# Change Log

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

[Full Changelog](https://github.com/sanger-pathogens/iva/compare/v1.0.9-2...HEAD)

**Merged pull requests:**

- Update readme [\#87](https://github.com/sanger-pathogens/iva/pull/87) ([ssjunnebo](https://github.com/ssjunnebo))
- Point install instruction to webpage [\#84](https://github.com/sanger-pathogens/iva/pull/84) ([ssjunnebo](https://github.com/ssjunnebo))
- update README and add to codecov [\#83](https://github.com/sanger-pathogens/iva/pull/83) ([ssjunnebo](https://github.com/ssjunnebo))
- Docker instructions [\#82](https://github.com/sanger-pathogens/iva/pull/82) ([ssjunnebo](https://github.com/ssjunnebo))
- Set up Docker [\#81](https://github.com/sanger-pathogens/iva/pull/81) ([ssjunnebo](https://github.com/ssjunnebo))

## [v1.0.9-2](https://github.com/sanger-pathogens/iva/tree/v1.0.9-2) (2018-02-02)
[Full Changelog](https://github.com/sanger-pathogens/iva/compare/v1.0.9-1...v1.0.9-2)

## [v1.0.9-1](https://github.com/sanger-pathogens/iva/tree/v1.0.9-1) (2018-02-02)
[Full Changelog](https://github.com/sanger-pathogens/iva/compare/v1.0.9...v1.0.9-1)

**Closed issues:**

- iva version check of external programs fails [\#78](https://github.com/sanger-pathogens/iva/issues/78)

## [v1.0.9](https://github.com/sanger-pathogens/iva/tree/v1.0.9) (2018-01-25)
[Full Changelog](https://github.com/sanger-pathogens/iva/compare/v1.0.8...v1.0.9)

**Closed issues:**

- kmc std::bad\_alloc [\#77](https://github.com/sanger-pathogens/iva/issues/77)
- samtools sort command fails for samtools 1.3.1 [\#75](https://github.com/sanger-pathogens/iva/issues/75)
- iva test failing with samtools1.4 [\#74](https://github.com/sanger-pathogens/iva/issues/74)
- IVA sensitivity threshold [\#72](https://github.com/sanger-pathogens/iva/issues/72)
- multithreading smalt error  [\#71](https://github.com/sanger-pathogens/iva/issues/71)

**Merged pull requests:**

- Prog versions [\#79](https://github.com/sanger-pathogens/iva/pull/79) ([andrewjpage](https://github.com/andrewjpage))
- test more samtools versions and pythons [\#76](https://github.com/sanger-pathogens/iva/pull/76) ([andrewjpage](https://github.com/andrewjpage))
- update LICENSE and AUTHORS [\#73](https://github.com/sanger-pathogens/iva/pull/73) ([ssjunnebo](https://github.com/ssjunnebo))

## [v1.0.8](https://github.com/sanger-pathogens/iva/tree/v1.0.8) (2017-01-12)
[Full Changelog](https://github.com/sanger-pathogens/iva/compare/v1.0.7...v1.0.8)

**Merged pull requests:**

- Embl no cds fix [\#70](https://github.com/sanger-pathogens/iva/pull/70) ([martinghunt](https://github.com/martinghunt))
- upstreaming some patches [\#69](https://github.com/sanger-pathogens/iva/pull/69) ([satta](https://github.com/satta))

## [v1.0.7](https://github.com/sanger-pathogens/iva/tree/v1.0.7) (2016-09-06)
[Full Changelog](https://github.com/sanger-pathogens/iva/compare/v1.0.6...v1.0.7)

**Merged pull requests:**

- Pysam 0.9.1.x [\#68](https://github.com/sanger-pathogens/iva/pull/68) ([martinghunt](https://github.com/martinghunt))

## [v1.0.6](https://github.com/sanger-pathogens/iva/tree/v1.0.6) (2016-05-12)
[Full Changelog](https://github.com/sanger-pathogens/iva/compare/v1.0.5...v1.0.6)

**Closed issues:**

- samtools errors caused by mapping.py  [\#59](https://github.com/sanger-pathogens/iva/issues/59)

