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Init
2025-04-17 16:17:44 +08:00
Noteworthy changes in release 1.21 (12th September 2024)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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)
Noteworthy changes in release 1.20 (15th April 2024)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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)
Noteworthy changes in release 1.19.1 (22nd January 2024)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* 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#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)
Noteworthy changes in release 1.19 (12th December 2023)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 https://github.com/samtools/hts-specs/pull/434).
(PR #1689)
* 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 samtools#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 samtools#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)
Noteworthy changes in release 1.18 (25th July 2023)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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)
Noteworthy changes in release 1.17 (21st February 2023)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* 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#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#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#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
---------
* 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)
Noteworthy changes in release 1.16 (18th August 2022)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* 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#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#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#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#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#1670. Reported by Gert Hulselmans;
PR#1478, fixes 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#1652. Reported by hd2326)
* Remove limit of returned size from fai_retrieve().
(PR#1446, fixes 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)
Noteworthy changes in release 1.15.1 (7th April 2022)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* Security fix: Fixed broken error reporting in the sam_prob_realn()
function, due to a missing hts_log() parameter. Prior to this fix
(i.e., in HTSlib versions 1.8 to 1.15) 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)
Noteworthy changes in release 1.15 (21st February 2022)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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)
Noteworthy changes in release 1.14 (22nd October 2021)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 (ENA). (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 @ryancaicse.
(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)
Noteworthy changes in release 1.13 (7th July 2021)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Features and Updates
--------------------
* In case a PG header line has multiple ID tags supplied by other applications,
the header API now selects the first one encountered as the identifying tag
and issues a warning when detecting subsequent ID tags.
(#1256; fixed samtools/samtools#1393)
* VCF header reading function (vcf_hdr_read) no longer tries to download a
remote index file by default.
(#1266; fixes #380)
* Support reading and writing FASTQ format in the same way as SAM, BAM or CRAM.
Records read from a FASTQ file will be treated as unmapped data.
(#1156)
* Added GCP requester pays bucket access. Thanks to @indraniel.
(#1255)
* Made mpileup's overlap removal choose which copy to remove at random instead
of always removing the second one. This avoids strand bias in experiments
where the +ve and -ve strand reads always appear in the same order.
(#1273; fixes samtools/bcftools#1459)
* It is now possible to use platform specific BAQ parameters. This also
selects long-read parameters for read lengths bigger than 1kb, which helps
bcftools mpileup call SNPs on PacBio CCS reads.
(#1275)
* Improved bcf_remove_allele_set. This fixes a bug that stopped iteration over
alleles prematurely, marks removed alleles as 'missing' and does automatic
lazy unpacking.
(#1288; fixes #1259)
* Improved compression metrics for unsorted CRAM files. This improves the
choice of codecs when handling unsorted data.
(#1291)
* Linear index entries for empty intervals are now initialised with the file
offset in the next non-empty interval instead of the previous one. This
may reduce the amount of data iterators have to discard before reaching
the desired region, when the starting location is in a sequence gap.
Thanks to @carsonh for reporting the issue.
(#1286; fixes #486)
* A new hts_bin_level API function has been added, to compute the level of a
given bin in the binning index.
(#1286)
* Related to the above, a new API method, hts_idx_nseq, now returns the total
number of contigs from an index.
(#1295 and #1299)
* Added bracket handling to bcf_hdr_parse_line, for use with ##META lines.
Thanks to Alberto Casas Ortiz.
(#1240)
Build changes
-------------
These are compiler, configuration and makefile based changes.
* HTSlib now uses libhtscodecs release 1.1.1.
* Added a curl/curl.h check to configure and improved INSTALL documentation on
build options. Thanks to Melanie Kirsche and John Marshall.
(#1265; fixes #1261)
* Some fixes to address GCC 11.1 warnings.
(#1280, #1284, #1285; fixes #1283)
* Supports building HTSlib in a separate directory. Thanks to John Marshall.
(#1277; fixes #231)
* Supports building HTSlib on MinGW 32-bit environments. Thanks to
John Marshall.
(#1301)
Bug fixes
---------
* Fixed hts_itr_query() et al region queries: fixed bug introduced in
HTSlib 1.12, which led to iterators producing very few reads for some
queries (especially for larger target regions) when unmapped reads were
present. HTSlib 1.11 had a related problem in which iterators would omit
a few unmapped reads that should have been produced; cf #1142.
Thanks to Daniel Cooke for reporting the issue.
(#1281; fixes #1279)
* Removed compressBound assertions on opening bgzf files. Thanks to
Gurt Hulselmans for reporting the issue.
(#1258; fixed #1257)
* Duplicate sample name error message for a VCF file now only displays the
duplicated name rather the entire same name list.
(#1262; fixes samtools/bcftools#1451)
* Fix to make samtools cat work on CRAMs again.
(#1276; fixes samtools/samtools#1420)
* Fix for a double memory free in SAM header creation. Thanks to @ihsineme.
(#1274)
* Prevent assert in bcf_sr_set_regions. Thanks to Dr K D Murray.
(#1270)
* Fixed crash in knet_open() etc stubs. Thanks to John Marshall.
(#1289)
* Fixed filter expression "cigar" on unmapped reads. Stop treating an empty
CIGAR string as an error. Thanks to Chang Y for reporting the issue.
(#1298, fixes samtools/samtools#1445)
* Bug fixes in the bundled copy of htscodecs:
- Fixed an uninitialized access in the name tokeniser decoder.
(samtools/htscodecs#23)
- Fixed a bug with name tokeniser and variable number of names per slice,
causing it to incorrectly report an error on certain valid inputs.
(samtools/htscodecs#24)
Noteworthy changes in release 1.12 (17th March 2021)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Features and Updates
--------------------
* Added experimental CRAM 3.1 and 4.0 support. (#929)
These should not be used for long term data storage as the
specification still needs to be ratified by GA4GH and may be subject
to changes in format. (This is highly likely for 4.0). However it
may be tested using:
test/test_view -t ref.fa -C -o version=3.1 in.bam -p out31.cram
For smaller but slower files, try varying the compression profile
with an additional "-o small". Profile choices are fast, normal,
small and archive, and can be applied to all CRAM versions.
* Added a general filtering syntax for alignment records in SAM/BAM/CRAM
readers. (#1181, #1203)
An example to find chromosome spanning read-pairs with high mapping
quality: 'mqual >= 30 && mrname != rname'
To find significant sized deletions:
'cigar =~ "[0-9]{2}D"' or 'rlen - qlen > 10'.
To report duplicates that aren't part of a "proper pair":
'flag.dup && !flag.proper_pair'
More details are in the samtools.1 man page under "FILTER EXPRESSIONS".
* The knet networking code has been removed. It only supported the http
and ftp protocols, and a better and safer alternative using libcurl
has been available since release 1.3. If you need access to ftp:// and
http:// URLs, HTSlib should be built with libcurl support. (#1200)
* The old htslib/knetfile.h interfaces have been marked as deprecated. Any
code still using them should be updated to use hFILE instead. (#1200)
* Added an introspection API for checking some of the capabilities provided
by HTSlib. (#1170) Thanks also to John Marshall for contributions. (#1222)
- `hfile_list_schemes`: returns the number of schemes found
- `hfile_list_plugins`: returns the number of plugins found
- `hfile_has_plugin`: checks if a specific plugin is available
- `hts_features`: returns a bit mask with all available features
- `hts_test_feature`: test if a feature is available
- `hts_feature_string`: return a string summary of enabled features
* Made performance improvements to `probaln_glocal` method, which
speeds up mpileup BAQ calculations. (#1188)
- Caching of reused loop variables and removal of loop invariants
- Code reordering to remove instruction latency.
