File: CHANGELOG.md

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# Change Log

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

[Full Changelog](https://github.com/sanger-pathogens/snp-sites/compare/v2.4.1...HEAD)

**Closed issues:**

- SegFault for unknown reason [\#72](https://github.com/sanger-pathogens/snp-sites/issues/72)

**Merged pull requests:**

- Include tests in README [\#73](https://github.com/sanger-pathogens/snp-sites/pull/73) ([ssjunnebo](https://github.com/ssjunnebo))

## [v2.4.1](https://github.com/sanger-pathogens/snp-sites/tree/v2.4.1) (2018-10-04)
[Full Changelog](https://github.com/sanger-pathogens/snp-sites/compare/v2.4.0...v2.4.1)

**Implemented enhancements:**

- Print to screen [\#63](https://github.com/sanger-pathogens/snp-sites/issues/63)

**Fixed bugs:**

- Docker file typo [\#60](https://github.com/sanger-pathogens/snp-sites/issues/60)

**Closed issues:**

- Info in VCF output format [\#68](https://github.com/sanger-pathogens/snp-sites/issues/68)

**Merged pull requests:**

- Include docker and conda badges [\#70](https://github.com/sanger-pathogens/snp-sites/pull/70) ([ssjunnebo](https://github.com/ssjunnebo))
- fixed Dockerfile [\#67](https://github.com/sanger-pathogens/snp-sites/pull/67) ([trstickland](https://github.com/trstickland))

## [v2.4.0](https://github.com/sanger-pathogens/snp-sites/tree/v2.4.0) (2018-01-29)
[Full Changelog](https://github.com/sanger-pathogens/snp-sites/compare/2.3.3...v2.4.0)

**Fixed bugs:**

- segmentation fault with `-b` option [\#58](https://github.com/sanger-pathogens/snp-sites/issues/58)
- Segmentation fault with larger sequences \(on Desktop and HPC\) [\#57](https://github.com/sanger-pathogens/snp-sites/issues/57)

**Closed issues:**

- Gaps not reported in output? [\#61](https://github.com/sanger-pathogens/snp-sites/issues/61)

**Merged pull requests:**

- update readme [\#65](https://github.com/sanger-pathogens/snp-sites/pull/65) ([ssjunnebo](https://github.com/ssjunnebo))
- Jk seg fault [\#59](https://github.com/sanger-pathogens/snp-sites/pull/59) ([andrewjpage](https://github.com/andrewjpage))

## [2.3.3](https://github.com/sanger-pathogens/snp-sites/tree/2.3.3) (2017-06-09)
[Full Changelog](https://github.com/sanger-pathogens/snp-sites/compare/2.3.2...2.3.3)

**Closed issues:**

- brew recipe needs to be updated to the latest release. [\#55](https://github.com/sanger-pathogens/snp-sites/issues/55)
- Linuxbrew installation issue \(links issue\) [\#54](https://github.com/sanger-pathogens/snp-sites/issues/54)

**Merged pull requests:**

- update LICENSE and AUTHORS [\#56](https://github.com/sanger-pathogens/snp-sites/pull/56) ([ssjunnebo](https://github.com/ssjunnebo))

## [2.3.2](https://github.com/sanger-pathogens/snp-sites/tree/2.3.2) (2016-05-12)
[Full Changelog](https://github.com/sanger-pathogens/snp-sites/compare/2.3.1...2.3.2)

**Closed issues:**

- Didn't mean to open this [\#52](https://github.com/sanger-pathogens/snp-sites/issues/52)
- Failing tests on various platforms [\#51](https://github.com/sanger-pathogens/snp-sites/issues/51)

## [2.3.1](https://github.com/sanger-pathogens/snp-sites/tree/2.3.1) (2016-03-18)
[Full Changelog](https://github.com/sanger-pathogens/snp-sites/compare/2.3.0...2.3.1)

**Merged pull requests:**

- allow pure bases and monomorphic, making it work with BEAST [\#50](https://github.com/sanger-pathogens/snp-sites/pull/50) ([andrewjpage](https://github.com/andrewjpage))

## [2.3.0](https://github.com/sanger-pathogens/snp-sites/tree/2.3.0) (2016-03-17)
[Full Changelog](https://github.com/sanger-pathogens/snp-sites/compare/2.2.2...2.3.0)

## [2.2.2](https://github.com/sanger-pathogens/snp-sites/tree/2.2.2) (2016-03-14)
[Full Changelog](https://github.com/sanger-pathogens/snp-sites/compare/2.2.1...2.2.2)

