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# Change Log

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

[Full Changelog](https://github.com/sanger-pathogens/pymummer/compare/v0.10.3...HEAD)

**Merged pull requests:**

- update README [\#29](https://github.com/sanger-pathogens/pymummer/pull/29) ([ssjunnebo](https://github.com/ssjunnebo))

## [v0.10.3](https://github.com/sanger-pathogens/pymummer/tree/v0.10.3) (2017-08-21)
[Full Changelog](https://github.com/sanger-pathogens/pymummer/compare/v0.10.2...v0.10.3)

**Merged pull requests:**

- Add diagfactor \(-d\) and maxgap \(-g\) options for nucmer [\#28](https://github.com/sanger-pathogens/pymummer/pull/28) ([Adamtaranto](https://github.com/Adamtaranto))
- update LICENSE [\#27](https://github.com/sanger-pathogens/pymummer/pull/27) ([ssjunnebo](https://github.com/ssjunnebo))

## [v0.10.2](https://github.com/sanger-pathogens/pymummer/tree/v0.10.2) (2017-02-02)
[Full Changelog](https://github.com/sanger-pathogens/pymummer/compare/v0.10.1...v0.10.2)

**Closed issues:**

- MUMmer programs not found in path  [\#21](https://github.com/sanger-pathogens/pymummer/issues/21)

**Merged pull requests:**

- Ref qry translate vars not in matches [\#26](https://github.com/sanger-pathogens/pymummer/pull/26) ([martinghunt](https://github.com/martinghunt))

## [v0.10.1](https://github.com/sanger-pathogens/pymummer/tree/v0.10.1) (2016-11-18)
[Full Changelog](https://github.com/sanger-pathogens/pymummer/compare/v0.10.0...v0.10.1)

**Merged pull requests:**

- Indels bug [\#25](https://github.com/sanger-pathogens/pymummer/pull/25) ([martinghunt](https://github.com/martinghunt))

## [v0.10.0](https://github.com/sanger-pathogens/pymummer/tree/v0.10.0) (2016-11-15)
[Full Changelog](https://github.com/sanger-pathogens/pymummer/compare/v0.9.0...v0.10.0)

**Merged pull requests:**

- Show snps expose C option [\#24](https://github.com/sanger-pathogens/pymummer/pull/24) ([martinghunt](https://github.com/martinghunt))

## [v0.9.0](https://github.com/sanger-pathogens/pymummer/tree/v0.9.0) (2016-10-17)
[Full Changelog](https://github.com/sanger-pathogens/pymummer/compare/v0.8.1...v0.9.0)

**Merged pull requests:**

- Expose mincluster [\#23](https://github.com/sanger-pathogens/pymummer/pull/23) ([martinghunt](https://github.com/martinghunt))

## [v0.8.1](https://github.com/sanger-pathogens/pymummer/tree/v0.8.1) (2016-08-23)
[Full Changelog](https://github.com/sanger-pathogens/pymummer/compare/v0.8.0...v0.8.1)

## [v0.8.0](https://github.com/sanger-pathogens/pymummer/tree/v0.8.0) (2016-08-23)
[Full Changelog](https://github.com/sanger-pathogens/pymummer/compare/v0.7.1...v0.8.0)

**Merged pull requests:**

- Ref coords from qry coord [\#22](https://github.com/sanger-pathogens/pymummer/pull/22) ([martinghunt](https://github.com/martinghunt))

## [v0.7.1](https://github.com/sanger-pathogens/pymummer/tree/v0.7.1) (2016-04-18)
[Full Changelog](https://github.com/sanger-pathogens/pymummer/compare/v0.7.0...v0.7.1)

**Merged pull requests:**

- Make  \_\_version\_\_  work [\#20](https://github.com/sanger-pathogens/pymummer/pull/20) ([martinghunt](https://github.com/martinghunt))

## [v0.7.0](https://github.com/sanger-pathogens/pymummer/tree/v0.7.0) (2016-02-09)
[Full Changelog](https://github.com/sanger-pathogens/pymummer/compare/v0.6.1...v0.7.0)

**Merged pull requests:**

- Coords finding in matches [\#19](https://github.com/sanger-pathogens/pymummer/pull/19) ([martinghunt](https://github.com/martinghunt))

## [v0.6.1](https://github.com/sanger-pathogens/pymummer/tree/v0.6.1) (2015-10-19)
[Full Changelog](https://github.com/sanger-pathogens/pymummer/compare/v0.6.0...v0.6.1)

