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# Change Log

## [Unreleased](https://github.com/sanger-pathogens/Bio-Tradis/tree/HEAD)

[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/v1.4.1...HEAD)

**Merged pull requests:**

- Include tests in README [\#97](https://github.com/sanger-pathogens/Bio-Tradis/pull/97) ([ssjunnebo](https://github.com/ssjunnebo))

## [v1.4.1](https://github.com/sanger-pathogens/Bio-Tradis/tree/v1.4.1) (2018-09-20)
[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/1.4.1...v1.4.1)

**Merged pull requests:**

- update version for cpan [\#96](https://github.com/sanger-pathogens/Bio-Tradis/pull/96) ([ssjunnebo](https://github.com/ssjunnebo))
- Add to codecov [\#95](https://github.com/sanger-pathogens/Bio-Tradis/pull/95) ([ssjunnebo](https://github.com/ssjunnebo))

## [1.4.1](https://github.com/sanger-pathogens/Bio-Tradis/tree/1.4.1) (2018-07-19)
[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/1.4.0...1.4.1)

**Closed issues:**

- Installation on Ubuntu 17.10 fails [\#84](https://github.com/sanger-pathogens/Bio-Tradis/issues/84)
- Port 18 volume discrepancy? [\#83](https://github.com/sanger-pathogens/Bio-Tradis/issues/83)

**Merged pull requests:**

- Change TryCatch to Try::Tiny [\#94](https://github.com/sanger-pathogens/Bio-Tradis/pull/94) ([ssjunnebo](https://github.com/ssjunnebo))
- fix typo in badge [\#93](https://github.com/sanger-pathogens/Bio-Tradis/pull/93) ([ssjunnebo](https://github.com/ssjunnebo))
- Include TOC [\#92](https://github.com/sanger-pathogens/Bio-Tradis/pull/92) ([ssjunnebo](https://github.com/ssjunnebo))
- 621538 docker [\#91](https://github.com/sanger-pathogens/Bio-Tradis/pull/91) ([ssjunnebo](https://github.com/ssjunnebo))
- 621538 docker [\#90](https://github.com/sanger-pathogens/Bio-Tradis/pull/90) ([ssjunnebo](https://github.com/ssjunnebo))
- include reference genome for cram [\#89](https://github.com/sanger-pathogens/Bio-Tradis/pull/89) ([ssjunnebo](https://github.com/ssjunnebo))
- Revert "Replace cram file without reads" [\#88](https://github.com/sanger-pathogens/Bio-Tradis/pull/88) ([ssjunnebo](https://github.com/ssjunnebo))
- Replace cram file without reads [\#87](https://github.com/sanger-pathogens/Bio-Tradis/pull/87) ([ssjunnebo](https://github.com/ssjunnebo))
- update tutorial for ENA switch to https \(from http\) [\#85](https://github.com/sanger-pathogens/Bio-Tradis/pull/85) ([lbarquist](https://github.com/lbarquist))

## [1.4.0](https://github.com/sanger-pathogens/Bio-Tradis/tree/1.4.0) (2017-11-28)
[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/v1.3.3...1.4.0)

**Closed issues:**

- Duplicate genes [\#81](https://github.com/sanger-pathogens/Bio-Tradis/issues/81)
- Installing Bio-Tradis Fail  [\#80](https://github.com/sanger-pathogens/Bio-Tradis/issues/80)

**Merged pull requests:**

- include last base of annotation in insertion count [\#82](https://github.com/sanger-pathogens/Bio-Tradis/pull/82) ([lbarquist](https://github.com/lbarquist))
- Rename license file' [\#79](https://github.com/sanger-pathogens/Bio-Tradis/pull/79) ([ssjunnebo](https://github.com/ssjunnebo))
- update AUTHORS and rename LICENSE [\#78](https://github.com/sanger-pathogens/Bio-Tradis/pull/78) ([ssjunnebo](https://github.com/ssjunnebo))
- Tmp file time stamp [\#77](https://github.com/sanger-pathogens/Bio-Tradis/pull/77) ([ssjunnebo](https://github.com/ssjunnebo))

## [v1.3.3](https://github.com/sanger-pathogens/Bio-Tradis/tree/v1.3.3) (2017-05-08)
[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/v1.3.2...v1.3.3)

**Merged pull requests:**

- try localtime for tmp file timestamp [\#76](https://github.com/sanger-pathogens/Bio-Tradis/pull/76) ([ssjunnebo](https://github.com/ssjunnebo))

## [v1.3.2](https://github.com/sanger-pathogens/Bio-Tradis/tree/v1.3.2) (2017-05-08)
[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/v1.3.1...v1.3.2)

**Closed issues:**

- cpan update? [\#75](https://github.com/sanger-pathogens/Bio-Tradis/issues/75)
- tradis\_comparison.R error [\#71](https://github.com/sanger-pathogens/Bio-Tradis/issues/71)

**Merged pull requests:**

- modified ranges to accommodate higher density insertion data [\#74](https://github.com/sanger-pathogens/Bio-Tradis/pull/74) ([lbarquist](https://github.com/lbarquist))
- removed File::Slurp [\#73](https://github.com/sanger-pathogens/Bio-Tradis/pull/73) ([vaofford](https://github.com/vaofford))
- dont add POD to R scripts [\#72](https://github.com/sanger-pathogens/Bio-Tradis/pull/72) ([andrewjpage](https://github.com/andrewjpage))

## [v1.3.1](https://github.com/sanger-pathogens/Bio-Tradis/tree/v1.3.1) (2016-09-23)
[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/v1.3.0...v1.3.1)

**Closed issues:**

- Mapping score always set to 1 if -m option used with plot\_tradis [\#66](https://github.com/sanger-pathogens/Bio-Tradis/issues/66)
- Error in step 3.5 of bacteria\_tradis, using samtools 1.3 [\#63](https://github.com/sanger-pathogens/Bio-Tradis/issues/63)

**Merged pull requests:**

- change to dist zilla starter bundle [\#70](https://github.com/sanger-pathogens/Bio-Tradis/pull/70) ([nds](https://github.com/nds))
- switch PCR primers [\#69](https://github.com/sanger-pathogens/Bio-Tradis/pull/69) ([andrewjpage](https://github.com/andrewjpage))
- updated readme [\#68](https://github.com/sanger-pathogens/Bio-Tradis/pull/68) ([lbarquist](https://github.com/lbarquist))
- Fix for bug \#66, change mapping\_score option spec in B::T::CL::PlotTradis [\#67](https://github.com/sanger-pathogens/Bio-Tradis/pull/67) ([RoyChaudhuri](https://github.com/RoyChaudhuri))