSE

@@ -3,7 +3,7 @@ according to the terms of the following MIT/Expat license.]
 
 The MIT/Expat License
 
-Copyright (C) 2012-2022 Genome Research Ltd.
+Copyright (C) 2012-2023 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) 2012-2022 Genome Research Ltd.
+Copyright (C) 2012-2023 Genome Research Ltd.
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:

Makefile

@@ -1,6 +1,6 @@
 # Makefile for htslib, a C library for high-throughput sequencing data formats.
 #
-#    Copyright (C) 2013-2022 Genome Research Ltd.
+#    Copyright (C) 2013-2023 Genome Research Ltd.
 #
 #    Author: John Marshall <[email protected]>
 #
@@ -39,6 +39,7 @@ CFLAGS   = -g -Wall -O2 -fvisibility=hidden
 EXTRA_CFLAGS_PIC = -fpic
 TARGET_CFLAGS =
 LDFLAGS  = -fvisibility=hidden
+VERSION_SCRIPT_LDFLAGS = -Wl,-version-script,$(srcprefix)htslib.map
 LIBS     = $(htslib_default_libs)
 
 prefix      = /usr/local
@@ -58,7 +59,8 @@ MKDIR_P = mkdir -p
 INSTALL = install -p
 INSTALL_DATA    = $(INSTALL) -m 644
 INSTALL_DIR     = $(MKDIR_P) -m 755
-INSTALL_LIB     = $(INSTALL_DATA)
+LIB_PERM        = 644
+INSTALL_LIB     = $(INSTALL) -m $(LIB_PERM)
 INSTALL_MAN     = $(INSTALL_DATA)
 INSTALL_PROGRAM = $(INSTALL)
 
@@ -80,6 +82,7 @@ BUILT_TEST_PROGRAMS = \
 	test/sam \
 	test/test_bgzf \
 	test/test_expr \
+	test/test_faidx \
 	test/test_kfunc \
 	test/test_kstring \
 	test/test_mod \
@@ -140,8 +143,8 @@ LIBHTS_SOVERSION = 3
 # is not strictly necessary and should be removed the next time
 # LIBHTS_SOVERSION is bumped (see #1144 and
 # https://developer.apple.com/library/archive/documentation/DeveloperTools/Conceptual/DynamicLibraries/100-Articles/DynamicLibraryDesignGuidelines.html#//apple_ref/doc/uid/TP40002013-SW23)
-MACH_O_COMPATIBILITY_VERSION = 3.1.16
-MACH_O_CURRENT_VERSION = 3.1.16
+MACH_O_COMPATIBILITY_VERSION = 3.1.17
+MACH_O_CURRENT_VERSION = 3.1.17
 
 # $(NUMERIC_VERSION) is for items that must have a numeric X.Y.Z string
 # even if this is a dirty or untagged Git working tree.
@@ -160,12 +163,20 @@ show-version:
 	@echo PACKAGE_VERSION = $(PACKAGE_VERSION)
 	@echo NUMERIC_VERSION = $(NUMERIC_VERSION)
 
+config_vars.h: override escape=$(subst ',\x27,$(subst ",\",$(subst \,\\,$(1))))
+config_vars.h: override hts_cc_escaped=$(call escape,$(CC))
+config_vars.h: override hts_cppflags_escaped=$(call escape,$(CPPFLAGS))
+config_vars.h: override hts_cflags_escaped=$(call escape,$(CFLAGS))
+config_vars.h: override hts_ldflags_escaped=$(call escape,$(LDFLAGS))
+config_vars.h: override hts_libs_escaped=$(call escape,$(LIBS))
+
 config_vars.h:
-	echo '#define HTS_CC "$(CC)"' > $@
-	echo '#define HTS_CPPFLAGS "$(CPPFLAGS)"' >> $@
-	echo '#define HTS_CFLAGS "$(CFLAGS)"' >> $@
-	echo '#define HTS_LDFLAGS "$(LDFLAGS)"' >> $@
-	echo '#define HTS_LIBS "$(LIBS)"' >> $@
+	printf '#define HTS_CC "%s"\n#define HTS_CPPFLAGS "%s"\n#define HTS_CFLAGS "%s"\n#define HTS_LDFLAGS "%s"\n#define HTS_LIBS "%s"\n' \
+	'$(hts_cc_escaped)' \
+	'$(hts_cppflags_escaped)' \
+	'$(hts_cflags_escaped)' \
+	'$(hts_ldflags_escaped)' \
+	'$(hts_libs_escaped)' > $@
 
