1.21

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.)

1.20

Download the source code here: htslib-1.20.tar.bz2.(The "Source code" downloads are generated by GitHub and are incomplete as they are missing some generated files.)

Updates

• When working on named files, bgzip now sets the modified and access times of the output files it makes to match those of the corresponding input. (PR #1727, feature request #1718. Requested by Gert Hulselmans)

• It's now possible to use a -o option to specify the output file name in bgzip. (PR #1747, feature request #1726. Requested by Gert Hulselmans)

• Improved error faidx error messages. (PR #1743, thanks to Nick Moore)

• Faster reading of SAM array (type "B") tags. These often turn up in ONT and PacBio data. (PR #1741)

• Improved validity checking of base modification tags. (PR #1749)

• mpileup overlap removal now works where one read has a deletion. (PR #1751, fixes samtools/samtools#1992. Reported by Long Tian)

• The S3 plugin can now find buckets via S3 access point aliases. (PR #1756, thanks to Matt Pawelczyk; fixes samtools/samtools#1984. Reported by Albert Li)

• Added a --threads option (and -@ short option) to tabix. (PR #1755, feature request #1735. Requested by Dan Bolser)

• tabix can now index Graph Alignment Format (GAF) files. (See https://github.com/lh3/gfatools/blob/master/doc/rGFA.md) (PR #1763, thanks to Adam Novak)

Bug fixes

• Security fix: Prevent possible heap overflow in cram_encode_aux() on bad RG:Z tags. (PR #1737)

• Security fix: Prevent attempts to call a NULL pointer if certain URL schemes are used in CRAM @SQ UR: tags. (PR #1757)

• Security fix: Fixed a bug where following certain AWS S3 redirects could downgrade the connection from TLS (i.e. https://) to unencrypted http://. This could happen when using path-based URLs and AWS_DEFAULT_REGION was set to a region other that the one where the data was stored. (PR #1762, fixes #1760. Reported by andaca)

• Fixed arithmetic overflow when loading very long references for CRAM. (PR #1738, fixes #1738. Reported by Shane McCarthy)

• Fixed faidx and CRAM reference look-ups on compressed fasta where the .fai index file was present, but the .gzi index of compressed offsets was not. (PR #1745, fixes #1744. Reported by Theodore Li)

• Fixed BCF indexing on-the-fly bug which produced invalid indexes when using multiple compression threads. (PR #1742, fixes #1740. Reported by graphenn)

• Ensure that pileup destructors are called by bam_plp_destroy(), to prevent memory leaks. (PR #1749, PR #1754)

• Ensure on-the-fly index timestamps are always older than the data file. Previously the files could be closed out of order, leading to warnings being printed when using the index. (PR #1753, fixes #1732. Reported by Gert Hulselmans)

• To prevent data corruption when reading (strictly invalid) VCF files with duplicated FORMAT tags, all but the first copy of the data associated with the tag are now dropped with a warning. (PR #1752, PR #1761, fixes #1733. Reported by anthakki)

• Fixed a bug introduced in release 1.19 (PR #1689) which broke variant record data if it tried to remove an over-long tag. (PR #1752, PR #1761)

• Changed error to warning when complaining about use of the CG tag in SAM or CRAM files. (PR #1758, fixes samtools/samtools#2002)

1.19.1

Download the source code here: htslib-1.19.1.tar.bz2.(The "Source code" downloads are generated by GitHub and are incomplete as they are missing some generated files.)

• Fixed a regression in release 1.19 that caused all aux records to be stored uncompressed in CRAM files. The resulting files were correctly formatted, but bigger than they needed to be. (PR #1729, fixes samtools/samtools#1968. Reported by Clockris)

• Fixed possible out-of-bounds reads due to an incorrect check on B tag lengths in cram_encode_aux(). (PR #1725)

• Fixed an incorrect check on tag length which could fail to catch a two byte out-of-bounds read in bam_get_aux(). (PR #1728)

• Made errors reported by hts_open_format() less confusing when it can't open the reference file. (PR #1724, fixes #1723. Reported by Alex Leonard)

• Made hts_close() fail more gracefully if it's passed a NULL pointer (PR #1724)

1.19

Download the source code here: htslib-1.19.tar.bz2.(The "Source code" downloads are generated by GitHub and are incomplete as they are missing some generated files.)

