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@daviesrob daviesrob released this 25 Jul 13:07
· 223 commits to develop since this release
1.18
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Download the source code here: htslib-1.18.tar.bz2.(The "Source code" downloads are generated by GitHub and are incomplete as they are missing some generated files.)

Updates

  • Using CRAM 3.1 no longer gives a warning about the specification being draft. Note CRAM 3.0 is still the default output format. (PR #1583)

  • Replaced use of sprintf with snprintf, to silence potential warnings from Apple's compilers and those who implement similar checks. (PR #1594, fixes #1586. Reported by Oleksii Nikolaienko)

  • Fastq output will now generate empty records for reads with no sequence data (i.e. sequence is * in SAM format). (PR #1576, fixes samtools/samtools#1576. Reported by Nils Homer)

  • CRAM decoding speed-ups. (PR #1580)

  • A new MN aux tag can now be used to verify that MM/ML base modification data has not been broken by hard clipping. (PR #1590, PR #1612. See also PR samtools/hts-specs#714 and issue samtools/hts-specs#646. Reported by Jared Simpson)

  • The base modification API has been improved to make it easier for callers to tell unchecked bases from unmodified ones. (PR #1636, fixes #1550. Requested by Chris Wright)

  • A new bam_mods_queryi() API has been added to return additional data about the i-th base modification returned by bam_mods_recorded(). (PR #1636, fixes #1550 and #1635. Requested by Jared Simpson)

  • Speed up index look-ups for whole-chromosome queries. (PR #1596)

  • Mpileup now merges adjacent (mis)match CIGAR operations, so CIGARs using the X/= operators give the same results as if the M operator was used. (PR #1607, fixes #1597. Reported by Marcel Martin)

  • It's now possible to call bcf_sr_set_regions() after adding readers using bcf_sr_add_reader() (previously this returned an error). Doing so will discard any unread data, and reset the readers so they iterate over the new regions. (PR #1624, fixes samtools/bcftools#1918. Reported by Gregg Thomas)

  • The synced BCF reader can now accept regions with reference names including colons and hyphens, by enclosing them in curly braces. For example, {chr_part:1-1001}:10-20 will return bases 10 to 20 from reference chr_part:1-1001. (PR #1630, fixes #1620. Reported by Bren)

  • Add a "samples" directory with code demonstrating usage of HTSlib plus a tutorial document. (PR #1589)

Build changes

  • Htscodecs has been updated to 1.5.1 (PR #1654)

  • Htscodecs SIMD code now works with Apple multiarch binaries. (PR #1587, HTSlib fix for samtools/htscodecs#76. Reported by John Marshall)

  • Improve portability of expr usage in version.sh. (PR #1593, fixes #1592. Reported by John Marshall)

  • Improve portability to *BSD targets by ensuring _XOPEN_SOURCE is defined correctly and that source files properly include "config.h". Perl scripts also now all use #!/usr/bin/env instead of assuming that it's in /usr/bin/perl. (PR #1628, fixes #1606. Reported by Robert Clausecker)

  • Fixed NAME entry in htslib-s3-plugin man page so the whatis and apropos commands find it. (PR #1634, thanks to Étienne Mollier)

  • Assorted dependency tracking fixes. (PR #1653, thanks to John Marshall)

Documentation updates

  • Changed Alpine build instructions as they've switched back to using openssl. (PR #1609)

  • Recommend using -rdynamic when statically linking a libhts.a with plugins enabled. (PR #1611, thanks to John Marshall. Fixes #1600, reported by Jack Wimberley)

  • Fixed example in docs for sam_hdr_add_line(). (PR #1618, thanks to kojix2)

  • Improved test harness for base modifications API. (PR #1648)

Bug fixes

  • Fix a major bug when searching against a CRAM index where one container has start and end coordinates entirely contained within the previous container. This would occasionally miss data, and sometimes return much more than required. The bug affected versions 1.11 to 1.17, although the change in 1.11 was bug-fixing multi-threaded index queries. This bug did not affect index building. There is no need to reindex your CRAM files. (PR #1574, PR #1640. Fixes #1569, #1639, samtools/samtools#1808, samtools/samtools#1819. Reported by xuxif, Jens Reeder and Jared Simpson)

  • Prevent CRAM blocks from becoming too big in files with short sequences but very long aux tags. (PR #1613)

  • Fix bug where the CRAM decoder for CONST_INT and CONST_BYTE codecs may incorrectly look for extra data in the CORE block. Note that this bug only affected the experimental CRAM v4.0 decoder. (PR #1614)

  • Fix crypt4gh redirection so it works in conjunction with non-file IO, such as using htsget. (PR #1577)

  • Improve error checking for the VCF POS column, when facing invalid data. (PR #1575, replaces #1570 originally reported and fixed by Colin Nolan.)

  • Improved error checking on VCF indexing to validate the data is BGZF compressed. (PR #1581)

  • Fix bug where bin number calculation could overflow when making iterators over regions that go to the end of a chromosome. (PR #1595)

  • Backport attractivechaos/klib#78 (by Pall Melsted) to HTSlib. Prevents infinite loops in kseq_read() when reading broken gzip files. (PR #1582, fixes #1579. Reported by Goran Vinterhalter)

  • Backport attractivechaos/klib@384277a (by innoink) to HTSlib. Fixes the kh_int_hash_func2() macro definition. (PR #1599, fixes #1598. Reported by fanxinping)

  • Remove a compilation warning on systems with newer libcurl releases. (PR #1572)

  • Windows: Fixed BGZF EOF check for recent MinGW releases. (PR #1601, fixes samtools/bcftools#1901)

  • Fixed bug where tabix would not return the correct regions for files where the column ordering is end, ..., begin instead of begin, ..., end. (PR #1626, fixes #1622. Reported by Hiruna Samarakoon)

  • sam_format_aux1() now always NUL-terminates Z/H tags. (PR #1631)

  • Ensure base modification iterator is reset when no MM tag is present. (PR #1631, PR #1647)

  • Fix segfault when attempting to write an uncompressed BAM file opened using hts_open(name, "wbu"). This was attempting to write BAM data without wrapping it in BGZF blocks, which is invalid according to the BAM specification. "wbu" is now internally converted to "wb0" to output uncompressed data wrapped in BGZF blocks. (PR #1632, fixes #1617. Reported by Joyjit Daw)

  • Fixed over-strict bounds check in probaln_glocal() which caused it to make sub-optimal alignments when the requested band width was greater than the query length. (PR #1616, fixes #1605. Reported by Jared Simpson)

  • Fixed possible double frees when handling errors in bcf_hdr_add_hrec(), if particular memory allocations fail. (PR #1637)

  • Ensure that bcf_hdr_remove() clears up all pointers to the items removed from dictionaries. Failing to do this could have resulted in a call requesting a deleted item via bcf_hdr_get_hrec() returning a stale pointer. (PR #1637)

  • Stop the gzip decompresser from finishing prematurely when an empty gzip block is followed by more data. (PR #1643, PR #1646)

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