- Other refactoring and tidyups.
* Added a public method for constructing a BAM record from the
component pieces. Thanks to Anders Kaplan. (#1159, #1164)
* Added two public methods, `sam_parse_cigar` and `bam_parse_cigar`, as part of
a small CIGAR API (#1169, #1182). Thanks to Daniel Cameron for input. (#1147)
* HTSlib, and the included htsfile program, will now recognise the old
RAZF compressed file format. Note that while the format is detected,
HTSlib is unable to read it. It is recommended that RAZF files are
uncompressed with `gunzip` before using them with HTSlib. Thanks to
John Marshall (#1244); and Matthew J. Oldach who reported problems
with uncompressing some RAZF files (samtools/samtools#1387).
* The S3 plugin now has options to force the address style. It will recognise
the addressing_style and host_bucket entries in the respective aws
.credentials and s3cmd .s3cfg files. There is also a new HTS_S3_ADDRESS_STYLE
environment variable. Details are in the htslib-s3-plugin.7 man file (#1249).
Build changes
-------------
These are compiler, configuration and makefile based changes.
* Added new Makefile targets for the applications that embed HTSlib and
want to run its test suite or clean its generated artefacts. (#1230, #1238)
* The CRAM codecs are now obtained via the htscodecs submodule, hence
when cloning it is now best to use "git clone --recursive". In an
existing clone, you may use "git submodule update --init" to obtain
the htscodecs submodule checkout.
* Updated CI test configuration to recurse HTSlib submodules. (#1359)
* Added Cirrus-CI integration as a replacement for Travis, which was
phased out. (#1175; #1212)
* Updated the Windows image used by Appveyor to 'Visual Studio 2019'. (#1172;
fixed #1166)
* Fixed a buglet in configure.ac, exposed by the release 2.70 of autoconf.
Thanks to John Marshall. (#1198)
* Fixed plugin linking on macOS, to prevent symbol conflict when linking
with a static HTSlib. Thanks to John Marshall. (#1184)
* Fixed a clang++9 error in `cram_io.h`. Thanks to Pjotr Prins. (#1190)
* Introduced $(ALL_CPPFLAGS) to allow for more flexibility in setting the
compiler flags. Thanks to John Marshall. (#1187)
* Added 'fall through' comments to prevent warnings issued by Clang on
intentional fall through case statements, when building with
`-Wextra flag`. Thanks to John Marshall. (#1163)
* Non-configure builds now define _XOPEN_SOURCE=600 to allow them to work
when the `gcc -std=c99` option is used. Thanks to John Marshall. (#1246)
Bug fixes
---------
* Fixed VCF `#CHROM` header parsing to only separate columns at tab characters.
Thanks to Sam Morris for reporting the issue.
(#1237; fixed samtools/bcftools#1408)
* Fixed a crash reported in `bcf_sr_sort_set`, which expects REF to be present.
(#1204; fixed samtools/bcftools#1361)
* Fixed a bcf synced reader bug when filtering with a region list, and
the first record for a chromosome had the same position as the last
record for the previous chromosome. (#1254; fixed samtools/bcftools#1441)
* Fixed a bug in the overlapping logic of mpileup, dealing with iterating over
CIGAR segments. Thanks to `@wulj2` for the analysis. (#1202; fixed #1196)
* Fixed a tabix bug that prevented setting the correct number of lines to be
skipped in a region file. Thanks to Jim Robinson for reporting it. (#1189;
fixed #1186)
* Made `bam_itr_next` an alias for `sam_itr_next`, to prevent it from crashing
when working with htsFile pointers. Thanks to Torbjörn Klatt for
reporting it. (#1180; fixed #1179)
* Fixed once per outgoing multi-threaded block `bgzf_idx_flush` assertion, to
accommodate situations when a single record could span multiple blocks.
Thanks to `@lacek`. (#1168; fixed samtools/samtools#1328)
* Fixed assumption of pthread_t being a non-structure, as permitted by POSIX.
Thanks also to John Marshall and Anders Kaplan. (#1167, #1153, #1153)
* Fixed the minimum offset of a BAI index bin, to account for unmapped reads.
Thanks to John Marshall for spotting the issue. (#1158; fixed #1142)
* Fixed the CRLF handling in `sam_parse_worker` method. Thanks to
Anders Kaplan. (#1149; fixed #1148)
* Included unistd.h and errno.h directly in HTSlib files, as opposed to
including them indirectly, via third party code. Thanks to
Andrew Patterson (#1143) and John Marshall (#1145).
Noteworthy changes in release 1.11 (22nd September 2020)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Features and Updates
--------------------
* Support added for remote reference files. fai_path() can take a remote
reference file and will return the corresponding index file. Remote indexes
can be handled by refs_load_fai(). UR tags in @SQ lines can now be set to
remote URIs. (#1017)
* Added tabix --separate-regions option, which adds header comment lines
separating different regions' output records when multiple target regions
are supplied on the command line. (#1108)
* Added tabix --cache option to set a BGZF block cache size. Most beneficial
when the -R option is used and the same blocks need to be re-read multiple
times. (#1053)
* Improved error checking in tabix and added a --verbosity option so
it is possible to change the amount of logging when it runs. (#1040)
* A note about the maximum chromosome length usable with TBI indexes has been
added to the tabix manual page. Thanks to John Marshall. (#1070)
* New method vcf_open_mode() changes the opening mode of a variant file
based on its file extension. Similar to sam_open_mode(). (#1096)
* The VCF parser has been made faster and easier to maintain. (#1057)
* bcf_record_check() has been made faster, giving a 15% speed increase when
reading an uncompressed BCF file. (#1130)
* The VCF parser now recognises the "<NON_REF>" symbolic allele produced
by GATK. (#1045)
* Support has been added for simultaneous reading of unindexed VCF/BCF files
when using the synced_bcf_reader interface. Input files must have the
chromosomes in the same order as each other and be consistent with the order
of sequences in the header. (#1089)
* The VCF and BCF readers will now attempt to fix up invalid INFO/END tags
where the stored END value is less than POS, resulting in an apparently
negative record length. Such files have been generated by programs which
used END incorrectly, and by broken lift-over processes that failed to
update any END tags present. (#1021; fixed samtools/bcftools#1154)
* The htsFile interface can now detect the crypt4gh encrypted format (see
https://samtools.github.io/hts-specs/crypt4gh.pdf). If HTSlib is
built with external plug-in support, and the hfile_crypt4gh plug-in is
present, the file will be passed to it for decryption. The plug-in
can be obtained from https://github.com/samtools/htslib-crypt4gh. (#1046)
* hts_srand48() now seeds the same POSIX-standard sequences of pseudo-random
numbers regardless of platform, including on OpenBSD where plain srand48()
produces a different cryptographically-strong non-deterministic sequence.
Thanks to John Marshall. (#1002)
* Iterators now work with 64 bit positions. (#1018)
* Improved the speed of range queries when using BAI indexes by
making better use of the linear index data included in the file.
The best improvement is on low-coverage data. (#1031)
* Alignments which consume no reference bases are now considered to have
length 1. This would make such alignments cover 1 reference position in
the same manner as alignments that are unmapped or have no CIGAR strings.