**Merged pull requests:**

- Flag reference opt as experimental [\#67](https://github.com/sanger-pathogens/iva/pull/67) ([martinghunt](https://github.com/martinghunt))
- Add travis files [\#66](https://github.com/sanger-pathogens/iva/pull/66) ([martinghunt](https://github.com/martinghunt))

## [v1.0.5](https://github.com/sanger-pathogens/iva/tree/v1.0.5) (2016-05-05)
[Full Changelog](https://github.com/sanger-pathogens/iva/compare/v1.0.4...v1.0.5)

**Closed issues:**

- Support samtools 1.3 [\#57](https://github.com/sanger-pathogens/iva/issues/57)

**Merged pull requests:**

- Version bump 1.0.5 [\#65](https://github.com/sanger-pathogens/iva/pull/65) ([martinghunt](https://github.com/martinghunt))
- fix spelling [\#64](https://github.com/sanger-pathogens/iva/pull/64) ([satta](https://github.com/satta))
- add copyright notices [\#62](https://github.com/sanger-pathogens/iva/pull/62) ([satta](https://github.com/satta))
- make IVA compatible with new 'samtools sort' syntax [\#61](https://github.com/sanger-pathogens/iva/pull/61) ([satta](https://github.com/satta))

## [v1.0.4](https://github.com/sanger-pathogens/iva/tree/v1.0.4) (2016-04-18)
[Full Changelog](https://github.com/sanger-pathogens/iva/compare/v1.0.3...v1.0.4)

**Closed issues:**

- IVA: error: unrecognized arguments: path\_to\_output\_directory [\#56](https://github.com/sanger-pathogens/iva/issues/56)
- thread option not passed to kmc [\#54](https://github.com/sanger-pathogens/iva/issues/54)

**Merged pull requests:**

- pysam 0.9.0 [\#58](https://github.com/sanger-pathogens/iva/pull/58) ([martinghunt](https://github.com/martinghunt))

## [v1.0.3](https://github.com/sanger-pathogens/iva/tree/v1.0.3) (2016-01-25)
[Full Changelog](https://github.com/sanger-pathogens/iva/compare/v1.0.2...v1.0.3)

**Closed issues:**

- support an explicit output argument  [\#53](https://github.com/sanger-pathogens/iva/issues/53)

**Merged pull requests:**

- Kmc threads [\#55](https://github.com/sanger-pathogens/iva/pull/55) ([martinghunt](https://github.com/martinghunt))

## [v1.0.2](https://github.com/sanger-pathogens/iva/tree/v1.0.2) (2015-10-28)
[Full Changelog](https://github.com/sanger-pathogens/iva/compare/v1.0.1...v1.0.2)

**Merged pull requests:**

- Check samtools version [\#52](https://github.com/sanger-pathogens/iva/pull/52) ([martinghunt](https://github.com/martinghunt))

## [v1.0.1](https://github.com/sanger-pathogens/iva/tree/v1.0.1) (2015-10-16)
[Full Changelog](https://github.com/sanger-pathogens/iva/compare/v1.0.0...v1.0.1)

**Merged pull requests:**

- Use pyfastaq 3.10.0 [\#51](https://github.com/sanger-pathogens/iva/pull/51) ([martinghunt](https://github.com/martinghunt))
- import stat required to stop --add\_to\_ref dying [\#50](https://github.com/sanger-pathogens/iva/pull/50) ([martinghunt](https://github.com/martinghunt))

## [v1.0.0](https://github.com/sanger-pathogens/iva/tree/v1.0.0) (2015-07-15)
[Full Changelog](https://github.com/sanger-pathogens/iva/compare/v0.11.7...v1.0.0)

**Merged pull requests:**

- Make tests pass from last merge [\#49](https://github.com/sanger-pathogens/iva/pull/49) ([martinghunt](https://github.com/martinghunt))
- No strand bias trim [\#48](https://github.com/sanger-pathogens/iva/pull/48) ([martinghunt](https://github.com/martinghunt))

## [v0.11.7](https://github.com/sanger-pathogens/iva/tree/v0.11.7) (2015-07-09)
[Full Changelog](https://github.com/sanger-pathogens/iva/compare/v0.11.6...v0.11.7)

**Merged pull requests:**

-  version bump, tweak setup.py [\#47](https://github.com/sanger-pathogens/iva/pull/47) ([martinghunt](https://github.com/martinghunt))
- Die nicely if input reads bad, or when no contigs made [\#46](https://github.com/sanger-pathogens/iva/pull/46) ([martinghunt](https://github.com/martinghunt))

