1.5

• 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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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.

1.4.1

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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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.

1.4

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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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.

1.3.2

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_LOCAL and RTLD_GLOBAL they wish to be opened with — previously they were always RTLD_LOCAL.

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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.

1.3.1

• 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.

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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.

1.3

• 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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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.

1.2.1

• 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 enviroment 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 occurences of 2²⁹ 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

The changes above are also present in release 1.2. The 1.2 release was immediately superseded by this release, which further includes the following:

• 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

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The htslib-1.2.1.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.