Release 1.23

Author: daviesrob

Makefile

@@ -1,6 +1,6 @@
 # Makefile for htslib, a C library for high-throughput sequencing data formats.
 #
-#    Copyright (C) 2013-2024 Genome Research Ltd.
+#    Copyright (C) 2013-2025 Genome Research Ltd.
 #
 #    Author: John Marshall <[email protected]>
 #
@@ -158,8 +158,8 @@ 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 = 3.1.22
-MACH_O_CURRENT_VERSION = 3.1.22
+MACH_O_COMPATIBILITY_VERSION = 3.1.23
+MACH_O_CURRENT_VERSION = 3.1.23
 
 # 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))
@@ -267,6 +267,7 @@ NONCONFIGURE_OBJS = hfile_libcurl.o
 PLUGIN_EXT  =
 PLUGIN_OBJS =
 
+bgzf_internal_h = bgzf_internal.h $(htslib_bgzf_h)
 cram_h = cram/cram.h $(cram_samtools_h) $(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 $(htslib_cram_h)
 cram_io_h = cram/cram_io.h $(cram_misc_h)
 cram_misc_h = cram/misc.h
@@ -276,7 +277,7 @@ cram_structs_h = cram/cram_structs.h $(htslib_thread_pool_h) $(htslib_cram_h) cr
 cram_open_trace_file_h = cram/open_trace_file.h cram/mFILE.h
 bcf_sr_sort_h = bcf_sr_sort.h $(htslib_synced_bcf_reader_h) $(htslib_kbitset_h)
 fuzz_settings_h = fuzz_settings.h
-header_h = header.h cram/string_alloc.h cram/pooled_alloc.h $(htslib_khash_h) $(htslib_kstring_h) $(htslib_sam_h)
+header_h = header.h cram/string_alloc.h cram/pooled_alloc.h $(htslib_khash_h) $(htslib_kstring_h) $(htslib_sam_h) $(htslib_hts_h)
 hfile_internal_h = hfile_internal.h $(htslib_hts_defs_h) $(htslib_hfile_h) $(textutils_internal_h)
 hts_internal_h = hts_internal.h $(htslib_hts_h) $(textutils_internal_h)
 hts_time_funcs_h = hts_time_funcs.h
@@ -328,13 +329,18 @@ config.h:
 	if [ "x$(HTS_BUILD_AVX512)" != "x" ] ; then \
 	    echo '#define HAVE_AVX512 1' >> $@ ; \
 	fi
+	echo '#if defined __x86_64__ && (defined HAVE_SSSE3 || defined HAVE_AVX2 || defined HAVE_AVX512)' >> $@
+	echo '#define HAVE_X86INTRIN_H 1' >> $@
+	echo '#endif' >> $@
 	echo '#if defined __x86_64__ || defined __arm__ || defined __aarch64__' >> $@
 	echo '#define HAVE_ATTRIBUTE_CONSTRUCTOR 1' >> $@
 	echo '#endif' >> $@
-	echo '#if (defined(__x86_64__) || defined(_M_X64))' >> $@
-	echo '#define HAVE_ATTRIBUTE_TARGET_SSSE3 1' >> $@
-	echo '#define HAVE_BUILTIN_CPU_SUPPORT_SSSE3 1' >> $@
-	echo '#endif' >> $@
+	if [ "x$(HTS_HAVE_SSSE3_BUILTINS)" != "x" ]; then \
+	    echo '#if (defined(__x86_64__) || defined(_M_X64))' >> $@ ; \
+	    echo '#define HAVE_ATTRIBUTE_TARGET_SSSE3 1' >> $@ ; \
+	    echo '#define HAVE_BUILTIN_CPU_SUPPORT_SSSE3 1' >> $@ ; \
+	    echo '#endif' >> $@ ; \
+	fi
 	echo '#if defined __linux__' >> $@
 	echo '#define HAVE_GETAUXVAL' >> $@
 	echo '#elif defined __FreeBSD__' >> $@
@@ -487,19 +493,18 @@ hts-object-files: $(LIBHTS_OBJS)
 	$(CC) -shared $(LDFLAGS) -o $@ $< hts.dll.a $(LIBS)
 