## [v0.11.6](https://github.com/sanger-pathogens/iva/tree/v0.11.6) (2015-05-12)
[Full Changelog](https://github.com/sanger-pathogens/iva/compare/v0.11.5...v0.11.6)

**Merged pull requests:**

- Bug reusing bad kmers [\#45](https://github.com/sanger-pathogens/iva/pull/45) ([martinghunt](https://github.com/martinghunt))
- Bug fix - min contig length now implemented properly [\#44](https://github.com/sanger-pathogens/iva/pull/44) ([martinghunt](https://github.com/martinghunt))

## [v0.11.5](https://github.com/sanger-pathogens/iva/tree/v0.11.5) (2015-03-27)
[Full Changelog](https://github.com/sanger-pathogens/iva/compare/v0.11.4...v0.11.5)

**Merged pull requests:**

- Increment version [\#43](https://github.com/sanger-pathogens/iva/pull/43) ([martinghunt](https://github.com/martinghunt))
- Qc input checks [\#42](https://github.com/sanger-pathogens/iva/pull/42) ([martinghunt](https://github.com/martinghunt))
- Fix gage bugs [\#41](https://github.com/sanger-pathogens/iva/pull/41) ([martinghunt](https://github.com/martinghunt))

## [v0.11.4](https://github.com/sanger-pathogens/iva/tree/v0.11.4) (2015-02-24)
[Full Changelog](https://github.com/sanger-pathogens/iva/compare/v0.11.3...v0.11.4)

**Merged pull requests:**

- No really, make all ratt script executable [\#40](https://github.com/sanger-pathogens/iva/pull/40) ([martinghunt](https://github.com/martinghunt))

## [v0.11.3](https://github.com/sanger-pathogens/iva/tree/v0.11.3) (2015-02-24)
[Full Changelog](https://github.com/sanger-pathogens/iva/compare/v0.11.2...v0.11.3)

**Merged pull requests:**

- bug fix running ratt scripts [\#39](https://github.com/sanger-pathogens/iva/pull/39) ([martinghunt](https://github.com/martinghunt))

## [v0.11.2](https://github.com/sanger-pathogens/iva/tree/v0.11.2) (2015-02-05)
[Full Changelog](https://github.com/sanger-pathogens/iva/compare/v0.11.0...v0.11.2)

**Merged pull requests:**

- Remove info that is on the gh-pages site [\#38](https://github.com/sanger-pathogens/iva/pull/38) ([martinghunt](https://github.com/martinghunt))
- Change to pyfastaq [\#37](https://github.com/sanger-pathogens/iva/pull/37) ([martinghunt](https://github.com/martinghunt))

## [v0.11.0](https://github.com/sanger-pathogens/iva/tree/v0.11.0) (2015-01-29)
[Full Changelog](https://github.com/sanger-pathogens/iva/compare/v0.10.3...v0.11.0)

**Merged pull requests:**

- Change default extension parameters, bump to version 0.11.0 [\#36](https://github.com/sanger-pathogens/iva/pull/36) ([martinghunt](https://github.com/martinghunt))

## [v0.10.3](https://github.com/sanger-pathogens/iva/tree/v0.10.3) (2015-01-14)
[Full Changelog](https://github.com/sanger-pathogens/iva/compare/v0.10.2...v0.10.3)

**Merged pull requests:**

- Allow gage to fail as long as we got the stats; v0.10.3 [\#35](https://github.com/sanger-pathogens/iva/pull/35) ([martinghunt](https://github.com/martinghunt))

## [v0.10.2](https://github.com/sanger-pathogens/iva/tree/v0.10.2) (2015-01-07)
[Full Changelog](https://github.com/sanger-pathogens/iva/compare/v0.10.1...v0.10.2)

**Merged pull requests:**

- version 0.10.2 [\#34](https://github.com/sanger-pathogens/iva/pull/34) ([martinghunt](https://github.com/martinghunt))

## [v0.10.1](https://github.com/sanger-pathogens/iva/tree/v0.10.1) (2014-12-05)
[Full Changelog](https://github.com/sanger-pathogens/iva/compare/v0.10.0...v0.10.1)

