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Change Log

All notable changes to this project will be documented in this file. This project adheres to Semantic Versioning.

0.47.0 (2024-05-22)

Features

  • Add fasta::build function + FaidxBuildError (#418) (7c575ef)
  • Add rust_htslib::bcf::index::build (#408) (79d70cd)
  • derive PartialEq and Eq for bam:: and bcf::Format (#428) (528e543)

Bug Fixes

  • bam::Record:new should return a valid record (#361) (87f2011)
  • build for macOS (#431) (d869fdd)
  • in bam record buffer, change the start of the window to the first added item in last iteration (#430) (56ee2bd)
  • Panic on trailing omitted FORMAT records (#417) (9f575ee)

0.46.0 (2024-02-22)

Features

  • making several RecordBuffer methods public (6757f52)

Bug Fixes

0.45.0 (2024-02-07)

Features

  • adding function to get sequence length to faidx mod (#410) (ae79eba)

Bug Fixes

  • Loosen acceptable types to support current linux build on aarch64 (#415) (1d78d12)

0.44.1 (2023-06-21)

Bug Fixes

  • use correct return value in bcf_get_format and bcf_get_info_values (#398) (f9a1981)

0.44.0 (2023-06-20)

Features

Bug Fixes

  • include doctests in test coverage calculations (#397) (8ed0837)

0.43.1 (2023-05-16)

Bug Fixes

  • implement Drop for faidx::Reader, destroying the fai handle (#391) (0e6d6ac)

0.43.0 (2023-05-12)

Features

0.42.0 (2023-03-30)

Features

  • Add ability to fetch number of sequences and I-th sequence from FAI index (#377) (6ecc4bd)

0.41.1 (2023-03-03)

Features

  • Revised calculation of leading- and trailing-softclips (#375) (b61dd2c)

Performance Improvements

  • update htslib and corresponding bindings to 1.16 (#366) (f597ce0)

0.40.2 (2022-10-13)

Performance Improvements

  • update htslib and corresponding bindings to 1.16 (#366) (f597ce0)

0.40.1 (2022-08-24)

Bug Fixes

  • Header::to_hashmap skips @CO tags, add comments() method (#363) (c24a7f6)

0.40.0 (2022-07-05)

Features

Bug Fixes

  • update to latest release-please (b130634)

0.39.5 (2022-05-09)

Bug Fixes

  • set path in release-please config (d8f7c6e)

0.39.4 (2022-05-09)

Bug Fixes

  • perform checkout before running release please (cbc6a0a)

0.39.3 (2021-11-20)

Bug Fixes

  • change the type to c_char so it can be compiled for aarch64 (#337) (a21aff2)

0.39.2 (2021-08-23)

Bug Fixes

  • Configuration when cross-compiling. Even when cross-compiling, build.rs runs on the build host. Hence within build.rs #[cfg(target_os)] always reflects the host, not the target. Use $CARGO_CFG_TARGET_OS instead to query target properties. (#329) (d5198e6)

0.39.1 (2021-07-06)

Bug Fixes

  • bump hts-sys version to 2.0.1 (336c8b8)

0.39.0 (2021-07-06)

⚠ BREAKING CHANGES

  • dummy major version bump to move away from previous versions that were following htslib versions.
  • bump to new major version (for technical reasons).
  • dummy breaking change to increase hts-sys major version.

Bug Fixes

  • bump to new major version (for technical reasons). (9c6db30)
  • dummy breaking change to increase hts-sys major version. (93415cb)
  • dummy changes (3af5ede)
  • dummy major version bump to move away from previous versions that were following htslib versions. (aaa70a8)
  • dummy release (74d1565)
  • dummy release (af2f84e)
  • dummy release (b97915f)
  • handle subcrate with release-please (0a4605f)
  • trigger dummy release (7c5a7de)
  • update changelog (deef08f)

0.38.3 (2021-07-06)

Bug Fixes

  • dummy fix for triggering release (e92e6b1)

0.38.2 (2021-07-06)

Bug Fixes

  • add ID to automatic release handling (1244393)

0.38.1 (2021-07-06)

Bug Fixes

0.38.0 (2021-07-06)

⚠ BREAKING CHANGES

  • Improve bcf Record filter interface and improve docs (#306)

Features

  • Improve bcf Record filter interface and improve docs (#306) (f45e91d)

Bug Fixes

Unreleased

Changes

  • bcf::Record methods has_filter, remove_filter, push_filter, and set_filter all now take a byte slice (&[u8]) or an Id.

[0.37.0] - 2021-07-05

Added

  • bcf::Record methods end, clear, and rlen (@mbhall88).