**Merged pull requests:**

- make sure original API is not changed [\#49](https://github.com/sanger-pathogens/snp-sites/pull/49) ([satta](https://github.com/satta))
- update to 2.2.1 [\#48](https://github.com/sanger-pathogens/snp-sites/pull/48) ([andrewjpage](https://github.com/andrewjpage))

## [2.2.1](https://github.com/sanger-pathogens/snp-sites/tree/2.2.1) (2016-03-11)
[Full Changelog](https://github.com/sanger-pathogens/snp-sites/compare/2.2.0...2.2.1)

**Merged pull requests:**

- adjust manpage [\#47](https://github.com/sanger-pathogens/snp-sites/pull/47) ([satta](https://github.com/satta))
- output reference and change name to snp-sites [\#46](https://github.com/sanger-pathogens/snp-sites/pull/46) ([andrewjpage](https://github.com/andrewjpage))

## [2.2.0](https://github.com/sanger-pathogens/snp-sites/tree/2.2.0) (2016-03-11)
[Full Changelog](https://github.com/sanger-pathogens/snp-sites/compare/2.1.3...2.2.0)

**Closed issues:**

- Build is failing on Mac OS [\#45](https://github.com/sanger-pathogens/snp-sites/issues/45)
- specify reference sequence [\#44](https://github.com/sanger-pathogens/snp-sites/issues/44)
- Add Arxiv paper link to README.md [\#43](https://github.com/sanger-pathogens/snp-sites/issues/43)

## [2.1.3](https://github.com/sanger-pathogens/snp-sites/tree/2.1.3) (2016-01-27)
[Full Changelog](https://github.com/sanger-pathogens/snp-sites/compare/2.1.1...2.1.3)

**Closed issues:**

- possible to convert to redhat? [\#39](https://github.com/sanger-pathogens/snp-sites/issues/39)

**Merged pull requests:**

- Ensure C99 compliance [\#42](https://github.com/sanger-pathogens/snp-sites/pull/42) ([AidanDelaney](https://github.com/AidanDelaney))
- Test data [\#41](https://github.com/sanger-pathogens/snp-sites/pull/41) ([andrewjpage](https://github.com/andrewjpage))
- Running the clang static analyser turns up an issue with unintialised… [\#40](https://github.com/sanger-pathogens/snp-sites/pull/40) ([AidanDelaney](https://github.com/AidanDelaney))

## [2.1.1](https://github.com/sanger-pathogens/snp-sites/tree/2.1.1) (2015-12-14)
[Full Changelog](https://github.com/sanger-pathogens/snp-sites/compare/2.1.0...2.1.1)

**Implemented enhancements:**

- Opens \<file\> twice? [\#26](https://github.com/sanger-pathogens/snp-sites/issues/26)

**Fixed bugs:**

- make check =\> cannot find -lsubunit [\#33](https://github.com/sanger-pathogens/snp-sites/issues/33)
- autoreconf -i warnings =\> option 'subdir-objects' is disabled [\#29](https://github.com/sanger-pathogens/snp-sites/issues/29)

**Merged pull requests:**

- Autotoolize checking for dependencies [\#38](https://github.com/sanger-pathogens/snp-sites/pull/38) ([satta](https://github.com/satta))

## [2.1.0](https://github.com/sanger-pathogens/snp-sites/tree/2.1.0) (2015-12-03)
[Full Changelog](https://github.com/sanger-pathogens/snp-sites/compare/2.0.3...2.1.0)

**Merged pull requests:**

- Reduce times input file is opened [\#37](https://github.com/sanger-pathogens/snp-sites/pull/37) ([andrewjpage](https://github.com/andrewjpage))

## [2.0.3](https://github.com/sanger-pathogens/snp-sites/tree/2.0.3) (2015-12-03)
[Full Changelog](https://github.com/sanger-pathogens/snp-sites/compare/2.0.2...2.0.3)

**Closed issues:**

- How do we run the tests? [\#30](https://github.com/sanger-pathogens/snp-sites/issues/30)
- Add a --version switch? [\#27](https://github.com/sanger-pathogens/snp-sites/issues/27)
- FYI - updated brew package to 2.x series [\#24](https://github.com/sanger-pathogens/snp-sites/issues/24)

