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The htslib-1.9.tar.bz2 download is the full source code release. The “Source code” downloads are generated by GitHub and are incomplete as they are missing some generated files.
makewill stop working until either configure is re-run successfully, or
make distcleanis 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.
Faidx can now index fastq files as well as fasta. The fastq index adds an extra column to the
.faiindex which gives the offset to the quality values. New interfaces have been added to
htslib/faidx.hto 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)
hts_set_opt()to allow the compression level to be set. Setting
level=0enables 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)
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 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 bug where cram range queries could incorrectly report an error when using multiple threads. (#734, reported by Brent Pedersen)
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)
The htslib-1.8.tar.bz2 download is the full source code release. The “Source code” downloads are generated by GitHub and are incomplete as they are missing some generated files.
- 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.
- 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.
- 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).
The htslib-1.7.tar.bz2 download is the full source code release. The “Source code” downloads are generated by GitHub and are incomplete as they are missing some generated files.
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
ESPIPEand 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.
The htslib-1.6.tar.bz2 download is the full source code release. The “Source code” downloads are generated by GitHub and are incomplete as they are missing some generated files.
Added a new file I/O option "block_size" (HTS_OPT_BLOCK_SIZE) to alter the hFILE buffer size.
The htslib-1.5.tar.bz2 download is the full source code release. The “Source code” downloads are generated by GitHub and are incomplete as they [don't bundle HTSlib and] are missing some generated files.
This is primarily a security bug fix update.
Fixed SECURITY 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)
Sanitise headers (#509)
The htslib-1.4.1.tar.bz2 download is the full source code release. The “Source code” downloads are generated by GitHub and are incomplete as they [don't bundle HTSlib and] are missing some generated files.
Relase 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
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 apparantly working but creating an invalid
VCF formatting is now approximately 4x faster. (Whether this is
noticable 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
The [foo-1.x].tar.bz2 download is the full source code release. The “Source code” downloads are generated by GitHub and are incomplete as they [don't bundle HTSlib and] are missing some generated files.
This is a very small bug fix release based on the 1.3.1 release. Compared to 1.3.1, the following two improvements have been made; there are no other changes in behaviour from the previous release.
- 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/samtools#574).
- Plugins can now signal to HTSlib which of
RTLD_GLOBALthey wish to be opened with — previously they were always
The htslib-1.3.2.tar.bz2 download is the full source code release. The “Source code” downloads are generated by GitHub and are incomplete as they are missing some generated files.
- 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
$HOMEdirectory. (No message is printed if you are using
$REF_CACHEto 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
- 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.
The htslib-1.3.1.tar.bz2 download is the full source code release. The “Source code” downloads are generated by GitHub and are incomplete as they are missing some generated files.
- 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.
samtools faidxnow accept initial whitespace in ">" headers (e.g., "> chr1 description" is taken to refer to "chr1").
tabix --only-headerworks 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.
The htslib-1.3.tar.bz2 download is the full source code release. The “Source code” downloads are generated by GitHub and are incomplete as they are missing some generated files.