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standage committed Jun 14, 2018
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17 changes: 15 additions & 2 deletions CHANGELOG.md
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All notable changes to this project will be documented in this file.
This project adheres to [Semantic Versioning](http://semver.org/).

## [Unreleased]

### Fixed
- Refined handling of mate read alignments (see #247, #250, #251, #255, and #263).

### Added
- Multithreading is now supported natively in `kevlar alac` (see #249 and unmerged `feed-thread` branch).
- A limited-scope VCF reader (see #256).
- Script for computing likelihood scores is now a first-class kevlar citizen as `kevlar simlike` (see #259).
- New `kevlar dist` subcommand for computing average and standard deviation of k-mer abundances for likelihood calculations (see #264).
- Paired-end awareness for `kevlar dump` (see #265).
- New `LikelihoodFail` filter for variant calls with a negative likelihood score (see #266).


## [0.4.2] 2018-04-16

### Fixed
- Much cleaner and more concise calling code from implementing "center aligned" gap alignment strategy, facilitated by new CIGAR tokenizer (see #242).
- Improved default behavior for `maxdiff` and splitting seed hits into distinct bins (#246).
- Improved default behavior for `maxdiff` and splitting seed hits into distinct bins (see #246).


## [0.4.1] 2018-04-04
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- A minor bug with banded mode in `kevlar novel`, various other minor fixes, and code that should have been removed previously (#239).



## [0.4.0] 2018-03-29

### Added
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