**Merged pull requests:**

- Remove numpy dependency [\#18](https://github.com/sanger-pathogens/pymummer/pull/18) ([martinghunt](https://github.com/martinghunt))

## [v0.6.0](https://github.com/sanger-pathogens/pymummer/tree/v0.6.0) (2015-10-14)
[Full Changelog](https://github.com/sanger-pathogens/pymummer/compare/v0.5.0...v0.6.0)

**Merged pull requests:**

- Convert to mspcrunch [\#17](https://github.com/sanger-pathogens/pymummer/pull/17) ([martinghunt](https://github.com/martinghunt))

## [v0.5.0](https://github.com/sanger-pathogens/pymummer/tree/v0.5.0) (2015-10-09)
[Full Changelog](https://github.com/sanger-pathogens/pymummer/compare/v0.4.0...v0.5.0)

**Merged pull requests:**

- Msp crunch output [\#16](https://github.com/sanger-pathogens/pymummer/pull/16) ([martinghunt](https://github.com/martinghunt))
- Add TravisCI support [\#15](https://github.com/sanger-pathogens/pymummer/pull/15) ([bewt85](https://github.com/bewt85))

## [v0.4.0](https://github.com/sanger-pathogens/pymummer/tree/v0.4.0) (2015-05-28)
[Full Changelog](https://github.com/sanger-pathogens/pymummer/compare/v0.3.0...v0.4.0)

**Merged pull requests:**

- Expose diagdiff to nucmer [\#14](https://github.com/sanger-pathogens/pymummer/pull/14) ([martinghunt](https://github.com/martinghunt))

## [v0.3.0](https://github.com/sanger-pathogens/pymummer/tree/v0.3.0) (2015-05-15)
[Full Changelog](https://github.com/sanger-pathogens/pymummer/compare/v0.2.0...v0.3.0)

## [v0.2.0](https://github.com/sanger-pathogens/pymummer/tree/v0.2.0) (2015-05-15)
[Full Changelog](https://github.com/sanger-pathogens/pymummer/compare/v0.1.0...v0.2.0)

**Merged pull requests:**

- Reverse alignments [\#13](https://github.com/sanger-pathogens/pymummer/pull/13) ([martinghunt](https://github.com/martinghunt))
- Fix constructing alignment from promer output [\#12](https://github.com/sanger-pathogens/pymummer/pull/12) ([martinghunt](https://github.com/martinghunt))
- Add promer option; version bump [\#11](https://github.com/sanger-pathogens/pymummer/pull/11) ([martinghunt](https://github.com/martinghunt))

## [v0.1.0](https://github.com/sanger-pathogens/pymummer/tree/v0.1.0) (2015-03-05)
[Full Changelog](https://github.com/sanger-pathogens/pymummer/compare/v0.0.2...v0.1.0)

**Merged pull requests:**

- minor version number incremented [\#10](https://github.com/sanger-pathogens/pymummer/pull/10) ([nds](https://github.com/nds))
- Added --nosimplify toggle to nucmer command [\#9](https://github.com/sanger-pathogens/pymummer/pull/9) ([nds](https://github.com/nds))

## [v0.0.2](https://github.com/sanger-pathogens/pymummer/tree/v0.0.2) (2015-02-02)
**Merged pull requests:**

- Change to pyfastaq; add to pypi [\#8](https://github.com/sanger-pathogens/pymummer/pull/8) ([martinghunt](https://github.com/martinghunt))
- put system call code in seprate module [\#7](https://github.com/sanger-pathogens/pymummer/pull/7) ([martinghunt](https://github.com/martinghunt))
- Add snp\_file to list of modules [\#6](https://github.com/sanger-pathogens/pymummer/pull/6) ([martinghunt](https://github.com/martinghunt))
- Added documentation in README file [\#5](https://github.com/sanger-pathogens/pymummer/pull/5) ([nds](https://github.com/nds))
- Add variant calling [\#4](https://github.com/sanger-pathogens/pymummer/pull/4) ([martinghunt](https://github.com/martinghunt))
- Added some doc lines [\#3](https://github.com/sanger-pathogens/pymummer/pull/3) ([nds](https://github.com/nds))
- Split into separate files [\#2](https://github.com/sanger-pathogens/pymummer/pull/2) ([martinghunt](https://github.com/martinghunt))
- Initial commit [\#1](https://github.com/sanger-pathogens/pymummer/pull/1) ([martinghunt](https://github.com/martinghunt))