Updates

• A temporary work-around has been put in the VCF parser so that it is less likely to fail on rows with a large number of ALT alleles, where Number=G tags like PL can expand beyond the 2Gb limit enforced by HTSlib. For now, where this happens the offending tag will be dropped so the data can be processed, albeit without the likelihood data.
  In future work, the library will instead convert such tags into their local alternatives (see samtools/hts-specs#434).

• New program. Adds annot-tsv which annotates regions in a destination file with texts from overlapping regions in a source file. (PR #1619)

• Change bam_parse_cigar() so that it can modify existing BAM records. This makes more useful as public API. Previously it could only handle partially formed BAM records. (PR #1651, fixes #1650. Reported by Oleksii Nikolaienko)

• Add "uncompressed" to hts_format_description() where appropriate. This adds an "uncompressed" description to uncompressed files that would normally be compressed, such as BAM and BCF. (PR #1656, in relation to samtools#1884. Thanks to John Marshall)

• Speed up to the VCF parser and writer. (PR #1644 and PR #1663)

• Add an hclen (hard clip length) SAM filter function. (PR #1660, with reference to #813)

• Avoid really closing stdin/stdout in hclose()/hts_close()/et al. See discussion in PR for details. (PR #1665. Thanks to John Marshall)

• Add support to handle multiple files in bgzip. (PR #1658, fixes #1642. Requested by bw2)

• Enable auto-vectorisation in CRAM 3.1 codecs. Speeds decoding on some sequencing platform data. (PR #1669)

• Speed up removal of lines in large headers. (PR #1662, fixes #1460. Reported by Anže Starič)

• Apply seqtk PR to improve kseq.h parsing performance. Port of Fabian Klötzl's (kloetzl) lh3/seqtk#123 and attractivechaos/klib#173 to HTSlib. (PR #1674. Thanks to John Marshall)

Build changes

• Updated htscodecs submodule to 1.6.0. (PR #1685, PR #1717, PR #1719)

• Apply the packed attribute to uint*_u types for Clang to prevent -fsanitize=alignment failures. (PR #1667. Thanks to Fangrui Song)

• Fuzz testing improvements. (PR #1664)

• Add C++ casts for external headers in klist.h and kseq.h. (PR #1683. See also PR #1674 and PR #1682)

• Add test case compiling the public headers as C++. (PR #1682. Thanks to John Marshall)

• Enable optimisation level -O3 for SAM QUAL+33 formatting. (PR #1679)

• Make compiler flag detection work with zig cc. (PR #1687)

• Fix unused value warnings when built with NDEBUG. (PR #1688)

• Remove some disused Makefile variables, fix typos and a warning. Improve bam_parse_basemod() documentation. (PR #1705, Thanks to John Marshall)

Bug fixes

• Fail bgzf_useek() when offset is above block limits. (PR #1668)

• Fix multi-threaded on-the-fly indexing problems. (PR #1672, fixes samtools#1861 and bcftools#1985. Reported by Mark Ebbert and lacek)

• Fix hfile_libcurl small seek bug. (PR #1676, fixes samtools#1918. Also may fix #1037, #1625 and #1622. Reported by Alex Reynolds, Mark Walker, Arthur Gilly and skatragadda-nygc. Thanks to John Marshall)

• Fix a minor memory leak in malformed CRAM EXTERNAL blocks. [fuzz] (PR #1671)

• Fix a cram decode hang from block_resize(). (PR #1680. Reported by Sebastian Deorowicz)

• Cram fuzzing improvements. Fixes a number of cram errors. (PR #1701, fixes #1691, #1692, #1693, #1696, #1697, #1698, #1699 and #1700. Thanks to Octavio Galland for finding and reporting all these)

