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CHANGELOG.md

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Change Log

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

[0.21.0] - 2018-08-01

Changes

  • 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).