Relase 1.5: Solstice

Author: valeriuo

Makefile

@@ -92,7 +92,7 @@ HTSPREFIX =
 include htslib_vars.mk
 
 
-PACKAGE_VERSION = 1.4.1
+PACKAGE_VERSION = 1.5
 LIBHTS_SOVERSION = 2
 
 
@@ -175,9 +175,7 @@ LIBHTS_OBJS = \
 	cram/pooled_alloc.o \
 	cram/rANS_static.o \
 	cram/sam_header.o \
-	cram/string_alloc.o \
-	cram/vlen.o \
-	cram/zfio.o
+	cram/string_alloc.o
 
 PLUGIN_EXT  =
 PLUGIN_OBJS =
@@ -292,13 +290,13 @@ cyghts-$(LIBHTS_SOVERSION).dll: $(LIBHTS_OBJS)
 bgzf.o bgzf.pico: bgzf.c config.h $(htslib_hts_h) $(htslib_bgzf_h) $(htslib_hfile_h) $(htslib_thread_pool_h) cram/pooled_alloc.h $(htslib_khash_h)
 errmod.o errmod.pico: errmod.c config.h $(htslib_hts_h) $(htslib_ksort_h)
 kstring.o kstring.pico: kstring.c config.h $(htslib_kstring_h)
-knetfile.o knetfile.pico: knetfile.c config.h $(htslib_knetfile_h)
+knetfile.o knetfile.pico: knetfile.c config.h $(htslib_hts_log_h) $(htslib_knetfile_h)
 hfile.o hfile.pico: hfile.c config.h $(htslib_hfile_h) $(hfile_internal_h) $(hts_internal_h) $(htslib_khash_h)
 hfile_gcs.o hfile_gcs.pico: hfile_gcs.c config.h $(htslib_hts_h) $(htslib_kstring_h) $(hfile_internal_h)
 hfile_libcurl.o hfile_libcurl.pico: hfile_libcurl.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h)
 hfile_net.o hfile_net.pico: hfile_net.c config.h $(hfile_internal_h) $(htslib_knetfile_h)
 hfile_s3.o hfile_s3.pico: hfile_s3.c config.h $(hts_internal_h) $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h)
-hts.o hts.pico: hts.c config.h $(htslib_hts_h) $(htslib_bgzf_h) $(cram_h) $(htslib_hfile_h) version.h $(hts_internal_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_ksort_h)
+hts.o hts.pico: hts.c config.h $(htslib_hts_h) $(htslib_bgzf_h) $(cram_h) $(hfile_internal_h) $(htslib_hfile_h) version.h $(hts_internal_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_ksort_h)
 vcf.o vcf.pico: vcf.c config.h $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(htslib_hfile_h) $(hts_internal_h) $(htslib_khash_str2int_h) $(htslib_kstring_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_hts_endian_h)
 sam.o sam.pico: sam.c config.h $(htslib_sam_h) $(htslib_bgzf_h) $(cram_h) $(hts_internal_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_kstring_h) $(htslib_hts_endian_h)
 tbx.o tbx.pico: tbx.c config.h $(htslib_tbx_h) $(htslib_bgzf_h) $(hts_internal_h) $(htslib_khash_h)
@@ -320,20 +318,18 @@ cram/cram_codecs.o cram/cram_codecs.pico: cram/cram_codecs.c config.h $(cram_h)
 cram/cram_decode.o cram/cram_decode.pico: cram/cram_decode.c config.h $(cram_h) $(cram_os_h) $(htslib_hts_h)
 cram/cram_encode.o cram/cram_encode.pico: cram/cram_encode.c config.h $(cram_h) $(cram_os_h) $(htslib_hts_h) $(htslib_hts_endian_h)
 cram/cram_external.o cram/cram_external.pico: cram/cram_external.c config.h $(htslib_hfile_h) $(cram_h)
-cram/cram_index.o cram/cram_index.pico: cram/cram_index.c config.h $(htslib_hfile_h) $(hts_internal_h) $(cram_h) $(cram_os_h) cram/zfio.h
+cram/cram_index.o cram/cram_index.pico: cram/cram_index.c config.h $(htslib_bgzf_h) $(htslib_hfile_h) $(hts_internal_h) $(cram_h) $(cram_os_h)
 cram/cram_io.o cram/cram_io.pico: cram/cram_io.c config.h $(cram_h) $(cram_os_h) $(htslib_hts_h) $(cram_open_trace_file_h) cram/rANS_static.h $(htslib_hfile_h) $(htslib_bgzf_h) $(htslib_faidx_h) $(hts_internal_h)
 cram/cram_samtools.o cram/cram_samtools.pico: cram/cram_samtools.c config.h $(cram_h) $(htslib_sam_h)
 cram/cram_stats.o cram/cram_stats.pico: cram/cram_stats.c config.h $(cram_h) $(cram_os_h)
 cram/files.o cram/files.pico: cram/files.c config.h $(cram_misc_h)
-cram/mFILE.o cram/mFILE.pico: cram/mFILE.c config.h $(cram_os_h) cram/mFILE.h cram/vlen.h
+cram/mFILE.o cram/mFILE.pico: cram/mFILE.c config.h $(cram_os_h) cram/mFILE.h
 cram/open_trace_file.o cram/open_trace_file.pico: cram/open_trace_file.c config.h $(cram_os_h) $(cram_open_trace_file_h) $(cram_misc_h) $(htslib_hfile_h)
 cram/pooled_alloc.o cram/pooled_alloc.pico: cram/pooled_alloc.c config.h cram/pooled_alloc.h $(cram_misc_h)
 cram/rANS_static.o cram/rANS_static.pico: cram/rANS_static.c config.h cram/rANS_static.h cram/rANS_byte.h
 cram/sam_header.o cram/sam_header.pico: cram/sam_header.c config.h $(cram_sam_header_h) cram/string_alloc.h
 cram/string_alloc.o cram/string_alloc.pico: cram/string_alloc.c config.h cram/string_alloc.h
 thread_pool.o thread_pool.pico: thread_pool.c config.h $(thread_pool_internal_h)
-cram/vlen.o cram/vlen.pico: cram/vlen.c config.h cram/vlen.h $(cram_os_h)
-cram/zfio.o cram/zfio.pico: cram/zfio.c config.h $(cram_os_h) cram/zfio.h
 
 
 bgzip: bgzip.o libhts.a
@@ -479,6 +475,7 @@ clean: mostlyclean clean-$(SHLIB_FLAVOUR)
 distclean maintainer-clean: clean
 	-rm -f config.cache config.h config.log config.mk config.status
 	-rm -f TAGS *.pc.tmp *-uninstalled.pc htslib_static.mk
+	-rm -rf autom4te.cache
 
 clean-so:
 	-rm -f libhts.so libhts.so.*

NEWS

@@ -1,3 +1,18 @@
+Noteworthy changes in release 1.5 (21st June 2017)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+* Added a new logging API: hts_log(), along with hts_log_error(),
+  hts_log_warn() etc. convenience macros.  Thanks go to Anders Kaplan
+  for the implementation. (#499, #543, #551)
+
+* Added a new file I/O option "block_size" (HTS_OPT_BLOCK_SIZE) to
+  alter the hFILE buffer size.
+
+* Fixed various bugs, including compilation issues samtools/bcftools#610,
+  samtools/bcftools#611 and robustness to corrupted data #537, #538,
+  #541, #546, #548, #549, #554.
+
+
 Noteworthy changes in release 1.4.1  (8th May 2017)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~