These alignments can now be returned by iterator-based queries. Thanks
to John Marshall. (#1063; fixed samtools/samtools#1240, see also
samtools/hts-specs#521).
* A bam_set_seqi() function to modify a single base in the BAM structure
has been added. This is a companion function to bam_seqi(). (#1022)
* Writing SAM format is around 30% faster. (#1035)
* Added sam_format_aux1() which converts a BAM aux tag to a SAM format string.
(#1134)
* bam_aux_update_str() no longer requires NUL-terminated strings. It
is also now possible to create tags containing part of a longer string.
(#1088)
* It is now possible to use external plug-ins in language bindings that
dynamically load HTSlib. Note that a side-effect of this change is that
some plug-ins now link against libhts.so, which means that they have to be
able to find the shared library when they are started up. Thanks to
John Marshall. (#1072)
* bgzf_close(), and therefore hts_close(), will now return non-zero when
closing a BGZF handle on which errors have been detected. (Part of #1117)
* Added a special case to the kt_fisher_exact() test for when the table
probability is too small to be represented in a double. This fixes a
bug where it would, for some inputs, fail to correctly determine which
side of the distribution the table was on resulting in swapped p-values
being returned for the left- and right-tailed tests. The two-tailed
test value was not affected by this problem. (#1126)
* Improved error diagnostics in the CRAM decoder (#1042), BGZF (#1049),
the VCF and BCF readers (#1059), and the SAM parser (#1073).
* ks_resize() now allocates 1.5 times the requested size when it needs
to expand a kstring instead of rounding up to the next power of two.
This has been done mainly to make the inlined function smaller, but it
also reduces the overhead of storing data in kstrings at the expense of
possibly needing a few more reallocations. (#1129)
CRAM improvements
-----------------
* Delay CRAM crc32 checks until the data actually needs to be used. With
other changes this leads to a 20x speed up in indexing and other sub-query
based actions. (#988)
* CRAM now handles the transition from mapped to unmapped data in a better
way, improving compression of the unmapped data. (#961)
* CRAM can now use libdeflate. (#961)
* Fixed bug in MD tag generation with "b" read feature codes, causing the
numbers in the tag to be too large. Note that HTSlib never uses this
feature code so it is unlikely that this bug would be seen on real data.
The problem was found when testing against hand-crafted CRAM files. (#1086)
* Fixed a regression where the CRAM multi-region iterator became much less
efficient when using threads. It now works more like the single iterator
and does not preemptively decode the next container unless it will be used.
(#1061)
* Set CRAM default quality in lossy quality modes. If lossy quality is enabled
and 'B', 'q' or 'Q' features are used, CRAM starts off with QUAL being all 255
(as per BAM spec and "*" quality) and then modifies individual qualities as
dictated by the specific features.
However that then produces ASCII quality " " (space, q=-1) for the unmodified
bases. Instead ASCII quality "?" (q=30) is used, as per HTSJDK. Quality 255
is still used for sequences with no modifications at all. (#1094)
Build changes
-------------
These are compiler, configuration and makefile based changes.
* `make all` now also builds htslib_static.mk and htslib-uninstalled.pc.
Thanks to John Marshall. (#1011)
* Various cppcheck-1.90 warnings have been fixed. (#995, #1011)
* HTSlib now prefers its own headers when being compiled, fixing build
failures on machines that already had a system-installed HTSlib. Thanks to
John Marshall. (#1078; fixed #347)
* Define HTSLIB_EXPORT without using a helper macro to reduce the length of
compiler diagnostics that mention exported functions. Thanks to
John Marshall. (#1029)
* Fix dirty default build by including latest pkg.m4 instead of using
aclocal.m4. Thanks to Damien Zammit. (#1091)
* Struct tags have been added to htslib/*.h public typedefs. This makes it
possible to forward declare htsFile without including htslib/hts.h. Thanks
to Lucas Czech and John Marshall. (#1115; fixed #1106)
* Fixed compiler warnings emitted by the latest gcc and clang releases
when compiling HTSlib, along with some -Wextra warnings in the public
include files. Thanks to John Marshall. (#1066, #1063, #1083)
Bug fixes
---------
* Fixed hfile_libcurl breakage when using libcurl 7.69.1 or later. Thanks to
John Marshall for tracking down the exact libcurl change that caused the
incompatibility. (#1105; fixed samtools/samtools#1254 and
samtools/samtools#1284)
* Fixed overflows kroundup32() and kroundup_size_t() which caused them to
return zero when rounding up values where the most significant bit was
set. When this happens they now return the highest value that can
be stored (#1044). All of the kroundup macro definitions have also been
gathered together into a unified implementation (#1051).
* Fixed missing return parameter value in idx_test_and_fetch(). Thanks to
Lilian Janin. (#1014)
* Fixed crashes due to inconsistent selection between BGZF and plain (hFILE)
interfaces when reading files. [fuzz] (#1019)
* Added and/or fixed byte swapping code for big-endian platforms. Thanks
to Jun Aruga, John Marshall, Michael R Crusoe and Gianfranco Costamagna
for their help. (#1023; fixed #119 and #355)
* Fixed a problem with multi-threaded on-the-fly indexes which would
occasionally write virtual offsets pointing at the end of a BGZF block.
Attempting to read from such an offset caused EOF to be incorrectly
reported. These offsets are now handled correctly, and the indexer
has been updated to avoid generating them. (#1028; fixed
samtools/samtools#1197)
* In sam_hdr_create(), free newly allocated SN strings when encountering an
error. [fuzz] (#1034)
* Prevent double free in case of idx_test_and_fetch() failure. Thanks to
@fanwayne for the bug report. (#1047; fixed #1033)
* In the header, link a new PG line only to valid chains. Prevents an
explosive growth of PG lines on headers where PG lines are already present
but not linked together correctly. (#1062; fixed samtools/samtools#1235)
* Also in the header, when calling sam_hdr_update_line(), update target arrays
only when the name or length is changed. (#1007)
* Fixed buffer overflows in CRAM MD5 calculation triggered by
files with invalid compression headers, or files with embedded
references that were one byte too short. [fuzz] (#1024, #1068)
* Fix mpileup regression between 1.9 and 1.10 where overlap detection
was incorrectly skipped on reads where RNEXT, PNEXT and TLEN were
set to the "unavailable" values ("*", 0, 0 in SAM). (#1097)
* kputs() now checks for null pointer in source string. [fuzz] (#1087)
* Fix potential bcf_update_alleles() crash on 0 alleles. Thanks to
John Marshall. (#994)
* Added bcf_unpack() calls to some bcf_update functions to fix a bug
where updates made after a call to bcf_dup() could be lost. (#1032;
fixed #1030)
* Error message typo "Number=R" instead of "Number=G" fixed in
bcf_remove_allele_set(). Thanks to Ilya Vorontsov. (#1100)
* Fixed crashes that could occur in BCF files that use IDX= header annotations
to create a sparse set of CHROM, FILTER or FORMAT indexes, and
include records that use one of the missing index values. [fuzz] (#1092)
* Fixed potential integer overflows in the VCF parser and ensured that
the total length of FORMAT fields cannot go over 2Gbytes. [fuzz] (#1044,
#1104; latter is CVE-2020-36403 affecting all HTSlib versions up to 1.10.2)
* Download index files atomically in idx_test_and_fetch(). This prevents
corruption when running parallel jobs on S3 files. Thanks to John Marshall.