 .SUFFIXES: .bundle .c .cygdll .dll .o .pico .so
 
@@ -344,7 +355,7 @@ print-config:
 # file used at runtime (when $LD_LIBRARY_PATH includes the build directory).
 
 libhts.so: $(LIBHTS_OBJS:.o=.pico)
-	$(CC) -shared -Wl,-soname,libhts.so.$(LIBHTS_SOVERSION) $(LDFLAGS) -o $@ $(LIBHTS_OBJS:.o=.pico) $(LIBS) -lpthread
+	$(CC) -shared -Wl,-soname,libhts.so.$(LIBHTS_SOVERSION) $(VERSION_SCRIPT_LDFLAGS) $(LDFLAGS) -o $@ $(LIBHTS_OBJS:.o=.pico) $(LIBS) -lpthread
 	ln -sf $@ libhts.so.$(LIBHTS_SOVERSION)
 
 # Similarly this also creates libhts.NN.dylib as a byproduct, so that programs
@@ -494,7 +505,7 @@ htsfile: htsfile.o libhts.a
 tabix: tabix.o libhts.a
 	$(CC) $(LDFLAGS) -o $@ tabix.o libhts.a $(LIBS) -lpthread
 
-bgzip.o: bgzip.c config.h $(htslib_bgzf_h) $(htslib_hts_h)
+bgzip.o: bgzip.c config.h $(htslib_bgzf_h) $(htslib_hts_h) $(htslib_hfile_h)
 htsfile.o: htsfile.c config.h $(htslib_hfile_h) $(htslib_hts_h) $(htslib_sam_h) $(htslib_vcf_h)
 tabix.o: tabix.c config.h $(htslib_tbx_h) $(htslib_sam_h) $(htslib_vcf_h) $(htslib_kseq_h) $(htslib_bgzf_h) $(htslib_hts_h) $(htslib_regidx_h) $(htslib_hts_defs_h) $(htslib_hts_log_h)
 
@@ -583,12 +594,13 @@ check test: all $(HTSCODECS_TEST_TARGETS)
 	fi
 	test/test_bgzf test/bgziptest.txt
 	test/test-parse-reg -t test/colons.bam
+	cd test/faidx && ./test-faidx.sh faidx.tst
 	cd test/sam_filter && ./filter.sh filter.tst
 	cd test/tabix && ./test-tabix.sh tabix.tst
 	cd test/mpileup && ./test-pileup.sh mpileup.tst
 	cd test/fastq && ./test-fastq.sh
 	cd test/base_mods && ./base-mods.sh base-mods.tst
-	REF_PATH=: test/sam test/ce.fa test/faidx.fa test/fastqs.fq
+	REF_PATH=: test/sam test/ce.fa test/faidx/faidx.fa test/faidx/fastqs.fq
 	test/test-regidx
 	cd test && REF_PATH=: ./test.pl $${TEST_OPTS:-}
 
@@ -622,6 +634,9 @@ test/test_bgzf: test/test_bgzf.o libhts.a
 test/test_expr: test/test_expr.o libhts.a
 	$(CC) $(LDFLAGS) -o $@ test/test_expr.o libhts.a -lz $(LIBS) -lpthread
 
+test/test_faidx: test/test_faidx.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ test/test_faidx.o libhts.a -lz $(LIBS) -lpthread
+
 test/test_kfunc: test/test_kfunc.o libhts.a
 	$(CC) $(LDFLAGS) -o $@ test/test_kfunc.o libhts.a -lz $(LIBS) -lpthread
 
