Release 1.3.1: bug fix release, notably error checking

.gitattributes

@@ -1,3 +1,11 @@
+# Ensure BAM and CRAM files are left as binary.  To display changes in them
+# by converting to SAM, add to your configuration (perhaps with --global):
+#
+#	git config diff.bam.textconv  "samtools view -h"
+#	git config diff.cram.textconv "samtools view -h"
+*.bam     -text diff=bam
+*.cram    -text diff=cram
+
 # Omit these files from release tarballs.
 .git*           export-ignore
 /.travis.yml    export-ignore

.gitignore

@@ -1,5 +1,7 @@
 *.o
 *.pico
+*.dSYM
+*.exe
 *-uninstalled.pc
 /version.h
 

Makefile

@@ -92,7 +92,7 @@ HTSPREFIX =
 include htslib_vars.mk
 
 
-PACKAGE_VERSION  = 1.3
+PACKAGE_VERSION  = 1.3.1
 LIBHTS_SOVERSION = 1
 
 
@@ -251,21 +251,21 @@ libhts.dylib: $(LIBHTS_OBJS)
 
 
 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)
+kstring.o kstring.pico: kstring.c config.h $(htslib_kstring_h)
+knetfile.o knetfile.pico: knetfile.c config.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_irods.o hfile_irods.pico: hfile_irods.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_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)
 hts.o hts.pico: hts.c config.h version.h $(htslib_hts_h) $(htslib_bgzf_h) $(cram_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_ksort_h) $(hts_internal_h)
-vcf.o vcf.pico: vcf.c config.h $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_kstring_h) $(htslib_khash_str2int_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_h) $(htslib_kseq_h) $(htslib_kstring_h) $(htslib_khash_str2int_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)
 tbx.o tbx.pico: tbx.c config.h $(htslib_tbx_h) $(htslib_bgzf_h) $(htslib_khash_h)
 faidx.o faidx.pico: faidx.c config.h $(htslib_bgzf_h) $(htslib_faidx_h) $(htslib_hfile_h) $(htslib_khash_h) $(htslib_kstring_h)
 synced_bcf_reader.o synced_bcf_reader.pico: synced_bcf_reader.c config.h $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(htslib_bgzf_h)
 vcf_sweep.o vcf_sweep.pico: vcf_sweep.c config.h $(htslib_vcf_sweep_h) $(htslib_bgzf_h)
 vcfutils.o vcfutils.pico: vcfutils.c config.h $(htslib_vcfutils_h) $(htslib_kbitset_h)
-kfunc.o kfunc.pico: kfunc.c $(htslib_kfunc_h)
+kfunc.o kfunc.pico: kfunc.c config.h $(htslib_kfunc_h)
 regidx.o regidx.pico: regidx.c config.h $(htslib_hts_h) $(htslib_kstring_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(htslib_regidx_h)
 md5.o md5.pico: md5.c config.h $(htslib_hts_h)
 plugin.o plugin.pico: plugin.c config.h $(hts_internal_h) $(htslib_kstring_h)
@@ -311,7 +311,6 @@ check test: htsfile $(BUILT_TEST_PROGRAMS)
 	test/hfile
 	test/sam test/ce.fa test/faidx.fa
 	test/test-regidx
-	cd test && REF_PATH=: ./test_view.pl
 	cd test && REF_PATH=: ./test.pl
 
 test/fieldarith: test/fieldarith.o libhts.a
@@ -335,13 +334,13 @@ test/test-vcf-api: test/test-vcf-api.o libhts.a
 test/test-vcf-sweep: test/test-vcf-sweep.o libhts.a
 	$(CC) -pthread $(LDFLAGS) -o $@ test/test-vcf-sweep.o libhts.a -lz $(LIBS)
 
-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_faidx_h) $(htslib_kstring_h)
-test/test-regidx.o: test/test-regidx.c $(htslib_regidx_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) $(htslib_kseq_h)
-test/test-vcf-sweep.o: test/test-vcf-sweep.c $(htslib_vcf_sweep_h)
+test/fieldarith.o: test/fieldarith.c config.h $(htslib_sam_h)
+test/hfile.o: test/hfile.c config.h $(htslib_hfile_h) $(htslib_hts_defs_h)
+test/sam.o: test/sam.c config.h $(htslib_hts_defs_h) $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h)
+test/test-regidx.o: test/test-regidx.c config.h $(htslib_regidx_h)
+test/test_view.o: test/test_view.c config.h $(cram_h) $(htslib_sam_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)
 
 
 install: libhts.a $(BUILT_PROGRAMS) $(BUILT_PLUGINS) installdirs install-$(SHLIB_FLAVOUR) install-pkgconfig

NEWS

@@ -1,3 +1,35 @@
+Noteworthy changes in release 1.3.1 (22 April 2016)
+
+* Improved error checking and reporting, especially of I/O errors when
+  writing output files (#17, #315, PR #271, PR #317).
+
+* Build fixes for 32-bit systems; be sure to run configure to enable
+  large file support and access to 2GiB+ files.
+
+* Numerous VCF parsing fixes (#321, #322, #323, #324, #325; PR #370).
+  Particular thanks to Kostya Kortchinsky of the Google Security Team
+  for testing and numerous input parsing bug reports.
+
+* HTSlib now prints an informational message when initially creating a
+  CRAM reference cache in the default location under your $HOME directory.
+  (No message is printed if you are using $REF_CACHE to specify a location.)
+
+* Avoided rare race condition when caching downloaded CRAM reference sequence
+  files, by using distinctive names for temporary files (in addition to O_EXCL,
+  which has always been used).  Occasional corruption would previously occur
+  when multiple tools were simultaneously caching the same reference sequences
+  on an NFS filesystem that did not support O_EXCL (PR #320).
+
+* Prevented race condition in file access plugin loading (PR #341).
+
+* Fixed mpileup memory leak, so no more "[bam_plp_destroy] memory leak [...]
+  Continue anyway" warning messages (#299).
+
+* Various minor CRAM fixes.
+
+* Fixed documentation problems #348 and #358.
+
+
 Noteworthy changes in release 1.3  (15 December 2015)
 
 * Files can now be accessed via HTTPS and Amazon S3 in addition to HTTP
@@ -9,6 +41,9 @@ Noteworthy changes in release 1.3  (15 December 2015)
   easily added and facilitates building tools that use HTSlib, as they
   don't need to be linked with the backends' various required libraries.
 
+* When writing CRAM output, sam_open() etc now default to writing CRAM v3.0
+  rather than v2.1.
+
 * fai_build() and samtools faidx now accept initial whitespace in ">"
   headers (e.g., "> chr1 description" is taken to refer to "chr1").