(#1112; samtools/samtools#1242).
* The pileup constructor callback is now given the copy of the bam1_t struct
made by pileup instead of the original one passed to bam_plp_push(). This
makes it the same as the one passed to the destructor and ensures that
cached data, for example the location of an aux tag, will remain valid.
(#1127)
* Fixed possible error in code_sort() on negative CRAM Huffman code
length. (#1008)
* Fixed possible undefined shift in cram_byte_array_stop_decode_init(). (#1009)
* Fixed a bug where range queries to the end of a given reference
would return incorrect results on CRAM files. (#1016;
fixed samtools/samtools#1173)
* Fixed an integer overflow in cram_read_slice(). [fuzz] (#1026)
* Fixed a memory leak on failure in cram_decode_slice(). [fuzz] (#1054)
* Fixed a regression which caused cram_transcode_rg() to fail, resulting
in a crash in "samtools cat" on CRAM files. (#1093;
fixed samtools/samtools#1276)
* Fixed an undersized string reallocation in the threaded SAM reader which
caused it to crash when reading SAM files with very long lines. Numerous
memory allocation checks have also been added. (#1117)
Noteworthy changes in release 1.10.2 (19th December 2019)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
This is a release fix that corrects minor inconsistencies discovered in
previous deliverables.
Noteworthy changes in release 1.10.1 (17th December 2019)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
The support for 64-bit coordinates in VCF brought problems for files
not conforming to VCF/BCF specification. While previous versions would
make out-of-range values silently overflow creating nonsense values
but parseable file, the version 1.10 would silently create an invalid BCF.
Noteworthy changes in release 1.10 (6th December 2019)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Brief summary
-------------
There are many changes in this release, so the executive summary is:
* Addition of support for references longer than 2Gb (NB: SAM and VCF
formats only, not their binary counterparts). This may need changes
in code using HTSlib. See README.large_positions.md for more information.
* Added a SAM header API.
* Major speed up to SAM reading and writing. This also now supports
multi-threading.
* We can now auto-index on-the-fly while writing a file. This also
includes to bgzipped SAM.gz.
* Overhaul of the S3 interface, which now supports version 4
signatures. This also makes writing to S3 work.
These also required some ABI changes. See below for full details.
Features / updates
------------------
* A new SAM/BAM/CRAM header API has been added to HTSlib, allowing header
data to be updated without having to parse or rewrite large parts of the
header text. See htslib/sam.h for function definitions and
documentation. (#812)
The header typedef and several pre-existing functions have been renamed
to have a sam_hdr_ prefix: sam_hdr_t, sam_hdr_init(), sam_hdr_destroy(),
and sam_hdr_dup(). (The existing bam_hdr_-prefixed names are still
provided for compatibility with existing code.) (#887, thanks to
John Marshall)
* Changes to hfile_s3, which provides support for the AWS S3 API. (#839)
- hfile_s3 now uses version 4 signatures by default. Attempting to write to
an S3 bucket will also now work correctly. It is possible to force
version 2 signatures by creating environment variable HTS_S3_V2 (the exact
value does not matter, it just has to exist). Note that writing depends
on features that need version 4 signatures, so forcing version 2 will
disable writes.
- hfile_s3 will automatically retry requests where the region endpoint
was not specified correctly, either by following the 301 redirect (when
using path-style requests) or reading the 400 response (when using
virtual-hosted style requests and version 4 signatures). The first
region to try can be set by using the AWS_DEFAULT_REGION environment
variable, by setting "region" in ".aws/credentials" or by setting
"bucket_location" in ".s3cfg".
- hfile_s3 now percent-escapes the path component of s3:// URLs. For
backwards-compatibility it will ignore any paths that have already
been escaped (detected by looking for '%' followed by two hexadecimal
digits.)
- New environment variables HTS_S3_V2, HTS_S3_HOST, HTS_S3_S3CFG
and HTS_S3_PART_SIZE to force version-2 signatures, control the
S3 server hostname, the configuration file and upload chunk
sizes respectively.
* Numerous SAM format improvements.
- Bgzipped SAM files can now be indexed and queried. The library now
recognises sam.gz as a format name to ease this usage. (#718, #916)
- The SAM reader and writer now supports multi-threading via the
thread-pool. (#916)
Note that the multi-threaded SAM reader does not currently support seek
operations. Trying to do this (for example with an iterator range request)
will result in the SAM readers dropping back to single-threaded mode.
- Major speed up of SAM decoding and encoding, by around 2x. (#722)
- SAM format can now handle 64-bit coordinates and references. This
has implications for the ABI too (see below). Note BAM and CRAM
currently cannot handle references longer than 2Gb, however given
the speed and threading improvements SAM.gz is a viable workaround. (#709)
* We can now automatically build indices on-the-fly while writing
SAM, BAM, CRAM, VCF and BCF files. (Note for SAM and VCF this only
works when bgzipped.) (#718)
* HTSlib now supports the @SQ-AN header field, which lists alternative names
for reference sequences. This means given "@SQ SN:1 AN:chr1", tools like
samtools can accept requests for "1" or "chr1" equivalently. (#931)
* Zero-length files are no longer considered to be valid SAM files
(with no header and no alignments). This has been changed so that pipelines
such as `somecmd | samtools ...` with `somecmd` aborting before outputting
anything will now propagate the error to the second command. (#721, thanks
to John Marshall; #261 reported by Adrian Tan)
* Added support for use of non-standard index names by pasting the
data filename and index filename with ##idx##. For example
"/path1/my_data.bam##idx##/path2/my_index.csi" will open bam file
"/path1/my_data.bam" and index file "/path2/my_index.csi". (#884)
This affects hts_idx_load() and hts_open() functions.
* Improved the region parsing code to handle colons in reference
names. Strings can be disambiguated by the use of braces, so for
example when reference sequences called "chr1" and "chr1:100-200"
are both present, the regions "{chr1}:100-200" and "{chr1:100-200}"
unambiguously indicate which reference is being used. (#708)
A new function hts_parse_region() has been added along with
specialisations for sam_parse_region() and fai_parse_region().
* CRAM encoding now has additional checks for MD/NM validity. If
they are incorrect, it stores the (incorrect copy) verbatim so
round-trips "work". (#792)
* Sped up decoding of CRAM by around 10% when the MD tag is being
generated. (#874)
* CRAM REF_PATH now supports %Ns (where N is a single digit)
expansion in http URLs, similar to how it already supported this
for directories. (#791)
* BGZF now permits indexing and seeking using virtual offsets in
completely uncompressed streams. (#904, thanks to Adam Novak)
* bgzip now asks for extra confirmation before decompressing files
that don't have a known compression extension (e.g. .gz). This avoids
`bgzip -d foo.bam.bai` producing a foo.bam file that is very much not
a BAM-formatted file. (#927, thanks to John Marshall)
* The htsfile utility can now copy files (including to/from URLs using
HTSlib's remote access facilities) with the --copy option, in
addition to its existing uses of identifying file formats and
displaying sequence or variant data. (#756, thanks to John Marshall)
* Added tabix --min-shift option. (#752, thanks to Garrett Stevens)
* Tabix now has an -D option to disable storing a local copy of a
remote index. (#870)
* Improved support for MSYS Windows compiler environment. (#966)
* External htslib plugins are now supported on Windows. (#966)
API additions and improvements
------------------------------
* New API functions bam_set_mempolicy() and bam_get_mempolicy() have
been added. These allow more control over the ownership of bam1_t
alignment record data; see documentation in htslib/sam.h for more
information. (#922)
* Added more HTS_RESULT_USED checks, this time for VCF I/O. (#805)
* khash can now hash kstrings. This makes it easier to hash
non-NUL-terminated strings. (#713)
* New haddextension() filename extension API function. (#788, thanks to
John Marshall)
* New hts_resize() macro, designed to replace uses of hts_expand()
and hts_expand0(). (#805)
* Added way of cleaning up unused jobs in the thread pool via the new
hts_tpool_dispatch3() function. (#830)
* New API functions hts_reglist_create() and sam_itr_regarray() are added
to create hts_reglist_t region lists from `chr:<from>-<to>` type region
specifiers. (#836)
* Ksort has been improved to facilitate library use. See KSORT_INIT2
(adds scope / namespace capabilities) and KSORT_INIT_STATIC interfaces.
