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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.

[0.30.0] - 2019-11-14

  • Bayesian models now allow to access internals.
  • Various small bug fixes.

[0.29.0] - 2019-09-27

  • Migrate error handling to the snafu crate (this is an API breaking change).
  • Fix edge cases in pairwise alignment.
  • Fix error in backward search if symbol isn't found.

[0.28.1] - 2019-06-28

  • Fix select in RankSelect in cases where many superblocks have the same rank.

[0.28.0] - 2019-06-19

  • Myers bit-parallel pattern matching now supports arbitrarily long patterns via bit vectors (thanks to @markschl).
  • Minor documentation updates (thanks to @anders-was-here).

[0.27.0] - 2019-05-31

  • Implement sequence-read-trait for FASTQ records.
  • Cleanup dependencies.

[0.26.1] - 2019-05-10

  • Fix a bug in select_1 and select_0 that would lead to too large answers.

[0.26.0] - 2019-05-09

  • Added a trait system for computing Bayesian statistical models.
  • Added an implementation of MSA via partial order alignment.
  • Performance improvements to FASTQ reader.

[0.25.0] - 2018-12-12

  • Added FQRead and FARead traits to FastaReader and FastqReader to be more flexible with input types. This allows to use readers on gzipped and on plain text input interchangeably.
  • Added an implementation of Bayes Factors and evidence scoring using the method of Kass and Raftery.

[0.24.0] - 2018-11-26

  • API overhaul to become more flexible when accepting text iterators. Now, anything that iterates over something can be borrowed as u8 is allowed.
  • FMIndex and FMDIndex now also allow plain owned versions of BWT, Less and Occ. This should greatly simplify their usage.
  • PairHMM and LogProb implementation has seen extensive performance improvements. Among that, (a) the usage of a fast approximation of exp() as presented by Kopczynsi 2017, and (b) banding of the pairHMM matrix with a given maximum edit distance.
  • All IO records now support serde.

[0.23.0] - 2018-11-06

  • Generalized Myers pattern matching algorithm to arbitrary unsigned integer types (u64, u128) (thanks to @markschl).
  • Implemented optional traceback and alignment output for Myers pattern matching algorithm (thanks to @markschl).
  • Use Strand type from bio-types crate in BED module (thanks to @ingolia).
  • Added an IntervalTree based data structure for looking up overlaps between annotation types (thanks to @ingolia).
  • Various bug fixes.

[0.22.0] - 2018-08-01

  • Added HMM implementation (thanks to @holtgrewe).
  • Moved Alignment types to bio_types crate (thanks to @pmarks).
  • Ignore comment lines in GTF/GFF files (thanks to Yasunobu Okamura).
  • API usability improvements.

[0.21.0] - 2018-06-19

  • Added PSSM implementation (thanks to @hervold).

[0.20.0] - 2018-06-01

  • Refactored RankSelect API to consistently use u64.
  • Use bv crate in suffix array implementation.

[0.19.0] - 2018-05-25

  • rank-0 and select-0 in RankSelect.
  • use bv crate for RankSelect.

[0.18.0] - 2018-05-04

  • More flexible FASTA API.
  • Fixed bug in KMP.

[0.17.0] - 2018-02-22

  • Bug fix in Ukkonen algorithm
  • Convenience improvements to API

[0.16.0] - 2018-01-05

  • Pairwise alignment has been rewritten to support banded alignment and clips.
  • Various minor API additions and improvements.
  • Several small bug fixes.

[0.15.0] - 2017-11-20

  • Add pair hidden markov model implementation to calculate the probability of two sequences being related.
  • Various minor bug fixes and usability improvements.

[0.14.2] - 2017-08-30

  • Improved numerical stability of CDF construction.
  • Speed improvements to occurrence array lookups in FM-index.
  • Improved GFF/GTF variant format handling.
  • Improved robustness of credible interval calculating in CDF.
  • Bug fixes for log probability implementation.

[0.14.1] - 2017-06-23

Changed

  • Replace nalgebra dependency with ndarray crate.

[0.14.0] - 2017-06-15

Changed

  • GTF/GFF reader can now handle duplicate keys.
  • Updated dependencies.
  • RNA alphabet.
  • Improved FASTQ reader.
  • Fixes in alignment algorithm.

[0.13.0] - 2017-05-09

Changed

  • fasta::IndexedReader now also provides an iterator.
  • IntervalTree provides a mutable iterator.
  • Various fixes to Fasta IO.
  • Fixed calculation of expected FDR.

[0.12.0] - 2017-04-03

Changed

  • Improved distance API.
  • Moved Strand into utils.
  • More robust gff/gtf parsing.

[0.11.0] - 2017-02-16

Changed

  • Improved IntervalTree API.
  • Updated dependencies.
  • Speed improvements in alignment module.
  • Improved test coverage.
  • Speed improvements in fmindex module.

[0.10.0] - 2016-11-02

Added

  • An interval tree implementation.
  • Initial utilities for bayesian statistics.

Changed

  • Various small improvements to log-space probability API.

[0.9.0] - 2016-08-18

Added

  • Implementation of discrete probability distributions via cumulative distribution functions.

Changed

  • Log-space probabilities have been refactored into newtypes.
  • Performance improvements for FMIndex implementation.
  • Improved documentation.

[0.8.0] - 2016-07-20

Changed

  • Writers in the io module no longer take ownership of the given record.
  • Various cosmetic changes.

[0.7.0] - 2016-07-06

Changed

  • Reverse complement API has been refactored into plain functions.
  • Reverse complement now supports the whole IUPAC alphabet.
  • Various algorithms take now IntoTextIterator instead of only slices.
  • Fasta reader and writer treat sequence names as strings.
  • Refactoring of suffix array + fmindex API to provide more flexibility.

[0.6.0] - 2016-05-09

Changed

  • Type aliases for various text representations.
  • Pattern matching algorithms take both iterators and slices where possible.
  • logprobs::cumsum has been refactored to return an iterator.
  • support for subtraction of logprobs.

[0.5.0] - 2016-02-24

Added

  • Support for serde serialization when used in combination with rust nightly (@dikaiosune).