• Fix crypt4gh redirection. (PR #1675, fixes grbot/crypt4gh-tutorial#2. Reported by hth4)

• Fix PG header linking when records make a loop. (PR #1702, fixes #1694. Reported by Octavio Galland)

• Prevent issues with no-stored-sequence records in CRAM files, by ensuring they are accounted for properly in block size calculations, and by limiting the maximum query length in the CIGAR data. Originally seen as an overflow by OSS-Fuzz / UBSAN, it turned out this could lead to excessive time and memory use by HTSlib, and could result in it writing out unreadable CRAM files. (PR #1710)

• Fix some illegal shifts and integer overflows found by OSS-Fuzz / UBSAN. (PR #1707, PR #1712, PR #1713)

htslib release 1.18:

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)

1.17

Download the source code here: htslib-1.17.tar.bz2.(The "Source code" downloads are generated by GitHub and are incomplete as they are missing some generated files.)

• A new API for iterating through a BAM record's aux field. (PR #1354, addresses #1319. Thanks to John Marshall)

• Text mode for bgzip. Allows bgzip to compress lines of text with block breaks at newlines. (PR #1493, thanks to Mike Lin for the initial version PR #1369)

• Make tabix support CSI indices with large positions. Unlike SAM and VCF files, BED files do not set a maximum reference length which hindered CSI support. This change sets an arbitrary large size of 100G to enable it to work. (PR #1506)

• Add a fai_line_length function. Exposes the internal line-wrap length. (PR #1516)

• Check for invalid barcode tags in fastq output. (PR #1518, fixes samtools/samtools#1728. Reported by Poshi)

• Warn if reference found in a CRAM file is not contained in the specified reference file. (PR #1517 and PR #1521, adds diagnostics for #1515. Reported by Wei WeiDeng)

• Add a faidx_seq_len64 function that can return sequence lengths longer than INT_MAX. At the same time limit faidx_seq_len to INT_MAX output. Also add a fai_adjust_region to ensure given ranges do not go beyond the end of the requested sequence. (PR #1519)

• Add a bcf_strerror function to give text descriptions of BCF errors. (PR #1510)

• Add CRAM SQ/M5 header checking when specifying a fasta file. This is to prevent creating a CRAM that cannot be decoded again. (PR #1522. In response to samtools/samtools#1748 though not a direct fix)

• Improve support for very long input lines (> 2Gbyte). This is mostly useful for tabix which does not do much interpretation of its input. (PR #1542, a partial fix for #1539)

• Speed up load_ref_portion. This function has been sped up by about 7x, which speeds up low-depth CRAM decoding by about 10%. (PR #1551)

• Expand CRAM API to cope with new samtools cram_size command. (PR #1546)

• Merges neighbouring I and D ops into one op within pileup. This means 4M1D1D1D3M is reported as 4M3D3M. Fixing this in sam.c means not only is samtools mpileup now looking better, but any tool using the mpileup API will be getting consistent results. (PR #1552, fixes the last remaining part of samtools/samtools#139)

• Update the API documentation for bgzf_mt as it refered to a previous iteration. (PR #1556, fixes #1553. Reported by Raghavendra Padmanabhan)

Build changes

• Use POSIX grep in testing as egrep and fgrep are considered obsolete. (PR #1509, thanks to David Seifert)

• Switch to building libdefalte with cmake for Cirris CI. (PR #1511)

• Ensure strings in config_vars.h are escaped correctly. (PR #1530, fixes #1527. Reported by Lucas Czech)

• Easier modification of shared library permissions during install. (PR #1532, fixes #1525. Reported by StephDC)

• Fix build on ancient compilers. Added -std=gnu90 to build tests so older C compilers will still be happy. (PR #1524, fixes #1523. Reported by Martin Jakt)

• Switch MacOS CI tests to an ARM-based image. (PR #1536)

• Cut down the number of embed_ref=2 tests that get run. (PR #1537)

