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@daviesrob daviesrob released this 27 Oct 12:04
· 13 commits to develop since this release
1.25
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Download the source code here: htslib-1.25.tar.bz2.(The "Source code" downloads are generated by GitHub and are incomplete as they are missing some generated files.)

  • NEW. Added environment variable HTS_GCS_HOST, analogous to the existing HTS_S3_HOST, to redirect gs:// URLs to a caller-specified endpoint.
    (PR #2051. Thanks to Peter Dowdy)

Updates

  • Various code quality improvements. Added memory and error checks. Some changes to better data types.
    (PR #2054, PR #2059, PR #2064, PR #2066, PR #2070, PR #2073, PR #2075, PR #2077, PR #2078)

  • Add a new format option to strip UR tags from CRAM.
    (PR #2056, partial fix for samtools/samtools#2327. Requested by Florian Plaza Oñate)

  • Report when khash can no longer expand.
    (PR #2063)

  • Use multi iterators in the synced reader. This adds bcf_itr_regions() and tbx_itr_regions() interfaces as BCF and tabix equivalents to sam_itr_regions(). This can speed up bcftools view.
    (PR #2052, fixes samtools/bcftools#2557. Reported by Carsten Erickson)

  • Apply CURL_CA_BUNDLE environment variable in the S3 backend.
    (PR #2069. Thanks to John Marshall)

  • Cram embed_ref=2 and huffman optimisation.
    (PR #2082)

  • API fix. Protect against out of bounds ref id in cram_put_bam_seq.
    (PR #2087)

  • Adds validation to options specified using hts_opt_add or cram_set_voption. Mostly for overflow detection.
    (PR #2095. Reported by Sn0wyDay)

  • Return an error instead of calling abort in hts_getline().
    (PR #2093, fixes #2091. Reported by an)

  • bcf_set_variant_type() now recognises single break-ends as described in section 5.4.9 of the VCF 4.5 specification.
    (PR #2115, fixes #2108)

Build Changes

  • Add more CI tests for a variety of Linux and non-Linux platforms.
    (PR #2053)

  • Update build badge, remove .cirrus.yml, spelling corrections.
    (PR #2071. Thanks to John Marshall)

  • Make check_copyright.pl better at skipping auto-generated files.
    (PR #2080)

  • Use bash and pipefail for tests using simple_test_driver.sh
    (PR #2083)

  • Add S3 integration tests.
    (PR #2067. Thanks to Peter Dowdy)

Bug fixes

  • Fix a use-after-free bug when renewing http authentication tokens. This could happen if the file used to supply a replacement token was not present at renewal time.
    (PR #2119 Reported by Xuqing Yang. GHSA-x79c-vxf6-6j9c)

  • Fix use-after-free and double free when handling file close errors in the preload:// file reader.
    (PR #2119 Reported by Xuqing Yang. GHSA-5cvj-m89h-h3cw)

  • Fix inconsistent region list clean-up on hts_itr_regions() failure. This function takes ownership of the region list passed to it, even if it fails due to out-of-memory conditions. Not accounting for this correctly led to a possible double free in the functions used to build multi-region iterators.
    (PR #2119. Reported by Xuqing Yang. GHSA-2r8w-wxh5-c7r8)

  • Fix a double free on out-of-memory conditions in the CRAM BYTE_ARRAY_LEN encoder.
    (PR #2119. Reported by Xuqing Yang. GHSA-2r8w-wxh5-c7r8)

  • Fix possible free of an uninitialised pointer if read errors occurred when loading .bai, .csi, or .tbx indexes.
    (PR #2119. Reported by maxmlz. GHSA-38qp-vpxq-r6xc)

  • Properly validate index metadata before attempting to access it.
    (PR #2119. GHSA-vhg8-qwm7-cv9m)

  • Fix use-after-free in bcf_sr_destroy1() if it tries to report an error on file close.
    (PR #2119. Reported by Junki Lee. GHSA-644m-mq4p-c7c6)

  • Reject VCF records containing ASCII NUL bytes in FORMAT data.
    (PR #2119. Reported by haehet. GHSA-6qq4-hj39-g6ph)

  • Validate tid value passed to hts_idx_get_stat() to prevent out-of-bounds reads.
    (PR #2119. Reported by haehet. GHSA-vhg8-qwm7-cv9m)

  • Fix an undefined behaviour in os/rand.c
    (PR #2050)

  • Fix heapsort bug and add ksort tests and improved documentation in comments.
    (PR #2055)

  • Fix possible leak of bgzidx_t::offs and changes to bgzidx_t::noffs and bgzidx_t::moffs data types.
    (PR #2057)

  • Remove an assert in cram_index_build and have it fail more gracefully.
    (PR #2061, fixes #2060. Reported and co-authored by Shujie Xiang)

  • Remove an infinite loop in bam_mods_at_qpos().
    (PR #2068)

  • Avoid calling libcurl functions if curl_global_init() failed.
    (Part of PR #2069. Thanks to John Marshall)

  • Make sam_format_aux1 'A' type be nul terminated.
    (PR #2079)

  • Fix multiple VCF header parsing bugs.
    (PR #2074, fixes #2065 Reported by Mark Woon)

  • Prevent integer overflow in resolve_cigar2().
    (PR #2072)

  • Improved code testing with the addition of a fuzzer for the expression filters (hts_expr). This resulted in the detection and correction of several serious expression parsing bugs.
    (PR #2076)

  • Fix leak of region list in hts_itr_multi_bam().
    (PR #2084)

  • Improve checking of SEQ/CIGAR consistency when processing records with CG tags.
    (PR # 2089. Fixes oss-fuzz issue 560967311)

  • Stop the CRAM zlib decoder from getting stuck in an endless loop.
    (PR #2085, fixes #2081. Reported by Sewon Ahn)

  • Fix hts_set_filter_expression(fp, NULL) so that it properly disables filtering without leaving a dangling pointer.
    (PR #2094. Reported and code fix suggestion by Sewon Ahn)

  • Tighten version number limits in bcf_get_version()
    (PR #2092, fixes #2088. Reported by an)

  • Fix CRAM query of unaligned ('*') reads.
    (PR #2100, fixes samtools/samtools#2396. Reported by Matt Sexton)

  • Fix hfile_s3 reads failing at EOF on a part boundary.
    (PR #2098, fixes #2097. Thanks to Peter Dowdy)

  • Reduce CRAM decode memory usage when multi-threading. Previous improvements to threaded throughput added greater memory usage, especially with long reads. This change mitigates that.
    (PR #2102, fixes samtools/samtools#2393. Reported by Matthieu Muffato)

  • Prevent negative range start in multi-region iterators, which could in some cases cause the index look-up to become stuck in an endless loop.
    (PR #2110. Reported by haehet)

  • Fix SQ line removal using sam_hdr_remove_lines(). It failed to update some internal sam_hdr_t structures, leading to deleted SQ lines reappearing, notably when writing BAM files.
    (PR #2105)

  • Fix the wildly incorrect length value returned by hfile_mem_get_buffer() and hfile_mem_steal_buffer().
    (PR #2109)

  • Fix a number of bugs that could be triggered by removing all samples with bcf_hdr_set_samples().
    (PR #2114)

  • Fix fai_load3() crash if a .fai index was present but it attempted a rebuild because it also needed a .gzi one, and the rebuild failed.
    (PR #2116)

Download the source code here: htslib-1.25.tar.bz2.(The "Source code" downloads are generated by GitHub and are incomplete as they are missing some generated files.)

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