**Merged pull requests:**

- Bump version to 2.0.3 [\#36](https://github.com/sanger-pathogens/snp-sites/pull/36) ([bewt85](https://github.com/bewt85))
- 496468: Allow '?' in fasta input [\#35](https://github.com/sanger-pathogens/snp-sites/pull/35) ([bewt85](https://github.com/bewt85))
- Major cleanup to use standard C string functions [\#34](https://github.com/sanger-pathogens/snp-sites/pull/34) ([tseemann](https://github.com/tseemann))
- Add -V version flag \(Issue \#27\) [\#32](https://github.com/sanger-pathogens/snp-sites/pull/32) ([tseemann](https://github.com/tseemann))
- Use stdio FILENAME\_MAX for path char\[\] sizes [\#31](https://github.com/sanger-pathogens/snp-sites/pull/31) ([tseemann](https://github.com/tseemann))
- fix recent compilation failure in Debian [\#23](https://github.com/sanger-pathogens/snp-sites/pull/23) ([satta](https://github.com/satta))

## [2.0.2](https://github.com/sanger-pathogens/snp-sites/tree/2.0.2) (2015-09-03)
[Full Changelog](https://github.com/sanger-pathogens/snp-sites/compare/2.0.1...2.0.2)

**Merged pull requests:**

- Remove a tab in VCF header [\#22](https://github.com/sanger-pathogens/snp-sites/pull/22) ([bewt85](https://github.com/bewt85))
- Added bt5 and Jorge emails \(Jorge as path-help\) [\#21](https://github.com/sanger-pathogens/snp-sites/pull/21) ([aslett1](https://github.com/aslett1))

## [2.0.1](https://github.com/sanger-pathogens/snp-sites/tree/2.0.1) (2015-07-17)
[Full Changelog](https://github.com/sanger-pathogens/snp-sites/compare/1.5.0...2.0.1)

**Merged pull requests:**

- Add reference sequence length to VCF output [\#20](https://github.com/sanger-pathogens/snp-sites/pull/20) ([bewt85](https://github.com/bewt85))
- Change output format to show Genotype rather than Alt Base [\#19](https://github.com/sanger-pathogens/snp-sites/pull/19) ([bewt85](https://github.com/bewt85))
- Reformat README [\#18](https://github.com/sanger-pathogens/snp-sites/pull/18) ([bewt85](https://github.com/bewt85))

## [1.5.0](https://github.com/sanger-pathogens/snp-sites/tree/1.5.0) (2014-02-01)
[Full Changelog](https://github.com/sanger-pathogens/snp-sites/compare/1.4.11...1.5.0)

## [1.4.11](https://github.com/sanger-pathogens/snp-sites/tree/1.4.11) (2014-01-24)
[Full Changelog](https://github.com/sanger-pathogens/snp-sites/compare/1.4.10...1.4.11)

## [1.4.10](https://github.com/sanger-pathogens/snp-sites/tree/1.4.10) (2014-01-24)
[Full Changelog](https://github.com/sanger-pathogens/snp-sites/compare/1.4.9...1.4.10)

## [1.4.9](https://github.com/sanger-pathogens/snp-sites/tree/1.4.9) (2014-01-24)
[Full Changelog](https://github.com/sanger-pathogens/snp-sites/compare/1.4.8...1.4.9)

## [1.4.8](https://github.com/sanger-pathogens/snp-sites/tree/1.4.8) (2014-01-23)
[Full Changelog](https://github.com/sanger-pathogens/snp-sites/compare/1.4.7...1.4.8)

## [1.4.7](https://github.com/sanger-pathogens/snp-sites/tree/1.4.7) (2014-01-23)
[Full Changelog](https://github.com/sanger-pathogens/snp-sites/compare/1.4.6...1.4.7)

## [1.4.6](https://github.com/sanger-pathogens/snp-sites/tree/1.4.6) (2014-01-23)
[Full Changelog](https://github.com/sanger-pathogens/snp-sites/compare/1.4.5...1.4.6)

## [1.4.5](https://github.com/sanger-pathogens/snp-sites/tree/1.4.5) (2014-01-23)
[Full Changelog](https://github.com/sanger-pathogens/snp-sites/compare/1.4.4...1.4.5)

## [1.4.4](https://github.com/sanger-pathogens/snp-sites/tree/1.4.4) (2014-01-23)
[Full Changelog](https://github.com/sanger-pathogens/snp-sites/compare/1.4.3...1.4.4)

## [1.4.3](https://github.com/sanger-pathogens/snp-sites/tree/1.4.3) (2014-01-23)
[Full Changelog](https://github.com/sanger-pathogens/snp-sites/compare/1.4.2...1.4.3)