• Add symbol versions to libhts.so. This is to aid package developers. (PR #1560 addresses #1505, thanks to John Marshall. Reported by Stefan Bruens)

• htscodecs now updated to v1.4.0. (PR #1563)

• Cleaned up misleading system error reports in test_bgzf. (PR #1565)
  Bug fixes

Bug fixes

• VCF. Fix n-squared complexity in sample line with many adjacent tabs [fuzz]. (PR #1503)

• Improved bcftools detection and reporting of bgzf decode errors. (PR #1504, thanks to Lilian Janin. PR #1529 thanks to Bergur Ragnarsson, fixes #1528. PR #1554)

• Prevent crash when the only FASTA entry has no sequence [fuzz]. (PR #1507)

• Fixed typo in sam.h documentation. (PR #1512, thanks to kojix2)

• Fix buffer read-overrun in bam_plp_insertion_mod. (PR #1520)

• Fix hash keys being left behind by bcf_hdr_remove. (PR #1535, fixes #1533. Reported by Giulio Genovese in #842)

• Make bcf_hdr_idinfo_exists more robust by checking id value exists. (PR #1544, fixes #1538. Reported by Giulio Genovese)

• CRAM improvements. Fixed crash with multi-threaded CRAM. Fixed a bug in the codec parameter learning for CRAM 3.1 name tokeniser. Fixed Cram compression container substitution matrix generation, (PR #1558, PR #1559 and PR #1562)

1.16

Download the source code here: htslib-1.16.tar.bz2.(The "Source code" downloads are generated by GitHub and are incomplete as they are missing some generated files.)

• Make hfile_s3 refresh AWS credentials on expiry in order to make HTSlib work better with AWS IAM credentials, which have a limited lifespan. (PR #1462 and PR #1474, addresses #344)

• Allow BAM headers between 2GB and 4GB in size once more. This is not permitted in the BAM specification but was allowed in an earlier version of HTSlib. There is now a warning at 2GB and a hard failure at 4GB. (PR #1421, fixes #1420 and samtools/samtools#1613. Reported by John Marshall and R C Mueller)

• Improve error message when failing to load an index. (PR #1468, example of the problem samtools/samtools#1637)

• Permit MM (base modification) tags containing . and ? suffixes. These define implicit vs explicit coordinates. See the SAM tags specification for details. (PR #1423 and PR #1426, fixes #1418. PR #1469, fixes #1466. Reported by cjw85)

• Warn if spaces instead of tabs are detected in a VCF file to prevent confusion. (PR #1328, fixes bcftools#1575. Reported by ketkijoshi278)

• Add an sclen filter expression keyword. This is the length of a soft-clip, both left and right end. It may be combined with qlen (qlen-sclen) to obtain the number of bases in the query sequence that have been aligned to the genome ie it provides a way to compare local-alignment vs global-alignment length. (PR #1441 and PR samtools/samtools#1661, fixes #1436. Requested by Chang Y)

• Improve error messages for CRAM reference mismatches. If the user specifies the wrong reference, the CRAM slice header MD5sum checks fail. We now report the SQ line M5 string too so it is possible to validate against the whole chr in the ref.fa file. The error message has also been improved to report the reference name instead of #num. Finally, we now hint at the likely cause, which counters the misleading samtools supplied error of "truncated or corrupt" file. (PR #1427, fixes samtools/samtools#1640. Reported by Jian-Guo Zhou)

• Expose more of the CRAM API and add new functionality to extract the reference from a CRAM file. (PR #1429 and PR #1442)

• Improvements to the implementation of embedded references in CRAM where no external reference is specified. (PR #1449, addresses some of the issues in #1445)

• The CRAM writer now allows alignment records with RG:Z: aux tags that don't have a corresponding @RG ID in the file header. Previously these tags would have been silently dropped. HTSlib will complain whenever it has to add one though, as such tags do not conform to recommended practice for the SAM, BAM and CRAM formats. (PR #1480, fixes #1479. Reported by Alex Leonard)

