update htslib

Author: Yenaled

.gitignore

@@ -15,6 +15,7 @@ ext/htslib/src/
 CMakeCache.txt
 CMakeFiles
 Makefile
+!ext/htslib/Makefile
 cmake_install.cmake
 CTestTestfile.cmake
 *~

ext/htslib/Makefile

@@ -0,0 +1,303 @@
+# Makefile for htslib, a C library for high-throughput sequencing data formats.
+#
+#    Copyright (C) 2013-2014 Genome Research Ltd.
+#
+#    Author: John Marshall <[email protected]>
+
+CC     ?= gcc
+AR     = ar
+RANLIB = ranlib
+
+# TODO: edit cram code to remove need for -DSAMTOOLS
+CPPFLAGS += -I. -DSAMTOOLS=1
+# TODO: probably update cram code to make it compile cleanly with -Wc++-compat
+CFLAGS   := -g -Wall -O2 $(CFLAGS)
+EXTRA_CFLAGS_PIC = -fpic
+LDFLAGS  =
+LDLIBS   =
+
+prefix      = /usr/local
+exec_prefix = $(prefix)
+bindir      = $(exec_prefix)/bin
+includedir  = $(prefix)/include
+libdir      = $(exec_prefix)/lib
+mandir      = $(prefix)/share/man
+man1dir     = $(mandir)/man1
+man5dir     = $(mandir)/man5
+
+INSTALL = install -p
+INSTALL_PROGRAM = $(INSTALL)
+INSTALL_DATA    = $(INSTALL) -m 644
+
+BUILT_PROGRAMS = \
+	bgzip \
+	tabix
+
+BUILT_TEST_PROGRAMS = \
+	test/fieldarith \
+	test/hfile \
+	test/sam \
+	test/test_view \
+	test/test-vcf-api \
+	test/test-vcf-sweep
+
+all: lib-static lib-shared $(BUILT_PROGRAMS) $(BUILT_TEST_PROGRAMS)
+
+HTSPREFIX =
+include htslib_vars.mk
+
+lib-static: libhts.a
+
+# $(shell), :=, and ifeq/.../endif are GNU Make-specific.  If you don't have
+# GNU Make, comment out the parts of this conditional that don't apply.
+PLATFORM := $(shell uname -s)
+ifeq "$(PLATFORM)" "Darwin"
+SHLIB_FLAVOUR = dylib
+lib-shared: libhts.dylib
+else
+SHLIB_FLAVOUR = so
+lib-shared: libhts.so
+endif
+
+
+PACKAGE_VERSION  = 0.0.1
+LIBHTS_SOVERSION = 0
+
+
+# $(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.
+NUMERIC_VERSION = $(PACKAGE_VERSION)
+
+# 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
+# as $(PACKAGE_VERSION) above, or an exact description likely based on a tag.
+# Much of this is also GNU Make-specific.  If you don't have GNU Make and/or
+# are not building from a Git repository, comment out this conditional.
+ifneq "$(wildcard .git)" ""
+original_version := $(PACKAGE_VERSION)
+PACKAGE_VERSION := $(shell git describe --always --dirty)
+
+# Unless the Git description matches /\d*\.\d*(\.\d*)?/, i.e., is exactly a tag
+# with a numeric name, revert $(NUMERIC_VERSION) to the original version number
+# written above, but with the patchlevel field bumped to 255.
+ifneq "$(subst ..,.,$(subst 0,,$(subst 1,,$(subst 2,,$(subst 3,,$(subst 4,,$(subst 5,,$(subst 6,,$(subst 7,,$(subst 8,,$(subst 9,,$(PACKAGE_VERSION))))))))))))" "."
+empty :=
+NUMERIC_VERSION := $(subst $(empty) ,.,$(wordlist 1,2,$(subst ., ,$(original_version))) 255)
+endif
+
+# Force version.h to be remade if $(PACKAGE_VERSION) has changed.
