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@daviesrob daviesrob released this 12 Sep 15:55
· 5 commits to develop since this release
1.21
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Download the source code here: htslib-1.21.tar.bz2.

The primary user-visible changes in this release are updates to the annot-tsv tool and some speed improvements. Full details of other changes and bugs fixed are below.

Notice: this is the last SAMtools / HTSlib release where CRAM 3.0 will be the default CRAM version. From the next we will change to CRAM 3.1 unless the version is explicitly specified, for example using samtools view -O cram,version=3.0.

Updates

  • Extend annot-tsv with several new command line options.
    --delim permits use of other delimiters.
    --headers for selection of other header formats.
    --no-header-idx to suppress column index numbers in header.
    Also removed -h as it is now short for --headers. Note --help still works. (PR #1779)

  • Allow annot-tsv -a to rename annotations. (PR #1709)

  • Extend annot-tsv --overlap to be able to specify the overlap fraction separately for source and target. (PR #1811)

  • Added new APIs to facilitate low-level CRAM container manipulations, used by the new samtools cat region filtering code. Functions are:

    cram_container_get_coords()
cram_filter_container()
cram_index_extents()
cram_container_num2offset()
cram_container_offset2num()
cram_num_containers()
cram_num_containers_between()

    Also improved cram_index_query() to cope with HTS_IDX_NOCOOR regions. (PR #1771)

  • Bgzip now retains file modification and access times when compressing and decompressing. (PR #1727, fixes #1718. Requested by Gert Hulselmans.)

  • Use FNV1a for string hashing in khash. The old algorithm was particularly weak with base-64 style strings and lead to a large number of collisions. (PR #1806. Fixes samtools/samtools#2066, reported by Hans-Joachim Ruscheweyh)

  • Improve the speed of the nibble2base() function on Intel (PR #1667, PR #1764, PR #1786, PR #1802, thanks to Ruben Vorderman) and ARM (PR #1795, thanks to John Marshall).

  • bgzf_getline() will now warn if it encounters UTF-16 data. (PR #1487, thanks to John Marshall)

  • Speed up bgzf_read(). While this does not reduce CPU significantly, it does increase the maximum parallelism available permitting 10-15% faster decoding. (PR #1772, PR #1800, Issue #1798)

  • Speed up faidx by use of better isgraph() methods (PR #1797) and whole-line reading (PR #1799, thanks to John Marshall).

  • Speed up kputll() function, speeding up BAM -> SAM conversion by about 5% and also samtools depth. (PR #1805)

  • Added more example code, covering fasta/fastq indexing, tabix indexing and use of the thread pool. (PR #1666)

Build Changes

  • Code warning fixes for pedantic compilers (PR #1777) and avoid some undefined behaviour (PR #1810, PR #1816, PR #1828).

  • Windows based CI has been migrated from AppVeyor to GitHub Actions. (PR #1796, PR #1803, PR #1808)

  • Miscellaneous minor build infrastructure and code fixes. (PR #1807, PR #1829, both thanks to John Marshall)

  • Updated htscodecs submodule to version 1.6.1 (PR #1828)

  • Fixed an awk script in the Makefile that only worked with gawk. (PR #1831)

Bug fixes

  • Fix small OSS-Fuzz reported issues with CRAM encoding and long CIGARS and/or illegal positions. (PR #1775, PR #1801, PR #1817)

  • Fix issues with on-the-fly indexing of VCF/BCF (bcftools --write-index) when not using multiple threads. (PR #1837. Fixes samtools/bcftools#2267, reported by Giulio Genovese)

  • Stricter limits on POS / MPOS / TLEN in sam_parse1(). This fixes a signed overflow reported by OSS-Fuzz and should help prevent other as-yet undetected bugs. (PR #1812)

  • Check that the underlying file open worked for preload: URLs. Fixes a NULL pointer dereference reported by OSS-Fuzz. (PR #1821)

  • Fix an infinite loop in hts_itr_query() when given extremely large positions which cause integer overflow. Also adds hts_bin_maxpos() and hts_idx_maxpos() functions. (PR #1774, thanks to John Marshall and reported by Jesus Alberto Munoz Mesa)

  • Fix an out of bounds read in hts_itr_multi_next() when switching chromosomes. This bug is present in releases 1.11 to 1.20. (PR #1788. Fixes samtools/samtools#2063, reported by acorvelo)

  • Work around parsing problems with colons in CHROM names. Fixes samtools/bcftools#2139. (PR #1781, John Marshall / James Bonfield)

  • Correct the CPU detection for Mac OS X 10.7. cpuid is used by htscodecs (see samtools/htscodecs#116), and the corresponding changes in htslib are PR #1785. Reported by Ryan Carsten Schmidt.

  • Make BAM zero-length intervals work the same as CRAM; permitted and returning overlapping records. (PR #1787. Fixes samtools/samtools#2060, reported by acorvelo)

  • Replace assert() with abort() in BCF synced reader. This is not an ideal solution, but it gives consistent behaviour when compiling with or without NDEBUG. (PR #1791, thanks to Martin Pollard)

  • Fixed failure to change the write block size on compressed SAM or VCF files due to an internal type confusion. (PR #1826)

  • Fixed an out-of-bounds read in cram_codec_iter_next() (PR #1832)

Download the source code here: htslib-1.21.tar.bz2. (The "Source code" downloads are generated by GitHub and are incomplete as they are missing some generated files.)

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