• Set tab delimiter in man page for tabix GFF3 sort. (PR #1457. Thanks to Colin Diesh)

• When using libdeflate, the 1...9 scale of BGZF compression levels is now remapped to the 1...12 range used by libdeflate instead of being passed directly. In particular, HTSlib levels 8 and 9 now map to libdeflate levels 10 and 12, so it is possible to select the highest (but slowest) compression offered by libdeflate. (PR #1488, fixes #1477. Reported by Gert Hulselmans)

• The VCF variant API has been extended so that it can return separate flags for INS and DEL variants as well as the existing INDEL one. These flags have not been added to the old bcf_get_variant_types() interface as it could break existing users. To access them, it is necessary to use new functions bcf_has_variant_type() and bcf_has_variant_types(). (PR #1467)

• The missing, but trivial, le_to_u8() function has been added to hts_endian. (PR #1494, Thanks to John Marshall)

• bcf_format_gt() now works properly on big-endian platforms. (PR #1495, Thanks to John Marshall)

Build changes

These are compiler, configuration and makefile based changes.

• Update htscodecs to version 1.3.0 for new SIMD code + various fixes. Updates the htscodecs submodule and adds changes necessary to make HTSlib build the new SIMD codec implementations. (PR #1438, PR #1489, PR #1500)

• Fix clang builds under mingw. Under mingw, clang requires dllexport to be applied to both function declarations and function definitions. (PR #1435, PR #1497, PR #1498 fixes #1433. Reported by teepean)

• Fix curl type warning with gcc 12.1 on Windows. (PR #1443)

• Detect ARM Neon support and only build appropriate SIMD object files. (PR #1451, fixes #1450. Thanks to John Marshall)

• make print-config now reports extra CFLAGS that are needed to build the SIMD parts of htscodecs. These may be of use to third-party build systems that don't use HTSlib's or htscodecs' build infrastructure. (PR #1485. Thanks to John Marshall)

• Fixed some Makefile dependency issues for the check/test targets and plugins. In particular, make check will now build the all target, if not done already, before running the tests. (PR #1496)

Bug fixes

• Fix bug when reading position -1 in BCF (0 in VCF), which is used to indicate telomeric regions. The BCF reader was incorrectly assuming the value stored in the file was unsigned, so a VCF->BCF->VCF round-trip would change it from 0 to 4294967296. (PR #1476, fixes #1475 and bcftools#1753. Reported by Rodrigo Martin)

• Various bugs and quirks have been fixed in the filter expression engine, mostly related to the handling of absent tags, and the is_true flag. Note that as a result of these fixes, some filter expressions may give different results:

  • Fixed and-expressions including aux tag values which could give an invalid true result depending on the order of terms.
  • The expression ![NM] is now true if only NM does not exist. In earlier versions it would also report true for tags like NM:i:0 which exist but have a value of zero.
  • The expression [X1] != 0 is now false when X1 does not exist. Earlier versions would return true for this comparison when the tag was missing.
  • NULL values due to missing tags now propagate through string, bitwise and mathematical operations. Logical operations always treat them as false. (PR #1463, fixes samtools/samtools#1670. Reported by Gert Hulselmans; PR #1478, fixes samtools/samtools#1677. Reported by johnsonzcode)

• Fix buffer overrun in bam_plp_insertion_mod. Memory now grows to the proper size needed for base modification data. (PR #1430, fixes samtools/samtools#1652. Reported by hd2326)

• Remove limit of returned size from fai_retrieve(). (PR #1446, fixes samtools/samtools#1660. Reported by Shane McCarthy)

• Cap hts_getline() return value at INT_MAX. Prevents hts_getline() from returning a negative number (a fail) for very long string length values. (PR #1448. Thanks to John Marshall)

• Fix breakend detection and test bcf_set_variant_type(). (PR #1456, fixes #1455. Thanks to Martin Pollard)

• Prevent arrays of BCF_BT_NULL values found in BCF files from causing bcf_fmt_array() to call exit() as the type is unsupported. These are now tested for and caught by bcf_record_check(), which returns an error code instead. (PR #1486)

• Improved detection of fasta and fastq files that have very long comments following identifiers. (PR #1491, thanks to John Marshall. Fixes samtools/samtools#1689, reported by cjw85)

• Fixed a SEGV triggered by giving a SAM file to samtools import. (PR #1492)

1.15.1

Download the source code here: htslib-1.15.1.tar.bz2.(The "Source code" downloads are generated by GitHub and are incomplete as they are missing some generated files.)