@@ -739,6 +754,7 @@ test/test-regidx.o: test/test-regidx.c config.h $(htslib_kstring_h) $(htslib_reg
 test/test_str2int.o: test/test_str2int.c config.h $(textutils_internal_h)
 test/test_time_funcs.o: test/test_time_funcs.c config.h $(hts_time_funcs_h)
 test/test_view.o: test/test_view.c config.h $(cram_h) $(htslib_sam_h) $(htslib_vcf_h) $(htslib_hts_log_h)
+test/test_faidx.o: test/test_faidx.c config.h $(htslib_faidx_h)
 test/test_index.o: test/test_index.c config.h $(htslib_sam_h) $(htslib_vcf_h)
 test/test-vcf-api.o: test/test-vcf-api.c config.h $(htslib_hts_h) $(htslib_vcf_h) $(htslib_kstring_h) $(htslib_kseq_h)
 test/test-vcf-sweep.o: test/test-vcf-sweep.c config.h $(htslib_vcf_sweep_h)
@@ -789,14 +805,39 @@ header-exports.txt: test/header_syms.pl htslib/*.h
 	test/header_syms.pl htslib/*.h | sort -u -o $@
 
 shlib-exports-so.txt: libhts.so
-	nm -D -g libhts.so | awk '$$2 == "T" { print $$3 }' | sort -u -o $@
+	nm -D -g libhts.so | awk '$$2 == "T" { sub("@.*", "", $$3); print $$3 }' | sort -u -o $@
 
 shlib-exports-dylib.txt: libhts.dylib
 	nm -Ug libhts.dylib | awk '$$2 == "T" { sub("^_", "", $$3); print $$3 }' | sort -u -o $@
 
 shlib-exports-dll.txt: hts.dll.a
 	nm -g hts.dll.a | awk '$$2 == "T" { print $$3 }' | sort -u -o $@
 
+$(srcprefix)htslib.map: libhts.so
+	LC_ALL=C ; export LC_ALL; \
+	curr_vers=`expr 'X$(PACKAGE_VERSION)' : 'X\([0-9]*\.[0-9.]*\)'` ; \
+	last_vers=`awk '/^HTSLIB_[0-9](\.[0-9]+)+/ { lv = $$1 } END { print lv }' htslib.map` ; \
+	if test "x$$curr_vers" = 'x' || test "x$$last_vers" = 'x' ; then \
+	    echo "Version check failed : $$curr_vers / $$las_vers" 1>&2 ; \
+	    exit 1 ; \
+	fi && \
+	if test "HTSLIB_$$curr_vers" = "$$last_vers" ; then \
+	    echo "Refusing to update $@ - HTSlib version not changed" 1>&2 ; \
+	    exit 1 ; \
+	fi && \
+	nm --with-symbol-versions -D -g libhts.so | awk '$$2 ~ /^[DGRT]$$/ && $$3 ~ /@@Base$$/ && $$3 !~ /^(_init|_fini|_edata)@@/ { sub(/@@Base$$/, ";", $$3); print "    " $$3 }' > $@.tmp && \
+	if [ -s $@.tmp ] ; then \
+	    cat $@ > $@.new.tmp && \
+	    printf '\n%s {\n' "HTSLIB_$$curr_vers" >> $@.new.tmp && \
+	    cat $@.tmp >> $@.new.tmp && \
+	    printf '} %s;\n' "$$last_vers" >> $@.new.tmp && \
+	        rm -f $@.tmp && \
+	        mv $@.new.tmp $@ ; \
+	    fi ; \
+	else \
+	    rm -f $@.tmp ; \
+	fi
+
 install: libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) installdirs install-$(SHLIB_FLAVOUR) install-pkgconfig
 	$(INSTALL_PROGRAM) $(BUILT_PROGRAMS) $(DESTDIR)$(bindir)
 	if test -n "$(BUILT_PLUGINS)"; then $(INSTALL_PROGRAM) $(BUILT_PLUGINS) $(DESTDIR)$(plugindir); fi
@@ -845,7 +886,9 @@ htslib-uninstalled.pc: htslib.pc.tmp
 
 
 testclean:
-	-rm -f test/*.tmp test/*.tmp.* test/longrefs/*.tmp.* test/tabix/*.tmp.* test/tabix/FAIL* header-exports.txt shlib-exports-$(SHLIB_FLAVOUR).txt
+	-rm -f test/*.tmp test/*.tmp.* test/faidx/*.tmp* test/faidx/FAIL* \
+               test/longrefs/*.tmp.* test/tabix/*.tmp.* test/tabix/FAIL* \
+               header-exports.txt shlib-exports-$(SHLIB_FLAVOUR).txt
 	-rm -rf htscodecs/tests/test.out
 
 # Only remove this in git checkouts