+version.h: $(if $(wildcard version.h),$(if $(findstring "$(PACKAGE_VERSION)",$(shell cat version.h)),,force))
+endif
+
+version.h:
+	echo '#define HTS_VERSION "$(PACKAGE_VERSION)"' > $@
+
+
+.SUFFIXES: .c .o .pico
+
+.c.o:
+	$(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ $<
+
+.c.pico:
+	$(CC) $(CFLAGS) $(CPPFLAGS) $(EXTRA_CFLAGS_PIC) -c -o $@ $<
+
+
+LIBHTS_OBJS = \
+	kfunc.o \
+	knetfile.o \
+	kstring.o \
+	bgzf.o \
+	faidx.o \
+	hfile.o \
+	hfile_net.o \
+	hts.o \
+	sam.o \
+	synced_bcf_reader.o \
+	vcf_sweep.o \
+	tbx.o \
+	vcf.o \
+	vcfutils.o \
+	cram/cram_codecs.o \
+	cram/cram_decode.o \
+	cram/cram_encode.o \
+	cram/cram_index.o \
+	cram/cram_io.o \
+	cram/cram_samtools.o \
+	cram/cram_stats.o \
+	cram/files.o \
+	cram/mFILE.o \
+	cram/md5.o \
+	cram/open_trace_file.o \
+	cram/pooled_alloc.o \
+	cram/sam_header.o \
+	cram/string_alloc.o \
+	cram/thread_pool.o \
+	cram/vlen.o \
+	cram/zfio.o
+
+
+libhts.a: $(LIBHTS_OBJS)
+	@-rm -f $@
+	$(AR) -rc $@ $(LIBHTS_OBJS)
+	-$(RANLIB) $@
+
+
+# The target here is libhts.so, as that is the built file that other rules
+# depend upon and that is used when -lhts appears in other program's recipes.
+# As a byproduct invisible to make, libhts.so.NN is also created, as it is the
+# 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) $(LDLIBS) -lz
+	ln -sf $@ libhts.so.$(LIBHTS_SOVERSION)
+
+# Similarly this also creates libhts.NN.dylib as a byproduct, so that programs
+# when run can find this uninstalled shared library (when $DYLD_LIBRARY_PATH
+# includes this project's build directory).
+
+libhts.dylib: $(LIBHTS_OBJS)
+	$(CC) -dynamiclib -install_name $(libdir)/libhts.$(LIBHTS_SOVERSION).dylib -current_version $(NUMERIC_VERSION) -compatibility_version $(LIBHTS_SOVERSION) $(LDFLAGS) -o $@ $(LIBHTS_OBJS) $(LDLIBS) -lz
+	ln -sf $@ libhts.$(LIBHTS_SOVERSION).dylib
+
+
+cram_h = cram/cram.h $(cram_samtools_h) $(cram_sam_header_h) $(cram_structs_h) $(cram_io_h) cram/cram_encode.h cram/cram_decode.h cram/cram_stats.h cram/cram_codecs.h cram/cram_index.h
+cram_io_h = cram/cram_io.h $(cram_misc_h)
+cram_misc_h = cram/misc.h cram/os.h
+cram_sam_header_h = cram/sam_header.h cram/string_alloc.h cram/pooled_alloc.h htslib/khash.h htslib/kstring.h
+cram_samtools_h = cram/cram_samtools.h $(htslib_sam_h) $(cram_sam_header_h)
+cram_structs_h = cram/cram_structs.h cram/thread_pool.h cram/string_alloc.h htslib/khash.h
+cram_open_trace_file_h = cram/open_trace_file.h cram/mFILE.h
+hfile_internal_h = hfile_internal.h $(htslib_hfile_h)
+
+bgzf.o bgzf.pico: bgzf.c config.h $(htslib_hts_h) $(htslib_bgzf_h) $(htslib_hfile_h) htslib/khash.h
+kstring.o kstring.pico: kstring.c htslib/kstring.h
+knetfile.o knetfile.pico: knetfile.c htslib/knetfile.h
+hfile.o hfile.pico: hfile.c $(htslib_hfile_h) $(hfile_internal_h)
+hfile_net.o hfile_net.pico: hfile_net.c $(hfile_internal_h) htslib/knetfile.h