## [1.4.2](https://github.com/sanger-pathogens/snp-sites/tree/1.4.2) (2014-01-23)
[Full Changelog](https://github.com/sanger-pathogens/snp-sites/compare/1.4.1...1.4.2)

## [1.4.1](https://github.com/sanger-pathogens/snp-sites/tree/1.4.1) (2014-01-21)
[Full Changelog](https://github.com/sanger-pathogens/snp-sites/compare/1.4...1.4.1)

## [1.4](https://github.com/sanger-pathogens/snp-sites/tree/1.4) (2014-01-20)
[Full Changelog](https://github.com/sanger-pathogens/snp-sites/compare/1.3...1.4)

## [1.3](https://github.com/sanger-pathogens/snp-sites/tree/1.3) (2014-01-15)
[Full Changelog](https://github.com/sanger-pathogens/snp-sites/compare/1.2...1.3)

## [1.2](https://github.com/sanger-pathogens/snp-sites/tree/1.2) (2014-01-14)
[Full Changelog](https://github.com/sanger-pathogens/snp-sites/compare/1.1...1.2)

## [1.1](https://github.com/sanger-pathogens/snp-sites/tree/1.1) (2014-01-13)
[Full Changelog](https://github.com/sanger-pathogens/snp-sites/compare/1.0...1.1)

## [1.0](https://github.com/sanger-pathogens/snp-sites/tree/1.0) (2014-01-06)
[Full Changelog](https://github.com/sanger-pathogens/snp-sites/compare/0.1...1.0)

## [0.1](https://github.com/sanger-pathogens/snp-sites/tree/0.1) (2013-07-25)
**Merged pull requests:**

- travis install check [\#17](https://github.com/sanger-pathogens/snp-sites/pull/17) ([andrewjpage](https://github.com/andrewjpage))
- travis autoreconf [\#16](https://github.com/sanger-pathogens/snp-sites/pull/16) ([andrewjpage](https://github.com/andrewjpage))
- travis ci [\#15](https://github.com/sanger-pathogens/snp-sites/pull/15) ([andrewjpage](https://github.com/andrewjpage))
- Update version and readme [\#14](https://github.com/sanger-pathogens/snp-sites/pull/14) ([andrewjpage](https://github.com/andrewjpage))
- Fix memory leaks [\#13](https://github.com/sanger-pathogens/snp-sites/pull/13) ([andrewjpage](https://github.com/andrewjpage))
- fix memory leaks and update make [\#12](https://github.com/sanger-pathogens/snp-sites/pull/12) ([andrewjpage](https://github.com/andrewjpage))
- GPL [\#11](https://github.com/sanger-pathogens/snp-sites/pull/11) ([andrewjpage](https://github.com/andrewjpage))
- rollback changes to fasta file parsing [\#10](https://github.com/sanger-pathogens/snp-sites/pull/10) ([andrewjpage](https://github.com/andrewjpage))
- print unequal length error message to stderr [\#9](https://github.com/sanger-pathogens/snp-sites/pull/9) ([andrewjpage](https://github.com/andrewjpage))
- vcf coords from 1 [\#8](https://github.com/sanger-pathogens/snp-sites/pull/8) ([andrewjpage](https://github.com/andrewjpage))
- speedup [\#7](https://github.com/sanger-pathogens/snp-sites/pull/7) ([andrewjpage](https://github.com/andrewjpage))
- print out an error if the sequence lengths are uneven [\#6](https://github.com/sanger-pathogens/snp-sites/pull/6) ([andrewjpage](https://github.com/andrewjpage))
- speedup phylip creation [\#5](https://github.com/sanger-pathogens/snp-sites/pull/5) ([andrewjpage](https://github.com/andrewjpage))
- output filename [\#4](https://github.com/sanger-pathogens/snp-sites/pull/4) ([andrewjpage](https://github.com/andrewjpage))
- Tests for when an N is present in input [\#3](https://github.com/sanger-pathogens/snp-sites/pull/3) ([andrewjpage](https://github.com/andrewjpage))
- Choose output file formats [\#2](https://github.com/sanger-pathogens/snp-sites/pull/2) ([andrewjpage](https://github.com/andrewjpage))
- Treat N as a gap [\#1](https://github.com/sanger-pathogens/snp-sites/pull/1) ([andrewjpage](https://github.com/andrewjpage))