(#851, thanks to John Marshall)
* New kstring functions (#879):
KS_INITIALIZE - Initializer for structure assignment
ks_initialize() - Initializer for pointed-to kstrings
ks_expand() - Increase kstring capacity by a given amount
ks_clear() - Set kstring length to zero
ks_free() - Free the underlying buffer
ks_c_str() - Returns the kstring buffer as a const char *,
or an empty string if the length is zero.
* New API functions hts_idx_load3(), sam_index_load3(), tbx_index_load3()
and bcf_index_load3() have been added. These allow control of whether
remote indexes should be cached locally, and allow the error message
printed when the index does not exist to be suppressed. (#870)
* Improved hts_detect_format() so it no longer assumes all text is
SAM unless positively identified otherwise. It also makes a stab
at detecting bzip2 format and identifying BED, FASTA and FASTQ
files. (#721, thanks to John Marshall; #200, #719 both reported by
Torsten Seemann)
* File format errors now set errno to EFTYPE (BSD, MacOS) when
available instead of ENOEXEC. (#721)
* New API function bam_set_qname (#942)
* In addition to the existing hts_version() function, which reflects the
HTSlib version being used at runtime, <htslib/hts.h> now also provides
HTS_VERSION, a preprocessor macro reflecting the HTSlib version that
a program is being compiled against. (#951, thanks to John Marshall; #794)
ABI changes
-----------
This release contains a number of things which change the Application
Binary Interface (ABI). This means code compiled against an earlier
library will require recompiling. The shared library soversion has
been bumped.
* On systems that support it, the default symbol visibility has been
changed to hidden and the only exported symbols are ones that form part
of the officially supported ABI. This is to make clear exactly which
symbols are considered parts of the library interface. It also
helps packagers who want to check compatibility between HTSlib versions.
(#946; see for example issues #311, #616, and #695)
* HTSlib now supports 64 bit reference positions. This means several
structures, function parameters, and return values have been made bigger
to allow larger values to be stored. While most code that uses
HTSlib interfaces should still build after this change, some alterations
may be needed - notably to printf() formats where the values of structure
members are being printed. (#709)
Due to file format limitations, large positions are only supported
when reading and writing SAM and VCF files.
See README.large_positions.md for more information.
* An extra field has been added to the kbitset_t struct so bitsets can
be made smaller (and later enlarged) without involving memory allocation.
(#710, thanks to John Marshall)
* A new field has been added to the bam_pileup1_t structure to keep track
of which CIGAR operator is being processed. This is used by a new
bam_plp_insertion() function which can be used to return the sequence of
any inserted bases at a given pileup location. If the alignment includes
CIGAR P operators, the returned sequence will include pads. (#699)
* The hts_itr_t and hts_itr_multi_t structures have been merged and can be
used interchangeably. Extra fields have been added to hts_itr_t to support
this. hts_itr_multi_t is now a typedef for hts_itr_t; sam_itr_multi_next()
is now an alias for sam_itr_next() and hts_itr_multi_destroy() is an alias
for hts_itr_destroy(). (#836)
* An improved regidx interface has been added. To allow this, struct
reg_t has been removed, regitr_t has been modified and various new
API functions have been added to htslib/regidx.h. While parts of
the old regidx API have been retained for backwards compatibility,
it is recommended that all code using regidx should be changed to use
the new interface. (#761)
* Elements in the hts_reglist_t structure have been reordered slightly
so that they pack together better. (#761)
* bgzf_utell() and bgzf_useek() now use type off_t instead of long for
the offset. This allows them to work correctly on files longer than
2G bytes on Windows and 32-bit Linux. (#868)
* A number of functions that used to return void now return int so that
they can report problems like memory allocation failures. Callers
should take care to check the return values from these functions. (#834)
The affected functions are:
ksort.h: ks_introsort(), ks_mergesort()
sam.h: bam_mplp_init_overlaps()
synced_bcf_reader.h: bcf_sr_regions_flush()
vcf.h: bcf_format_gt(), bcf_fmt_array(),
bcf_enc_int1(), bcf_enc_size(),
bcf_enc_vchar(), bcf_enc_vfloat(), bcf_enc_vint(),
bcf_hdr_set_version(), bcf_hrec_format()
vcfutils.h: bcf_remove_alleles()
* bcf_set_variant_type() now outputs VCF_OVERLAP for spanning
deletions (ALT=*). (#726)
* A new field (hrecs) has been added to the bam_hdr_t structure for
use by the new header API. The old sdict field is now not used and
marked as deprecated. The l_text field has been changed from uint32_t
to size_t, to allow for very large headers in SAM files. The text
and l_text fields have been left for backwards compatibility, but
should not be accessed directly in code that uses the new header API.
To access the header text, the new functions sam_hdr_length() and
sam_hdr_str() should be used instead. (#812)
* The old cigar_tab field is now marked as deprecated; use the new
bam_cigar_table[] instead. (#891, thanks to John Marshall)
* The bam1_core_t structure's l_qname and l_extranul fields have been
rearranged and enlarged; l_qname still includes the extra NULs.
(Almost all code should use bam_get_qname(), bam_get_cigar(), etc,
and has no need to use these fields directly.) HTSlib now supports
the SAM specification's full 254 QNAME length again. (#900, thanks
to John Marshall; #520)
* bcf_index_load() no longer tries the '.tbi' suffix when looking for
BCF index files (.tbi indexes are for text files, not binary BCF). (#870)
* htsFile has a new 'state' member to support SAM multi-threading. (#916)
* A new field has been added to the bam1_t structure, and others
have been rearranged to remove structure holes. (#709; #922)
Bug fixes
---------
* Several BGZF format fixes:
- Support for multi-member gzip files. (#744, thanks to Adam Novak; #742)
- Fixed error handling code for native gzip formatted files. (64c4927)
- CRCs checked when threading too (previously only when non-threaded). (#745)
- Made bgzf_useek function work with threads. (#818)
- Fixed rare threading deadlocks. (#831)
- Reading of very short files (<28 bytes) that do not contain an EOF block.
(#910)
* Fixed some thread pool deadlocks caused by race conditions. (#746, #906)
* Many additional memory allocation checks in VCF, BCF, SAM and CRAM
code. This also changes the return type of some functions. See ABI
changes above. (#920 amongst others)
* Replace some sam parsing abort() calls with proper errors.