 
-bgzf.o bgzf.pico: bgzf.c config.h $(htslib_hts_h) $(htslib_bgzf_h) $(htslib_hfile_h) $(htslib_thread_pool_h) $(htslib_hts_endian_h) cram/pooled_alloc.h $(hts_internal_h) $(htslib_khash_h)
+bgzf.o bgzf.pico: bgzf.c config.h $(htslib_hts_h) $(htslib_bgzf_h) $(htslib_hfile_h) $(htslib_thread_pool_h) $(htslib_hts_endian_h) cram/pooled_alloc.h $(hts_internal_h) $(bgzf_internal_h) $(htslib_khash_h)
 errmod.o errmod.pico: errmod.c config.h $(htslib_hts_h) $(htslib_ksort_h) $(htslib_hts_os_h)
 kstring.o kstring.pico: kstring.c config.h $(htslib_kstring_h)
-header.o header.pico: header.c config.h $(textutils_internal_h) $(header_h)
+header.o header.pico: header.c config.h $(textutils_internal_h) $(header_h) $(htslib_bgzf_h) $(htslib_hfile_h) $(htslib_kseq_h)
 hfile.o hfile.pico: hfile.c config.h $(htslib_hfile_h) $(hfile_internal_h) $(htslib_kstring_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) $(htslib_khash_h)
-hfile_s3_write.o hfile_s3_write.pico: hfile_s3_write.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h) $(htslib_khash_h)
 hfile_s3.o hfile_s3.pico: hfile_s3.c config.h $(hfile_internal_h) $(htslib_hts_h) $(htslib_kstring_h) $(hts_time_funcs_h)
 hts.o hts.pico: hts.c config.h os/lzma_stub.h $(htslib_hts_h) $(htslib_bgzf_h) $(cram_h) $(htslib_hfile_h) $(htslib_hts_endian_h) version.h config_vars.h $(hts_internal_h) $(hfile_internal_h) $(sam_internal_h) $(htslib_hts_expr_h) $(htslib_hts_os_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_ksort_h) $(htslib_tbx_h) $(htscodecs_htscodecs_h)
 hts_expr.o hts_expr.pico: hts_expr.c config.h $(htslib_hts_expr_h) $(htslib_hts_log_h) $(textutils_internal_h)
 hts_os.o hts_os.pico: hts_os.c config.h $(htslib_hts_defs_h) os/rand.c
-vcf.o vcf.pico: vcf.c config.h $(fuzz_settings_h) $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(htslib_hfile_h) $(hts_internal_h) $(htslib_khash_str2int_h) $(htslib_kstring_h) $(htslib_sam_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_hts_endian_h)
+vcf.o vcf.pico: vcf.c config.h $(fuzz_settings_h) $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(htslib_hfile_h) $(hts_internal_h) $(htslib_khash_str2int_h) $(htslib_kstring_h) $(htslib_sam_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_hts_endian_h) $(bgzf_internal_h)
 sam.o sam.pico: sam.c config.h $(fuzz_settings_h) $(htslib_hts_defs_h) $(htslib_sam_h) $(htslib_bgzf_h) $(cram_h) $(hts_internal_h) $(sam_internal_h) $(htslib_hfile_h) $(htslib_hts_endian_h) $(htslib_hts_expr_h) $(header_h) $(htslib_khash_h) $(htslib_kseq_h) $(htslib_kstring_h)
 sam_mods.o sam_mods.pico: sam_mods.c config.h $(htslib_sam_h) $(textutils_internal_h)
 simd.o simd.pico: simd.c config.h $(htslib_sam_h) $(sam_internal_h)
@@ -520,7 +525,7 @@ realn.o realn.pico: realn.c config.h $(htslib_hts_h) $(htslib_sam_h)
 textutils.o textutils.pico: textutils.c config.h $(htslib_hfile_h) $(htslib_kstring_h) $(htslib_sam_h) $(hts_internal_h)
 
