Tags give the ability to mark specific points in history as being important
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1.5
49fdfbda · ·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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1.4.1
6c068335 · ·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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debian/1.4-2
903f2b3b · · -
debian/1.4-1
d6ae67da · · -
1.4
d2d9c76a · ·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. -
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1.3.2
6bed35a3 · ·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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debian/1.3.1-1_bpo8+1
83fbdd99 · ·htslib (1.3.1-1~bpo8+1) jessie-backports; urgency=medium * Rebuild for jessie-backports. -- Charles Plessy <plessy@debian.org> Sun, 08 May 2016 21:28:33 +0900
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debian/1.3.1-1
68a17aa2 · ·htslib (1.3.1-1) unstable; urgency=medium 36bf59a Merge tag '1.3.1' into debian/unstable 559f8b4 Remove add_largefile.patch, applied upstream. 7163afb Update symbols file. Missing _vcf_parse_format@Base and fai_read@Base. c2c1df3 Build-depend on libcurl4-gnutls-dev and libssl-dev. 3b219b8 Enable libcurl. 9101580 Conforms to the Policy version 3.9.8. -- Charles Plessy <plessy@debian.org> Mon, 25 Apr 2016 22:28:11 +0900
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1.3.1
0f298ce2 · ·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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