+hts.o hts.pico: hts.c version.h $(htslib_hts_h) $(htslib_bgzf_h) $(cram_h) $(htslib_hfile_h) htslib/khash.h htslib/kseq.h htslib/ksort.h
+vcf.o vcf.pico: vcf.c $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(htslib_hfile_h) htslib/khash.h htslib/kseq.h htslib/kstring.h
+sam.o sam.pico: sam.c $(htslib_sam_h) $(htslib_bgzf_h) $(cram_h) $(htslib_hfile_h) htslib/khash.h htslib/kseq.h htslib/kstring.h
+tbx.o tbx.pico: tbx.c $(htslib_tbx_h) $(htslib_bgzf_h) htslib/khash.h
+faidx.o faidx.pico: faidx.c config.h $(htslib_bgzf_h) $(htslib_faidx_h) htslib/khash.h htslib/knetfile.h
+synced_bcf_reader.o synced_bcf_reader.pico: synced_bcf_reader.c $(htslib_synced_bcf_reader_h) htslib/kseq.h htslib/khash_str2int.h
+vcf_sweep.o vcf_sweep.pico: vcf_sweep.c $(htslib_vcf_sweep_h) $(htslib_bgzf_h)
+vcfutils.o vcfutils.pico: vcfutils.c $(htslib_vcfutils_h)
+kfunc.o kfunc.pico: kfunc.c htslib/kfunc.h
+
+cram/cram_codecs.o cram/cram_codecs.pico: cram/cram_codecs.c $(cram_h)
+cram/cram_decode.o cram/cram_decode.pico: cram/cram_decode.c $(cram_h) cram/os.h cram/md5.h
+cram/cram_encode.o cram/cram_encode.pico: cram/cram_encode.c $(cram_h) cram/os.h cram/md5.h
+cram/cram_index.o cram/cram_index.pico: cram/cram_index.c $(htslib_hfile_h) $(cram_h) cram/os.h cram/zfio.h
+cram/cram_io.o cram/cram_io.pico: cram/cram_io.c $(cram_h) cram/os.h cram/md5.h $(cram_open_trace_file_h) $(htslib_hfile_h)
+cram/cram_samtools.o cram/cram_samtools.pico: cram/cram_samtools.c $(cram_h) $(htslib_sam_h)
+cram/cram_stats.o cram/cram_stats.pico: cram/cram_stats.c $(cram_h) cram/os.h
+cram/files.o cram/files.pico: cram/files.c $(cram_misc_h)
+cram/mFILE.o cram/mFILE.pico: cram/mFILE.c cram/os.h cram/mFILE.h cram/vlen.h
+cram/md5.o cram/md5.pico: cram/md5.c cram/md5.h
+cram/open_trace_file.o cram/open_trace_file.pico: cram/open_trace_file.c $(cram_open_trace_file_h) $(cram_misc_h)
+cram/pooled_alloc.o cram/pooled_alloc.pico: cram/pooled_alloc.c cram/pooled_alloc.h
+cram/sam_header.o cram/sam_header.pico: cram/sam_header.c $(cram_sam_header_h) cram/string_alloc.h
+cram/string_alloc.o cram/string_alloc.pico: cram/string_alloc.c cram/string_alloc.h
+cram/thread_pool.o cram/thread_pool.pico: cram/thread_pool.c cram/thread_pool.h
+cram/vlen.o cram/vlen.pico: cram/vlen.c cram/vlen.h cram/os.h
+cram/zfio.o cram/zfio.pico: cram/zfio.c cram/os.h cram/zfio.h
+
+
+bgzip: bgzip.o libhts.a
+	$(CC) -pthread $(LDFLAGS) -o $@ bgzip.o libhts.a $(LDLIBS) -lz
+
+tabix: tabix.o libhts.a
+	$(CC) -pthread $(LDFLAGS) -o $@ tabix.o libhts.a $(LDLIBS) -lz
+
+bgzip.o: bgzip.c $(htslib_bgzf_h) $(htslib_hts_h)
+tabix.o: tabix.c $(htslib_tbx_h) $(htslib_sam_h) $(htslib_vcf_h) htslib/kseq.h $(htslib_bgzf_h) $(htslib_hts_h)
+
+
+check test: $(BUILT_TEST_PROGRAMS)
+	test/fieldarith test/fieldarith.sam
+	test/hfile
+	test/sam
+	cd test && ./test_view.pl
+	cd test && ./test.pl
+
+test/fieldarith: test/fieldarith.o libhts.a