 cram/cram_codecs.o cram/cram_codecs.pico: cram/cram_codecs.c config.h $(fuzz_settings_h) $(htslib_hts_endian_h) $(htscodecs_varint_h) $(htscodecs_pack_h) $(htscodecs_rle_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_decode.o cram/cram_decode.pico: cram/cram_decode.c config.h $(cram_h) $(cram_os_h) $(htslib_hts_h) $(htslib_hfile_h)
 cram/cram_encode.o cram/cram_encode.pico: cram/cram_encode.c config.h $(cram_h) $(cram_os_h) $(sam_internal_h) $(htslib_hts_h) $(htslib_hts_endian_h) $(textutils_internal_h)
 cram/cram_external.o cram/cram_external.pico: cram/cram_external.c config.h $(htscodecs_rANS_static4x16_h) $(htslib_hfile_h) $(cram_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)
@@ -699,6 +704,7 @@ check test: all $(HTSCODECS_TEST_TARGETS)
 	cd test/mpileup && ./test-pileup.sh mpileup.tst
 	cd test/fastq && ./test-fastq.sh
 	cd test/base_mods && ./base-mods.sh base-mods.tst
+	cd test/tlen && ./tlen.sh tlen.tst
 	REF_PATH=: test/sam test/ce.fa test/faidx/faidx.fa test/faidx/fastqs.fq
 	test/test-regidx
 	cd test && \
@@ -872,7 +878,7 @@ 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-api.o: test/test-vcf-api.c config.h $(htslib_hts_h) $(htslib_vcf_h) $(htslib_vcfutils_h) $(htslib_kbitset_h) $(htslib_kstring_h) $(htslib_kseq_h)
 test/test-vcf-sweep.o: test/test-vcf-sweep.c config.h $(htslib_vcf_sweep_h)
 test/test-bcf-sr.o: test/test-bcf-sr.c config.h $(htslib_hts_defs_h) $(htslib_synced_bcf_reader_h) $(htslib_hts_h) $(htslib_vcf_h)
 test/test-bcf-translate.o: test/test-bcf-translate.c config.h $(htslib_vcf_h)
@@ -946,7 +952,7 @@ $(srcprefix)htslib.map: libhts.so
 	    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 && \
+	nm --defined-only --with-symbol-versions -D -g libhts.so | awk '$$2 ~ /^[DGRT]$$/ && ($$3 ~ /@@Base$$/ || $$3 !~ /@/) && $$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 && \

