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Change Log

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

1.6.0 (2024-02-07)

Features

  • POA semi-global, local, and custom alignment (#569) (440cb1c)

1.5.0 (2023-12-09)

Features

Bug Fixes

1.4.0 (2023-09-12)

Features

Bug Fixes

  • include doctests in the test coverage of code that tarpaulin calculates (#533) (29cf0f5)
  • make dependabot commit message follow conventional commits (#542) (bb88281)

1.3.1 (2023-06-23)

Performance Improvements

  • improve alignment::distance::levenshtein and alignment::distance::bounded_levenshtein on strrings where distance is small (#522) (da7daea)

1.3.0 (2023-06-14)

Features

1.2.0 (2023-06-06)

Features

Bug Fixes

  • edge cases on partial order alignment (#515) (0181829)

Performance Improvements

1.1.0 (2022-12-13)

Features

  • add standard derives to all public types (#505) (c08623b)

1.0.0 (2022-09-29)

⚠ BREAKING CHANGES

  • update to latest ordered-float (#503)

Features

Bug Fixes

0.42.0 (2022-08-30)

⚠ BREAKING CHANGES

  • Update strum and ordered-float dependencies and change From into TryFrom for NotNan. (#491)

Features

  • Update strum and ordered-float dependencies and change From into TryFrom for NotNan. (#491) (57ccf8f)

Miscellaneous Chores

0.41.0 (2022-03-30)

Features

  • adaptive integration of density functions using a binary search approach that tries to achieve good resolution around the maximum (#486) (207b76f)

0.40.0 (2022-02-25)

Features

  • base specific hop parameters in homopoly-pair-hmm (#480) (cf75b6c)

Miscellaneous Chores

0.39.2 (2022-02-09)

Bug Fixes

  • Make QGramIndex use less memory; fix bug; improve tests&docs (#471) (48bac1c)
  • overflow in qgrams for k=32 (#478) (8048eb8)

0.39.1 (2022-01-12)

Bug Fixes

  • added code to ignore commented lines in a bed file (#474) (d17f823)

0.39.0 (2021-10-20)

Features

0.38.0 (2021-10-04)

Features

  • adds iupac amino acid alpha (#444) (f4b7a7c)
  • Allow to compute bayesian model via the exploration of the marginal distribution. (#453) (d09033c)

Bug Fixes

  • backward search yielding potentially incorrect positions on FM-Index (#454) (#455) (3489e6a)

0.37.1 (2021-08-23)

Bug Fixes

  • One Simple Trick to significantly improve the speed and memory usage of Occ (#448) (9aa79cb)
  • sampled suffix array (#447) (00f9846)

0.37.0 (2021-07-09)

Features

  • add method to retrieve all event posteriors from Bayesian model. (e5feda8)

0.36.0 (2021-07-06)

Features

  • Baum-Welch algorithm for Discrete HMM (#432) (eb8b8cb)

[0.35.0] - 2021-07-05

  • Improved buffer control in Fasta and Fastq API (@natir).
  • Fixed an indexing bug in ArrayBackedIntervalTree (@wabain).
  • Fixed a corner case where the FASTX parser could have looped infinitely (@morsecodist).
  • Fixed compiler warnings (@fxwiegand).
  • Improved documentation for FASTA index (@mbhall88).

[0.34.0] - 2021-05-04

  • Bayesian model framework now relies on Hash instead of Ord for accessing events (@johanneskoester).
  • Added wavelet matrix datastructure (@Identi, @tedil).

[0.33.0] - 2021-03-09

  • Fixed a floating point error in gcn_content (@tedil).
  • Improved error messages in io module (@fxwiegand).
  • Better memory usage of HomopolypairHMM (@tedil).
  • Improved documentation (@TianShi2001, @m0ssc0de, @dcroote).
  • Support for reading compact BED files (@manzt).
  • API improvements for Alphabet and GFF reader (@tshauck).
  • Switched to thiserror for error handling (@delehef).
  • Removed unsafe code (@huonw).
  • Fixed overflow in ShiftAnd algorithm (@dcroote).
  • Various additional test cases (@dcroote).
  • Extended API for SMEM computation on FMDIndex (@Identi).
  • Added a parser for Newick phylogenetic trees (@delehef).

[0.32.0] - 2020-07-28

This release mostly comprises of the documentation improvements made by the recent Docathon. Lots of new doctests and a bunch of time and memory complexity annotations. Big thanks to @tedil, @dcroote, @TomKellyGenetics, @natir, @thomasmulvaney, @mbhall88, @jafors, @HenningTimm, @luizirber, @dlaehnemann, @johanneskoester. Further additions in this release are:

  • homopolymer-error-aware pairHMM implementation (thanks to @tedil).
  • SIMD-accelerated edit distance routines (thanks to @Daniel-Liu-c0deb0t).
  • BitEnc derives more traits (thanks to @FelixMoelder).
  • wider pinning of some dependencies' version numbers (thanks to @pmarks).

[0.31.0] - 2020-06-02

  • Bugfix for pHMM implementation (thanks to @tedil).
  • Sorted array-backed interval trees (thanks to @tedil).

[0.30.1] - 2020-05-13

  • Improved occ counting speed for FM index (thanks to @thomasmulvaney)
  • Various small bug fixes and code cleanups and linter fixes.

[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).