+	$(CC) -pthread $(LDFLAGS) -o $@ test/fieldarith.o libhts.a $(LDLIBS) -lz
+
+test/hfile: test/hfile.o libhts.a
+	$(CC) $(LDFLAGS) -o $@ test/hfile.o libhts.a $(LDLIBS) -lz
+
+test/sam: test/sam.o libhts.a
+	$(CC) -pthread $(LDFLAGS) -o $@ test/sam.o libhts.a $(LDLIBS) -lz
+
+test/test_view: test/test_view.o libhts.a
+	$(CC) -pthread $(LDFLAGS) -o $@ test/test_view.o libhts.a $(LDLIBS) -lz
+
+test/test-vcf-api: test/test-vcf-api.o libhts.a
+	$(CC) -pthread $(LDFLAGS) -o $@ test/test-vcf-api.o libhts.a $(LDLIBS) -lz
+
+test/test-vcf-sweep: test/test-vcf-sweep.o libhts.a
+	$(CC) -pthread $(LDFLAGS) -o $@ test/test-vcf-sweep.o libhts.a $(LDLIBS) -lz
+
+test/fieldarith.o: test/fieldarith.c $(htslib_sam_h)
+test/hfile.o: test/hfile.c $(htslib_hfile_h) $(htslib_hts_defs_h)
+test/sam.o: test/sam.c $(htslib_sam_h) htslib/kstring.h
+test/test_view.o: test/test_view.c $(cram_h) $(htslib_sam_h)
+test/test-vcf-api.o: test/test-vcf-api.c $(htslib_hts_h) $(htslib_vcf_h) htslib/kstring.h
+test/test-vcf-sweep.o: test/test-vcf-sweep.c $(htslib_vcf_sweep_h)
+
+
+install: installdirs install-$(SHLIB_FLAVOUR)
+	$(INSTALL_PROGRAM) $(BUILT_PROGRAMS) $(DESTDIR)$(bindir)
+	$(INSTALL_DATA) htslib/*.h $(DESTDIR)$(includedir)/htslib
+	$(INSTALL_DATA) libhts.a $(DESTDIR)$(libdir)/libhts.a
+	$(INSTALL_DATA) *.1 $(DESTDIR)$(man1dir)
+	$(INSTALL_DATA) *.5 $(DESTDIR)$(man5dir)
+
+installdirs:
+	mkdir -p $(DESTDIR)$(bindir) $(DESTDIR)$(includedir)/htslib $(DESTDIR)$(libdir) $(DESTDIR)$(man1dir) $(DESTDIR)$(man5dir)
+
+# After installation, the real file in $(libdir) will be libhts.so.X.Y.Z,
+# with symlinks libhts.so (used via -lhts during linking of client programs)
+# and libhts.so.NN (used by client executables at runtime).
+
+install-so: libhts.so installdirs
+	$(INSTALL_DATA) libhts.so $(DESTDIR)$(libdir)/libhts.so.$(PACKAGE_VERSION)
+	ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so
+	ln -sf libhts.so.$(PACKAGE_VERSION) $(DESTDIR)$(libdir)/libhts.so.$(LIBHTS_SOVERSION)
+
+install-dylib: libhts.dylib installdirs
+	$(INSTALL_PROGRAM) libhts.dylib $(DESTDIR)$(libdir)/libhts.$(PACKAGE_VERSION).dylib
+	ln -sf libhts.$(PACKAGE_VERSION).dylib $(DESTDIR)$(libdir)/libhts.dylib
+	ln -sf libhts.$(PACKAGE_VERSION).dylib $(DESTDIR)$(libdir)/libhts.$(LIBHTS_SOVERSION).dylib
+
+
+testclean:
+	-rm -f test/*.tmp test/*.tmp.*
+
+mostlyclean: testclean
+	-rm -f *.o *.pico cram/*.o cram/*.pico test/*.o test/*.dSYM version.h
+
+clean: mostlyclean clean-$(SHLIB_FLAVOUR)
+	-rm -f libhts.a $(BUILT_PROGRAMS) $(BUILT_TEST_PROGRAMS)
+
+distclean: clean
+	-rm -f TAGS
+
+clean-so:
+	-rm -f libhts.so libhts.so.*
+
+clean-dylib:
+	-rm -f libhts.dylib libhts.*.dylib
+
+
+tags:
+	ctags -f TAGS *.[ch] cram/*.[ch] htslib/*.h
+
+
+force:
+
+
+.PHONY: all check clean distclean force install installdirs
+.PHONY: lib-shared lib-static mostlyclean tags test testclean
+.PHONY: clean-so install-so
+.PHONY: clean-dylib install-dylib