NEWS

@@ -1,3 +1,126 @@
+Noteworthy changes in release 1.23 (16th December 2025)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Updates
+-------
+
+* HTSlib 1.22 changed the VCF reader so that it stored GT prefixed phasing
+  information, but only for files specifying `fileformat=VCFv4.4` or higher.
+  This caused problems when merging files with different versions, so the
+  VCF reader will now store prefixed phasing information irrespective of
+  the VCF version listed in the file headers.  For files up to VCFv4.3, the
+  first phasing bit will be set if all other alleles are phased, and cleared
+  otherwise (following the rules for VCFv4.4 onwards where no explicit
+  phasing symbol is present).  This will also happen when reading BCF.
+
+  When accessing GT data, it is no longer safe to assume that the phasing
+  is set to zero even if the file reports a version earlier than VCFv4.4.
+  Interfaces such as `bcf_gt_allele()` should always be used to access
+  GT allele data.
+
+  For compatibility, prefixed phasing will be stripped when writing VCF
+  files with version 4.3 or earlier.
+  (PR #1938, fixes #1932)
+
+* Add support for VCFv4.4 / VCFv4.5 "Number=" fields.
+  (PR #1874)
+
+* Consolidate and simplify SAM header parsing.  This considerably speeds up
+  parsing files with many SQ lines.
+  (PR #1947. PR #1953 fixes oss-fuzz issues 444492071, 444492076, 444547724,
+   444490034, PR #1977)
+
+* Switch from strtol to hts_str2uint in mod parsing for speed increase.
+  (PR #1957.  Thanks to Chris Wright)
+
+* Add UMI support to FASTQ input and output.  See samtools/samtools#2270.
+  (PR #1960, fixes samtools/samtools#2259.  Requested by Poshi)
+
+* Removed direct access to htsFile struct members in some sample functions.
+  (PR #1963, fixes #1961.  Reported by John Marshall)
+
+* Improved operation of filters that work with header data.  Filter expressions
+  set as an `HTS_OPT_FILTER` on a BAM or CRAM iterator failed to return
+  records matching on `rname`, `mrname`, `rnext` or `library`.
+  (PR #1959)
+
+* Add Type to the INFO/FORMAT sanity check.  This produces a warning on
+  incorrect Type usage.
+  (PR #1967, fixes #1937 and samtools/bcftools#2431.
+   Reported by Jukka Matilainen)
+
+* S3 reading code now reads in `chunks` to limit the amount of data read (and
+  therefore egress costs) from the object store when doing a range request.
+  Also this combines the reading, writing and authorisation code into a single
+  file.
+  (PR #1958, fixes #1670.  Reported by Stephan Drukewitz)
+
+Build Changes
+-------------
+
+* Change optimisation for -fsanitize=address,undefined test build to counter
+  slow build and high compiler memory use.
+  (PR #1924)
+
+* Fix compilation failure on MacOS X 10.9 (and likely other very old platforms).
+  (PR #1945, fixes #1941.  Reported by Ryan Carsten Schmidt)
+
+* Fix htslib.map update due to recent change in nm behaviour.
+  (PR #1975, fixes #1971.  Reported by John Marshall).
+
+* The htscodecs submodule is updated to v1.6.5.
+  This includes a fix to the rANS encoder when running on x86-64
+  hardware with some SIMD features disabled.
+  (Fixes samtools/samtools#2256. Reported by Ran Fan)
+
+Bug fixes
+---------
+
+* Fix segfault on an empty valid MM tag.
+  (PR #1939, fixes #1936.  Reported by John Marshall)
+
+* Fix bam_next_basemod + HTS_MOD_REPORT_UNCHECKED flag.
+  (PR #1946, fixes #1943)
+
+* For the VCF rlen calculation, only use SVLEN for DEL, DUP and CNV symbolic
+  alleles.  A bug is also fixed on big-endian platforms where INFO and FORMAT
+  values were being accessed incorrectly.
+  (PR #1942, fixes #1940)
+
+* Correct TLEN assignment in CRAM decode.  Also improve decoder when dealing
+  with multiple secondary alignments.  See also samtools/hts-specs#842.
+  (PR #1951, fixes #1948.  Reported by Matt Sexton)
+
+* Make tabix skip comments (-c) wherever they occur, not just at the start of
+  the file.
+  (PR #1952, fixes #1950.  Reported by Victor Negîrneac)
+
+* Update htscodecs for better AVX2 / AVX512 runtime detection.
+  (PR #1954, fixes samtools/samtools#2256.  Reported by Ran Fan)
+
+* Fix embed_ref=2 on SEQ * and MD:Z tag. The combination of no sequence and
+  MD:Z with embed_ref=2 caused the slice extents to be miscalculated,
+  causing invalid CRAM output to be written.
+  (PR #1964, fixes samtools/samtools#2277.  Reported by fo40225)
+
+* Try to ensure CSI indexes are built with valid parameters.  Adjusts the
+  min_shift and n_lvls to cover the size of the genome.  This may override the
+  user setting of min_shift (with warning) if needed.
+  (PR #1968, fixes #1966. Reported by Marc Sturm)
+
+* Fix bug where multi-threaded CRAM iterators could drop long alignments
+  starting significantly before, but overlapping, the region of interest.
+  (PR #1973, fixes samtools/samtools#2285,  Reported by Nick Owens)
+
+Documentation updates
+---------------------
+
+* Added support information and samtools email for security issues.
+  (PR #1956)
+
+* Fix spelling in function name in sam.h.
+  (PR #1972.  Thanks to Jack Turpitt)
+
 Noteworthy changes in release 1.22.1 (14th July 2025)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 

README.md

@@ -61,3 +61,9 @@ Please cite this paper when using HTSlib for your publications.
     eprint = {https://academic.oup.com/gigascience/article-pdf/10/2/giab007/36332285/giab007.pdf},
 }
 ```
+
+### Support
+
+If you have found a bug or would like a new feature, please report the same in the GitHub [HTSlib](https://github.com/samtools/htslib/issues) issue tracker.
+
+For any security related issue, please send a mail to [[email protected]](mailto:[email protected]) instead of reporting in the GitHub issue tracker. 

annot-tsv.1

@@ -1,5 +1,5 @@
 '\" t
-.TH annot-tsv 1 "14 July 2025" "htslib-1.22.1" "Bioinformatics tools"
+.TH annot-tsv 1 "16 December 2025" "htslib-1.23" "Bioinformatics tools"
 .\"
 .\" Copyright (C) 2015, 2017-2018, 2023-2024 Genome Research Ltd.
 .\"