Changes

  • bcf::IndexReader::fetch parameter end is now an Option<u64>. This is inline with htslib regions, which do not require an end position (@mbhall88)
  • Removed unused dependencies (@sreenathkrishnan).
  • Improved documentation (@mbhall88).
  • Improved error message when failing to load index files (@johanneskoester).
  • Improved API for accessing AUX fields in BAM records (@jch-13).
  • Fixed compiler warnings (@fxwiegand).
  • BAM header representation is now always kept in sync between textual and binary (@jch-13).

[0.36.0] - 2020-11-23

Changes

  • Improved genotype API in VCF/BCF records (@MaltheSR).
  • Read pair orientation inference for BAM records (@johanneskoester).

[0.35.2] - 2020-11-23

Changes

  • let hts-sys dependency comply to semver.

[0.35.1] - 2020-11-23

Changes

  • Fixed wrongly define missing value constants in bcf::record (@johanneskoester).
  • Bump hts-sys depedency to the latest version, containing build fixes for macOS (@johanneskoester).

[0.35.0] - 2020-11-19

Changes

  • BREAKING: info and format field access in BCF records now allocates a separate buffer each time. In addition, it is also possible to pass a buffer that has been created manually before (@johanneskoester)
  • Fixes for building on macOS (@brainstorm)

Added

  • ability to push genotypes into BCF record (@MaltheSR, @tedil).

[0.34.0] - 2020-11-13

Added

  • Ability to set minimum refetch distance in bam::RecordBuffer.

[0.33.0] - 2020-11-04

Changes

  • BREAKING: Rename feature 'serde' as 'serde_feature' (for technical reasons)
  • BREAKING: Consolidate module-wide errors into a crate-wide error module
  • Making bcf::IndexedReader always unpack records to reflect the behaviour of bcf::Reader.
  • Adding bcf::errors::Error::FileNotFound and using it.
  • Fixes for musl compilation (@brainstorm).
  • Improved BCF constants handling (@juliangehring)
  • Fixes for tabix reader (@felix-clark, @brainstorm).
  • Fixes for BCF handling (@holtgrewe, @tedil).
  • Documentation improvements (@vsoch, @brainstorm, @edmundlth).
  • BREAKING: Improved, more ergonomic BAM fetch API (@TiberiusPrime, @brainstorm, @tedil).
  • BREAKING: Let BamRecordExtensions return iterators instead of vectors (@TiberiusPrime).
  • Handle all errors via a unified single thiserror based enum (@landesfeind).
  • BREAKING: BAM read API now returns Option (@slazicoicr).

Added

  • Support for reading indexed FASTA files (@landesfeind, @pmarks, @brainstorm).
  • Support for shared threadpools when reading and writing BAM (@pmarks, @nlhepler).
  • Serde support for Cigar strings (@FelixMoelder, @pmarks, @johanneskoester).
  • Expose bgzf functionality (@landesfeind).
  • Iterator over BAM records using Rc-pointers (@TiberiusPrime, @tedil).
  • Ability to obtain pairs of read and genome intervals from BAM (aligned_block_pairs) (@TiberiusPrime, @brainstorm).

[0.32.0] - 2020-07-09

Changes

  • Method seq_len() of bam::Record is now public.
  • Speedup when parsing BAM headers (thanks to @juliangehring).
  • Compatibility fixes for older rust versions (thanks to @pmarks and @brainstorm).

[0.31.0] - 2020-06-22

Changes

  • Bam record buffer now returns reference counted (Rc) objects. This makes the API more ergonomic to use.
  • Switched to thiserror instead of snafu for error handling.
  • Various cleanups and little fixes.

[0.30.0] - 2020-04-03

Changes

  • Removed fn header_mut() from bam::Read trait.
  • Fixed a major performance regression when reading bam files (issue #195).

[0.29.0] - 2020-03-26

Changes

  • Migrate buffer intervals to u64.

[0.28.0] - 2020-03-26

Changes

  • Return u64 wherever htslib has migrated to using 64 bit.
  • Implement more bio-types (Interval, Locus, Strand).

[0.27.0] - 2020-03-17

Changes

  • Updated to Htslib 1.10.2.
  • bam::Record.set() will panic if seq.len() != qual.len(). Previously, mismatched length would cause uninitialized memory to be written into the BAM file.
  • use serde_bytes to serialize .data section of bam::Record when using serde - large speed improvement.
  • change build.rs to avoid re-running when htslib or wrapper.h haven't changed.
  • update some dependencies.
  • refactor native dependency into htslib-sys crate, for greater versioning flexibility
  • Record::from_sam require &mut HeaderView. Provide the appropriate accessor.
  • set() no longer invalidates tag data.
  • Various minor improvements.

[0.26.1] - 2019-12-03

Changes

  • Various bug fixes in CIGAR string handling, INFO tag reading and FORMAT tag reading.

[0.26.0] - 2019-09-27

Changes

  • Allow caching of CIGAR in bam::RecordBuffer.

