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1.8be22a2a1 · ·
htslib release 1.8: * 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)
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1.7209f94ba · ·
HTSlib release 1.7: long CIGAR support, multi-region iterator * 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). -
1.6746549da · ·
Release 1.6: hfile_libcurl improvements; more checks on input 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 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.
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1.549fdfbda · ·
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.
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1.4.16c068335 · ·
Noteworthy changes in release 1.4.1 (8th May 2017) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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) * Compilation / portability improvements. (#255, #423, #498, #488) * Miscellaneous bug fixes (#482, #521, #522, #523, #524). * Sanitise headers (#509)
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1.4d2d9c76a · ·
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 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 apparantly working but creating an invalid index entry. * 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 hts_open_format() function. -
1.3.26bed35a3 · ·
HTSlib patch release 1.3.2: bin bug fix, RTLD_GLOBAL plugins * 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.
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1.3.10f298ce2 · ·
HTSlib release 1.3.1: bug fix release, notably error checking * 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.
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1.387141ea6 · ·
HTSlib release 1.3, plugins, libcurl, CRAM v3.0, bug fixes * 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. * 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.
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