(#721, thanks to John Marshall; #576)
* Fixed to permit SAM read names of length 252 to 254 (the maximum
specified by the SAM specification). (#900, thanks to John Marshall)
* Fixed mpileup overlap detection heuristic to work with BAMs having
long CIGARs (more than 65536 operations). (#802)
* Security fix: CIGAR strings starting with the "N" operation can no
longer cause underflow on the bam CIGAR structure. Similarly CIGAR
strings that are entirely "D" ops could leak the contents of
uninitialised variables. (#699)
* Fixed bug where alignments starting 0M could cause an invalid
memory access in sam_prob_realn(). (#699)
* Fixed out of bounds memory access in mpileup when given a reference
with binary characters (top-bit set). (#808, thanks to John Marshall)
* Fixed crash in mpileup overlap_push() function. (#882; #852 reported
by Pierre Lindenbaum)
* Fixed various potential CRAM memory leaks when recovering from
error cases.
* Fixed CRAM index queries for unmapped reads (#911; samtools/samtools#958
reported by @acorvelo)
* Fixed the combination of CRAM embedded references and multiple
slices per container. This was incorrectly setting the header
MD5sum. (No impact on default CRAM behaviour.) (b2552fd)
* Removed unwanted explicit data flushing in CRAM writing, which on
some OSes caused major slowdowns. (#883)
* Fixed inefficiencies in CRAM encoding when many small references
occur within the middle of large chromosomes. Previously it
switched into multi-ref mode, but not back out of it which caused
the read POS field to be stored poorly. (#896)
* Fixed CRAM handling of references when the order of sequences in a
supplied fasta file differs to the order of the @SQ headers. (#935)
* Fixed BAM and CRAM multi-threaded decoding when used in conjunction
with the multi-region iterator. (#830; #577, #822, #926 all reported by
Brent Pedersen)
* Removed some unaligned memory accesses in CRAM encoder and
undefined behaviour in BCF reading (#867, thanks to David Seifert)
* Repeated calling of bcf_empty() no longer crashes. (#741)
* Fixed bug where some 8 or 16-bit negative integers were stored using values
reserved by the BCF specification. These numbers are now promoted to the
next size up, so -121 to -128 are stored using at least 16 bits, and -32761
to -32768 are stored using 32 bits.
Note that while BCF files affected by this bug are technically incorrect,
it is still possible to read them. When converting to VCF format,
HTSlib (and therefore bcftools) will interpret the values as intended
and write out the correct negative numbers. (#766, thanks to John Marshall;
samtools/bcftools#874)
* Allow repeated invocations of bcf_update_info() and bcf_update_format_*()
functions. (#856, thanks to John Marshall; #813 reported by Steffen Möller)
* Memory leak removed in knetfile's kftp_parse_url() function. (#759, thanks
to David Alexander)
* Fixed various crashes found by libfuzzer (invalid data leading to
errors), mostly but not exclusively in CRAM, VCF and BCF decoding. (#805)
* Improved robustness of BAI and CSI index creation and loading. (#870; #967)
* Prevent (invalid) creation of TBI indices for BCF files.
(#837; samtools/bcftools#707)
* Better parsing of handling of remote URLs with ?param=val
components and their interaction with remote index URLs. (#790; #784
reported by Mark Ebbert)
* hts_idx_load() now checks locally for all possible index names before
attempting to download a remote index. It also checks that the remote
file it downloads is actually an index before trying to save and use
it. (#870; samtools/samtools#1045 reported by Albert Vilella)
* hts_open_format() now honours the compression field, no longer also
requiring an explicit "z" in the mode string. Also fixed a 1 byte
buffer overrun. (#880)
* Removed duplicate hts_tpool_process_flush prototype. (#816, reported by
James S Blachly)
* Deleted defunct cram_tell declaration. (66c41e2; #915 reported by
Martin Morgan)
* Fixed overly aggressive filename suffix checking in bgzip. (#927, thanks to
John Marshall; #129, reported by @hguturu)
* Tabix and bgzip --help output now goes to standard output. (#754, thanks to
John Marshall)
* Fixed bgzip index creation when using multiple threads. (#817)
* Made bgzip -b option honour -I (index filename). (#817)
* Bgzip -d no longer attempts to unlink(NULL) when decompressing stdin. (#718)
Miscellaneous other changes
---------------------------
* Integration with Google OSS fuzzing for automatic detection of
more bugs. (Thanks to Google for their assistance and the bugs it
has found.) (#796, thanks to Markus Kusano)
* aclocal.m4 now has the pkg-config macros. (6ec3b94d; #733 reported by
Thomas Hickman)
* Improved C++ compatibility of some header files. (#772; #771 reported
by @cwrussell)
* Improved strict C99 compatibility. (#860, thanks to John Marshall)
* Travis and AppVeyor improvements to aid testing. (#747; #773 thanks to
Lennard Berger; #781; #809; #804; #860; #909)
* Various minor compiler warnings fixed. (#708; #765; #846, #860, thanks to
John Marshall; #865; #966; #973)
* Various new and improved error messages.
* Documentation updates (mostly in the header files).
* Even more testing with "make check".
* Corrected many copyright dates. (#979)
* The default non-configure Makefile now uses libcurl instead of
knet, so it can support https. (#895)
Noteworthy changes in release 1.9 (18th July 2018)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* If `./configure` fails, `make` will stop working until either configure
is re-run successfully, or `make distclean` is used. This makes
configuration failures more obvious. (#711, thanks to John Marshall)
* The default SAM version has been changed to 1.6. This is in line with the
latest version specification and indicates that HTSlib supports the
CG tag used to store long CIGAR data in BAM format.
* bgzip integrity check option '--test' (#682, thanks to @sd4B75bJ, @jrayner)
* Faidx can now index fastq files as well as fasta. The fastq index adds
an extra column to the `.fai` index which gives the offset to the quality
values. New interfaces have been added to `htslib/faidx.h` to read the
fastq index and retrieve the quality values. It is possible to open
a fastq index as if fasta (only sequences will be returned), but not
the other way round. (#701)
* New API interfaces to add or update integer, float and array aux tags. (#694)
* Add `level=<number>` option to `hts_set_opt()` to allow the compression
level to be set. Setting `level=0` enables uncompressed output. (#715)
* Improved bgzip error reporting.
* Better error reporting when CRAM reference files can't be opened. (#706)
* Fixes to make tests work properly on Windows/MinGW - mainly to handle
line ending differences. (#716)
* Efficiency improvements:
- Small speed-up for CRAM indexing.
- Reduce the number of unnecessary wake-ups in the thread pool. (#703)
- Avoid some memory copies when writing data, notably for uncompressed
BGZF output. (#703)
* Bug fixes:
- Fix multi-region iterator bugs on CRAM files. (#684)
- Fixed multi-region iterator bug that caused some reads to be skipped
incorrectly when reading BAM files. (#687)
- Fixed synced_bcf_reader() bug when reading contigs multiple times. (#691,
reported by @freeseek)
- Fixed bug where bcf_hdr_set_samples() did not update the sample dictionary
when removing samples. (#692, reported by @freeseek)
- Fixed bug where the VCF record ref length was calculated incorrectly
if an INFO END tag was present. (71b00a)
- Fixed warnings found when compiling with gcc 8.1.0. (#700)
- sam_hdr_read() and sam_hdr_write() will now return an error code
if passed a NULL file pointer, instead of crashing.