[0.25.0] - 2019-09-27

Changes

  • Migrated error handling to the snafu crate: https://docs.rs/snafu.
  • Cleaned up and simplified API (including breaking changes).
  • Allow writing SAM files from the bam::Writer.

[0.24.0] - 2019-05-31

Added

  • Allow setting unmapped BAM record (without Cigar string).
  • Various bug fixes and error handling improvements.
  • Various Pysam-derived methods for interpreting Cigar strings.

[0.23.0] - 2019-05-02

Added

  • Support for BAM indices that are not placed beside a file.bam as file.bam.bai
  • Implement SequenceRead trait for BAM records.
  • Add function to build an index for a BAM file.
  • CRAM support for BAM reader and writer.

Changes

  • Allow to specify particular index filename when instantiating a BAM reader.
  • Various bug and API fixes.

[0.22.0] - 2018-11-02

Changes

  • Support compilation against musl.
  • Support for removing alleles.
  • Improvements to SyncedReader API.

[0.21.0] - 2018-08-01

Changes

  • Adding bcf::synced::SyncedReader::fetch(), changing error type for bcf::synced::SyncedReader::read_next().
  • Adding bcf::Record::unpack() for explicitely unpacking BCF records.
  • Fixed bcf::synced::SyncedReader::record().
  • bam::Record::cigar() now returns a reference (in constant time) and needs bam::Record::unpack_cigar() to be called first.
  • Allow to create Cigar string from bio_types::Alignment.
  • Provide a cached variant of obtaining cigar string.
  • Lots of small usability improvements.

[0.20.0] - 2018-06-18

Added

  • Initial implementation of synced BCF reader interface.
  • Several small helper methods for BAM readers.

Changes

  • Not skipping fileformat= header any more.
  • BCF records are always unpacked when reading.

[0.19.1] - 2018-06-07

Changed

  • Moved unpacking of BCF records into constructor to prevent race conditions.
  • Fixed bug in retrieving BCF record id.
  • Fixed bug in the filter iterator of BCF.

[0.19.0] - 2018-06-01

Added

  • more push functions for BCF.

[0.18.0] - 2018-05-04

Added

  • bcf::IndexedReader
  • support for writing bcf FILTER field
  • setting thread count in all readers and writers
  • setting ID and alleles in bcf records
  • support for tabix indexes
  • convert CIGAR to and from strings

[0.17.0] - 2018-02-22

Added

  • Serde support for bam records.

Changed

  • Various convenience improvements in the API.

[0.16.0] - 2018-01-05

Changed

  • Raw Htslib bindings are now generated on the fly.
  • Switched to Htslib 1.6.
  • Fixed a potential dangling pointer to the header in bcf records.
  • Various small API improvements.

[0.15.0] - 2017-12-05

Changed

  • HeaderView of bam and bcf can now be cloned.

[0.14.0] - 2017-12-03

Added

  • An efficient ringbuffer for accessing BCF regions
  • An efficient ringbuffer for accessing BAM regions

Changed

  • Improved mutability annotation for readers.

[0.13.0] - 2017-09-22

Added

  • Ability to clone bam records.
  • Ability to set only qname.

Changed

  • Further improved CIGAR string API.
  • Improved documentation.

[0.12.1] - 2017-06-12

Changed

  • Adapt to changes in Rust 1.18 that caused compilation issues.

[0.12.0] - 2017-06-01

Added

  • Support seek and tell to handle virtual offsets.

Changed

  • Renamed previous seek method into fetch (in line with pysam).
  • Improved CIGAR API.
  • Updated dependencies.

[0.11.0] - 2017-05-01

Added

  • A SAM writer.

Changed

  • Improved CIGAR string API using a newtype wrapper.
  • Improved pileup API.
  • Support threaded writing for BAM files.

[0.10.0] - 2016-11-10

Added

  • Prelude module to easily import all relevant traits.

Changed

  • fine-grained constructors for STDIN/STDOUT, paths and URLs
  • better template handling with bam files

[0.9.0] - 2016-11-02

Changed

  • improved genotype handling
  • improved error handling
  • improved missing value handling

[0.8.1] - 2016-08-17

Changed

  • Finally converted the last unit error types to real error types (really now!).

[0.8.0] - 2016-08-17

Changed

  • More error types.

[0.7.0] - 2016-08-16

Changed

  • Error types now properly implement the Display and the Error trait.

[0.6.2] - 2016-07-22

Changed

  • Mark all records as Send and Sync.

[0.6.1] - 2016-07-20

Changed

  • Improved error messages.
  • Check existence of BAM when instantiating Readers.

[0.6.0] - 2016-06-01

Changed

  • Improved handling of memory allocation for BCF and BAM records.
  • Fixed a memory leak occuring when creating a new BAM record (thanks to @andrelmartins).