• Security fix: Fixed broken error reporting in the sam_cap_mapq() function, due to a missing hts_log() parameter. Prior to this fix it was possible to abuse the log message format string by passing a specially crafted alignment record to this function. (PR#1406)

• HTSlib now uses libhtscodecs release 1.2.2. This fixes a number of bugs where invalid compressed data could trigger usage of uninitialised values. (PR#1416)

• Fixed excessive memory used by multi-threaded SAM output on long reads. (Part of PR#1384)

• Fixed a bug where tabix would misinterpret region specifiers starting at position 0. It will also now warn if the file being indexed is supposed to be 1-based but has positions less than or equal to 0. (PR#1411)

• The VCF header parser will now issue a warning if it finds an INFO header with Type=Flag but Number not equal to 0. It will also ignore the incorrect Number so the flag can be used. (PR#1415)

1.15

Download the source code here: htslib-1.15.tar.bz2.(The "Source code" downloads are generated by GitHub and are incomplete as they are missing some generated files.)

Features and Updates

• Bgzip now has a --keep option to not remove the input file after compressing. (PR #1331)

• Improved file format detection so some BED files are no longer detected as FASTQ or FASTA. (PR #1350, thanks to John Marshall)

• Added xz (lzma), zstd and D4 formats to the file type detection functions. We don't actively support reading these data types, but function calls and htsfile can detect them. (PR #1340, thanks to John Marshall)

• CRAM now also uses libdeflate for read-names if the libdeflate version is new enough (1.9 onwards). Previously we used zlib for this due to poor performance of libdeflate. This gives a slight speed up and reduction in file size. (PR #1383)

• The VCF and BCF readers will now issue a warning if contig, INFO or FORMAT IDs do not match the formats described in the VCFv4.3 specification. Note that while the invalid names will mostly still be accepted, future updates will convert the warnings to errors causing files including invalid names to be rejected. (PR #1389)

Build changes

These are compiler, configuration and makefile based changes.

• HTSlib now uses libhtscodecs release 1.2.1.

• Improved support for compiling and linking against HTSlib with Microsoft Visual Studio. (PR #1380, #1377, #1375. Thanks to Aidan Bickford and John Marshall)

• Various internal CI improvements.

Bug fixes

• Fixed CRAM index queries for HTSJDK output (PR #1388, reported by Chris Norman). Note this also fixes writing CRAM writing, to match the specification (and HTSJDK), from version 3.1 onwards.

• Fixed CRAM index queries when required-fields settings are selected to ignore CIGARs (PR #1372, reported by Giulio Genovese).

• Unmapped but placed (having chr/pos) are now included in the BAM indices. (PR #1352, thanks to John Marshall)

• CRAM now honours the filename##idx##index nomenclature for specifying non-standard index locations. (PR #1360, reported by Michael Cariaso)

• Minor CRAM v1.0 read-group fix (PR #1349, thanks to John Marshall)

• Permit .fa and .fq file type detection as synonyms for FASTA and FASTQ. (PR#1386).

• Empty VCF format fields are now output ":.:" as instead of "::". (PR #1370)

• Repeated bcf_sr_seek calls now work. (PR #1363, reported by Giulio Genovese)

• bcf_remove_allele_set now works on unpacked BCF records. (PR #1358, reported by Brent Pedersen).

• The hts_parse_decimal() function used to read numbers in region lists is now better at rejecting non-numeric values. In particular it now rejects a lone 'G' instead of interpreting it as '0G', i.e. zero. (PR #1396, PR #1400, reported by SSSimon Yang; thanks to John Marshall).