- Fixed possible negative array look-up in sam_parse1() that somehow escaped
previous fuzz testing. (CVE-2018-13845, #731, reported by @fCorleone)
- Fixed bug where cram range queries could incorrectly report an error
when using multiple threads. (#734, reported by Brent Pedersen)
- Fixed very rare rANS normalisation bug that could cause an assertion
failure when writing CRAM files. (#739, reported by @carsonhh)
Noteworthy changes in release 1.8 (3rd April 2018)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* The URL to get sequences from the EBI reference server has been changed
to https://. This is because the EBI no longer serve sequences via
plain HTTP - requests to the http:// endpoint just get redirected.
HTSlib needs to be linked against libcurl to download https:// URLs,
so CRAM users who want to get references from the EBI will need to
run configure and ensure libcurl support is enabled using the
--enable-libcurl option.
* Added libdeflate as a build option for alternative faster compression and
decompression. Results vary by CPU but compression should be twice as fast
and decompression faster.
* It is now possible to set the compression level in bgzip. (#675; thanks
to Nathan Weeks).
* bgzip now gets its own manual page.
* CRAM encoding now stored MD and NM tags verbatim where the reference
contains 'N' characters, to work around ambiguities in the SAM
specification (samtools #717/762).
Also added "store_md" and "store_nm" cram-options for forcing these
tags to be stored at all locations. This is best when combined with
a subsequent decode_md=0 option while reading CRAM.
* Multiple CRAM bug fixes, including a fix to free and the subsequent reuse of
references with `-T ref.fa`. (#654; reported by Chris Saunders)
* CRAM multi-threading bugs fixed: don't try to call flush on reading;
processing of multiple range queries; problems with multi-slice containers.
* Fixed crashes caused when decoding some cramtools produced CRAM files.
* Fixed a couple of minor rANS issues with handling invalid data.
* Fixed bug where probaln_glocal() tried to allocate far more memory than
needed when the query sequence was much longer than the reference. This
caused crashes in samtools and bcftools mpileup when used on data with very
long reads. (#572, problem reported by Felix Bemm via minimap2).
* sam_prop_realn() now returns -1 (the same value as for unmapped reads)
on reads that do not include at least one 'M', 'X' or '=' CIGAR operator,
and no longer adds BQ or ZQ tags. BAQ adjustments are only made to bases
covered by these operators so there is no point in trying to align
reads that do not have them. (#572)
Noteworthy changes in release 1.7 (26th January 2018)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* BAM: HTSlib now supports BAMs which include CIGARs with more than
65535 operations as per HTS-Specs 18th November (dab57f4 and 2f915a8).
* BCF/VCF:
- Removed the need for long double in pileup calculations.
- Sped up the synced reader in some situations.
- Bug fixing: removed memory leak in bcf_copy.
* CRAM:
- Added support for HTS_IDX_START in cram iterators.
- Easier to build when lzma header files are absent.
- Bug fixing: a region query with REQUIRED_FIELDS option to
disable sequence retrieval now gives correct results.
- Bug fixing: stop queries to regions starting after the last
read on a chromosome from incorrectly reporting errors
(#651, #653; reported by Imran Haque and @egafni via pysam).
* Multi-region iterator: The new structure takes a list of regions and
iterates over all, deduplicating reads in the process, and producing a
full list of file offset intervals. This is usually much faster than
repeatedly using the old single-region iterator on a series of regions.
* Curl improvements:
- Add Bearer token support via HTS_AUTH_LOCATION env (#600).
- Use CURL_CA_BUNDLE environment variable to override the CA (#622;
thanks to Garret Kelly & David Alexander).
- Speed up (removal of excessive waiting) for both http(s) and ftp.
- Avoid repeatedly reconnecting by removal of unnecessary seeks.
- Bug fixing: double free when libcurl_open fails.
* BGZF block caching, if enabled, now performs far better (#629; reported
by Ram Yalamanchili).
* Added an hFILE layer for in-memory I/O buffers (#590; thanks to Thomas
Hickman).
* Tidied up the drand48 support (intended for systems that do not
provide this function).
Noteworthy changes in release 1.6 (28th September 2017)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* Fixed bug where iterators on CRAM files did not propagate error return
values to the caller correctly. Thanks go to Chris Saunders.
* Overhauled Windows builds. Building with msys2/mingw64 now works
correctly and passes all tests.
* More improvements to logging output (thanks again to Anders Kaplan).
* Return codes from sam_read1() when reading cram have been made
consistent with those returned when reading sam/bam. Thanks to
Chris Saunders (#575).
* BGZF CRC32 checksums are now always verified.
* It's now possible to set nthreads = 1 for cram files.
* hfile_libcurl has been modified to make it thread-safe. It's also
better at handling web servers that do not honour byte range requests
when attempting to seek - it now sets errno to ESPIPE and keeps
the existing connection open so callers can revert to streaming mode
it they want to.
* hfile_s3 now recalculates access tokens if they have become stale. This
fixes a reported problem where authentication failed after a file
had been in use for more than 15 minutes.
* Fixed bug where remote index fetches would fail to notice errors when
writing files.
* bam_read1() now checks that the query sequence length derived from the
CIGAR alignment matches the sequence length in the BAM record.
Noteworthy changes in release 1.5 (21st June 2017)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
* Added a new logging API: hts_log(), along with hts_log_error(),
hts_log_warn() etc. convenience macros. Thanks go to Anders Kaplan
for the implementation. (#499, #543, #551)
* Added a new file I/O option "block_size" (HTS_OPT_BLOCK_SIZE) to
alter the hFILE buffer size.
* Fixed various bugs, including compilation issues samtools/bcftools#610,
samtools/bcftools#611 and robustness to corrupted data #537, #538,
#541, #546, #548, #549, #554.
Noteworthy changes in release 1.4.1 (8th May 2017)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
This is primarily a security bug fix update.
* Fixed SECURITY (CVE-2017-1000206) issue with buffer overruns with
malicious data. (#514)
* S3 support for non Amazon AWS endpoints. (#506)
* Support for variant breakpoints in bcftools. (#516)
* Improved handling of BCF NaNs. (#485)
* Compilation / portability improvements. (#255, #423, #498, #488)
* Miscellaneous bug fixes (#482, #521, #522, #523, #524).
* Sanitise headers (#509)
Release 1.4 (13 March 2017)
* Incompatible changes: several functions and data types have been changed
in this release, and the shared library soversion has been bumped to 2.
- bam_pileup1_t has an additional field (which holds user data)
- bam1_core_t has been modified to allow for >64K CIGAR operations
and (along with bam1_t) so that CIGAR entries are aligned in memory
- hopen() has vararg arguments for setting URL scheme-dependent options
- the various tbx_conf_* presets are now const
- auxiliary fields in bam1_t are now always stored in little-endian byte
order (previously this depended on if you read a bam, sam or cram file)
- index metadata (accessible via hts_idx_get_meta()) is now always
stored in little-endian byte order (previously this depended on if
the index was in tbi or csi format)
- bam_aux2i() now returns an int64_t value
- fai_load() will no longer save local copies of remote fasta indexes
- hts_idx_get_meta() now takes a uint32_t * for l_meta (was int32_t *)
* HTSlib now links against libbz2 and liblzma by default. To remove these
dependencies, run configure with options --disable-bz2 and --disable-lzma,
but note that this may make some CRAM files produced elsewhere unreadable.
* Added a thread pool interface and replaced the bgzf multi-threading
code to use this pool. BAM and CRAM decoding is now multi-threaded
too, using the pool to automatically balance the number of threads
between decode, encode and any data processing jobs.
* New errmod_cal(), probaln_glocal(), sam_cap_mapq(), and sam_prob_realn()
functions, previously internal to SAMtools, have been added to HTSlib.
* Files can now be accessed via Google Cloud Storage using gs: URLs, when
HTSlib is configured to use libcurl for network file access rather than
the included basic knetfile networking.
* S3 file access now also supports the "host_base" setting in the
$HOME/.s3cfg configuration file.
* Data URLs ("data:,text") now follow the standard RFC 2397 format and may
be base64-encoded (when written as "data:;base64,text") or may include
percent-encoded characters. HTSlib's previous over-simplified "data:text"
format is no longer supported -- you will need to add an initial comma.
* When plugins are enabled, S3 support is now provided by a separate
hfile_s3 plugin rather than by hfile_libcurl itself as previously.
When --enable-libcurl is used, by default both GCS and S3 support
and plugins will also be built; they can be individually disabled
via --disable-gcs and --disable-s3.
* The iRODS file access plugin has been moved to a separate repository.
Configure no longer has a --with-irods option; instead build the plugin
found at <https://github.com/samtools/htslib-plugins>.
* APIs to portably read and write (possibly unaligned) data in little-endian
byte order have been added.
* New functions bam_auxB_len(), bam_auxB2i() and bam_auxB2f() have been
added to make accessing array-type auxiliary data easier. bam_aux2i()
can now return the full range of values that can be stored in an integer
tag (including unsigned 32 bit tags). bam_aux2f() will return the value
of integer tags (as a double) as well as floating-point ones. All of
the bam_aux2 and bam_auxB2 functions will set errno if the requested
conversion is not valid.
* New functions fai_load3() and fai_build3() allow fasta indexes to be
stored in a different location to the indexed fasta file.
* New functions bgzf_index_dump_hfile() and bgzf_index_load_hfile()
allow bgzf index files (.gzi) to be written to / read from an existing
hFILE handle.
* hts_idx_push() will report when trying to add a range to an index that
is beyond the limits that the given index can handle. This means trying
to index chromosomes longer than 2^29 bases with a .bai or .tbi index
will report an error instead of apparently working but creating an invalid
index entry.
* VCF formatting is now approximately 4x faster. (Whether this is
noticeable depends on what was creating the VCF.)
* CRAM lossy_names mode now works with TLEN of 0 or TLEN within +/- 1
of the computed value. Note in these situations TLEN will be
generated / fixed during CRAM decode.
* CRAM now supports bzip2 and lzma codecs. Within htslib these are
disabled by default, but can be enabled by specifying "use_bzip2" or
"use_lzma" in an hts_opt_add() call or via the mode string of the
hts_open_format() function.
Noteworthy changes in release 1.3.2 (13 September 2016)
* Corrected bin calculation when converting directly from CRAM to BAM.
Previously a small fraction of converted reads would fail Picard's
validation with "bin field of BAM record does not equal value computed"
(SAMtools issue #574).
* Plugins can now signal to HTSlib which of RTLD_LOCAL and RTLD_GLOBAL
they wish to be opened with -- previously they were always RTLD_LOCAL.
Noteworthy changes in release 1.3.1 (22 April 2016)
* Improved error checking and reporting, especially of I/O errors when
writing output files (#17, #315, PR #271, PR #317).
* Build fixes for 32-bit systems; be sure to run configure to enable
large file support and access to 2GiB+ files.
* Numerous VCF parsing fixes (#321, #322, #323, #324, #325; PR #370).
Particular thanks to Kostya Kortchinsky of the Google Security Team
for testing and numerous input parsing bug reports.
* HTSlib now prints an informational message when initially creating a
CRAM reference cache in the default location under your $HOME directory.
(No message is printed if you are using $REF_CACHE to specify a location.)
* Avoided rare race condition when caching downloaded CRAM reference sequence
files, by using distinctive names for temporary files (in addition to O_EXCL,
which has always been used). Occasional corruption would previously occur
when multiple tools were simultaneously caching the same reference sequences
on an NFS filesystem that did not support O_EXCL (PR #320).
* Prevented race condition in file access plugin loading (PR #341).
* Fixed mpileup memory leak, so no more "[bam_plp_destroy] memory leak [...]
Continue anyway" warning messages (#299).
* Various minor CRAM fixes.
* Fixed documentation problems #348 and #358.
Noteworthy changes in release 1.3 (15 December 2015)
* Files can now be accessed via HTTPS and Amazon S3 in addition to HTTP
and FTP, when HTSlib is configured to use libcurl for network file access
rather than the included basic knetfile networking.
* HTSlib can be built to use remote access hFILE backends (such as iRODS
and libcurl) via a plugin mechanism. This allows other backends to be
easily added and facilitates building tools that use HTSlib, as they
don't need to be linked with the backends' various required libraries.
* When writing CRAM output, sam_open() etc now default to writing CRAM v3.0
rather than v2.1.
* fai_build() and samtools faidx now accept initial whitespace in ">"
headers (e.g., "> chr1 description" is taken to refer to "chr1").
* tabix --only-header works again (was broken in 1.2.x; #249).
* HTSlib's configure script and Makefile now fully support the standard
convention of allowing CC/CPPFLAGS/CFLAGS/LDFLAGS/LIBS to be overridden
as needed. Previously the Makefile listened to $(LDLIBS) instead; if you
were overriding that, you should now override LIBS rather than LDLIBS.
* Fixed bugs #168, #172, #176, #197, #206, #225, #245, #265, #295, and #296.
Noteworthy changes in release 1.2.1 (3 February 2015)
* Reinstated hts_file_type() and FT_* macros, which were available until 1.1
but briefly removed in 1.2. This function is deprecated and will be removed
in a future release -- you should use hts_detect_format() etc instead
Noteworthy changes in release 1.2 (2 February 2015)
* HTSlib now has a configure script which checks your build environment
and allows for selection of optional extras. See INSTALL for details
* By default, reference sequences are fetched from the EBI CRAM Reference
Registry and cached in your $HOME cache directory. This behaviour can
be controlled by setting REF_PATH and REF_CACHE environment variables
(see the samtools(1) man page for details)
* Numerous CRAM improvements:
- Support for CRAM v3.0, an upcoming revision to CRAM supporting
better compression and per-container checksums
- EOF checking for v2.1 and v3.0 (similar to checking BAM EOF blocks)
- Non-standard values for PNEXT and TLEN fields are now preserved
- hts_set_fai_filename() now provides a reference file when encoding
- Generated read names are now numbered from 1, rather than being
labelled 'slice:record-in-slice'
- Multi-threading and speed improvements
* New htsfile command for identifying file formats, and corresponding
file format detection APIs
* New tabix --regions FILE, --targets FILE options for filtering via BED files
* Optional iRODS file access, disabled by default. Configure with --with-irods
to enable accessing iRODS data objects directly via 'irods:DATAOBJ'
* All occurrences of 2^29 in the source have been eliminated, so indexing
and querying against reference sequences larger than 512Mbp works (when
using CSI indices)
* Support for plain GZIP compression in various places
* VCF header editing speed improvements
* Added seq_nt16_int[] (equivalent to the samtools API's bam_nt16_nt4_table)
* Reinstated faidx_fetch_nseq(), which was accidentally removed from 1.1.
Now faidx_fetch_nseq() and faidx_nseq() are equivalent; eventually
faidx_fetch_nseq() will be deprecated and removed [#156]
* Fixed bugs #141, #152, #155, #158, #159, and various memory leaks