• Improve support for GPU issues listed by -Wdouble-promotion. (PR #1365, reported by David Seisert)

• Fix example code in header file documentation. (PR #1381, Thanks to Aidan Bickford)

1.14

Download the source code here: htslib-1.14.tar.bz2.(The "Source code" downloads are generated by GitHub and are incomplete as they are missing some generated files.)

Features and Updates

• Added a keep option to bgzip to leave the original file untouched. This brings bgzip into line with gzip. (PR #1331, thanks to Alex Petty)

• endpos has been added to the filter language, giving the position of the rightmost mapped base as measured by the CIGAR string. For unmapped reads it is the same as pos. (PR #1307, thanks to John Marshall)

• Interfaces have been added to interpret the new base modification tags added to the SAMtags document in samtools/hts-specs#418. (PR #1132)

• New API functions hts_flush()/sam_flush()/bcf_flush() for flushing output htsFile/samFile/vcfFile streams. (PR #1326, thanks to John Marshall)

• The synced_bcf_reader now sorts lines with symbolic alleles by END tag as well as POS. (PR #1321)

• Added synced_bcf_reader options BCF_SR_REGIONS_OVERLAP and BCF_SR_TARGETS_OVERLAP for better control of records that start outside the desired region but overlap it are handled. Fixes samtools/bcftools#1420 and samtools/bcftools#1421 raised by John Marshall. (PR #1327)

• HTSlib will now accept long-cigar CG:B: tags made by htsjdk which don't quite follow the specification properly (using signed values instead of unsigned). Thanks to Colin Diesh for reporting an example file. (PR #1317)

• The warning printed when the BGZF reader finds a file with no EOF block has been changed to be less alarming. Unfortunately some third-party BGZF encoders don't write EOF blocks at the end of files. Thanks to Keiran Raine for reporting an example file. (PR #1323)

• The FASTA and FASTQ readers get an option to skip over the first item on the header line, and use the second as the read name. It allows the original name to be restored on some of the fastq files served from the European Nucleotide Archive. (PR #1325)

• HTSlib is now more strict when parsing the VCF samples line (beginning #CHROM). It will only accept tabs between the mandatory field names and sample names must be separated with tabs. (PR #1328)

• HTSlib will now warn if it looks like the header has been corrupted by diagnostic messages from the program that made it. This can happen when using nohup, which by default mixes stdout and stderr into the same stream. (PR#1339, thanks to John Marshall)

• File format detection will now recognise signatures for XZ, Zstd and D4 files (note that HTSlib will not read them yet). (PR #1340, thanks to John Marshall)

Build changes

These are compiler, configuration and makefile based changes.

• Some redundant tests have been removed from the test harness, speeding it up. (PR #1308)

• The version.sh script now works better on shallow checkouts. (PR #1324)

• A check-untracked Makefile target has been added to catch untracked files (mostly) left by the test harness. (PR #1324)

Bug fixes

• Fixed a case where flushing the thread pool could very occasionally cause a deadlock. (PR #1309)

• Fixed a bug where some CRAM files could fail to decode if the required_fields option was in use. Thanks to Matt Sexton for reporting the issue. (PR #1314, fixes samtools/samtools#1475)

• Fixed a regression where the S3 plugin could not read public files unless you supplied some Amazon credentials. Thanks to Chris Saunders for reporting. (PR #1332, fixes samtools/samtools#1491)

• Fixed a possible CRAM thread deadlock discovered by Ryan Cai. (PR #1330, fixes #1329)

• Some set-but-unused variables have been removed. (PR #1334)

• Fixed a bug which prevented flag.read2 from working in the filter language unless it was at the end of the expression. Thanks to Vamsi Kodali for reporting the issue. (PR #1342)

• Fixed a memory leak that could happen if CRAM fails to inflate a LZMA block. (PR #1340, thanks to John Marshall)