**Merged pull requests:**

- Bug fixes: string decoding and qc write contigs file [\#33](https://github.com/sanger-pathogens/iva/pull/33) ([martinghunt](https://github.com/martinghunt))
- Link to the pathogens VM [\#32](https://github.com/sanger-pathogens/iva/pull/32) ([martinghunt](https://github.com/martinghunt))

## [v0.10.0](https://github.com/sanger-pathogens/iva/tree/v0.10.0) (2014-11-06)
[Full Changelog](https://github.com/sanger-pathogens/iva/compare/v0.9.0...v0.10.0)

**Merged pull requests:**

- Improve read trimming; version 0.10.0 [\#31](https://github.com/sanger-pathogens/iva/pull/31) ([martinghunt](https://github.com/martinghunt))

## [v0.9.0](https://github.com/sanger-pathogens/iva/tree/v0.9.0) (2014-10-02)
[Full Changelog](https://github.com/sanger-pathogens/iva/compare/1.5.0...v0.9.0)

## [1.5.0](https://github.com/sanger-pathogens/iva/tree/1.5.0) (2014-10-02)
[Full Changelog](https://github.com/sanger-pathogens/iva/compare/v0.8.0...1.5.0)

**Merged pull requests:**

- version 0.9.0 [\#30](https://github.com/sanger-pathogens/iva/pull/30) ([martinghunt](https://github.com/martinghunt))
- write contigs that do not match reference [\#29](https://github.com/sanger-pathogens/iva/pull/29) ([martinghunt](https://github.com/martinghunt))
- Add ubuntu installation wiki link [\#28](https://github.com/sanger-pathogens/iva/pull/28) ([martinghunt](https://github.com/martinghunt))
- Contig trim [\#27](https://github.com/sanger-pathogens/iva/pull/27) ([martinghunt](https://github.com/martinghunt))

## [v0.8.0](https://github.com/sanger-pathogens/iva/tree/v0.8.0) (2014-09-11)
[Full Changelog](https://github.com/sanger-pathogens/iva/compare/v0.7.2...v0.8.0)

**Merged pull requests:**

- Pcr primer [\#26](https://github.com/sanger-pathogens/iva/pull/26) ([martinghunt](https://github.com/martinghunt))
- Added AUTHORS file [\#25](https://github.com/sanger-pathogens/iva/pull/25) ([aslett1](https://github.com/aslett1))

## [v0.7.2](https://github.com/sanger-pathogens/iva/tree/v0.7.2) (2014-08-27)
[Full Changelog](https://github.com/sanger-pathogens/iva/compare/v0.7.1...v0.7.2)

## [v0.7.1](https://github.com/sanger-pathogens/iva/tree/v0.7.1) (2014-08-05)
[Full Changelog](https://github.com/sanger-pathogens/iva/compare/v0.7.0...v0.7.1)

## [v0.7.0](https://github.com/sanger-pathogens/iva/tree/v0.7.0) (2014-08-01)
[Full Changelog](https://github.com/sanger-pathogens/iva/compare/v0.6.0...v0.7.0)

## [v0.6.0](https://github.com/sanger-pathogens/iva/tree/v0.6.0) (2014-07-25)
[Full Changelog](https://github.com/sanger-pathogens/iva/compare/v0.5.1...v0.6.0)

## [v0.5.1](https://github.com/sanger-pathogens/iva/tree/v0.5.1) (2014-06-17)
[Full Changelog](https://github.com/sanger-pathogens/iva/compare/v0.5.0...v0.5.1)

## [v0.5.0](https://github.com/sanger-pathogens/iva/tree/v0.5.0) (2014-06-12)
[Full Changelog](https://github.com/sanger-pathogens/iva/compare/v0.4.0...v0.5.0)

**Merged pull requests:**

- Version 0.5.0 [\#24](https://github.com/sanger-pathogens/iva/pull/24) ([martinghunt](https://github.com/martinghunt))
- Qc cleanup [\#23](https://github.com/sanger-pathogens/iva/pull/23) ([martinghunt](https://github.com/martinghunt))

## [v0.4.0](https://github.com/sanger-pathogens/iva/tree/v0.4.0) (2014-06-11)
[Full Changelog](https://github.com/sanger-pathogens/iva/compare/v0.3.0...v0.4.0)

**Merged pull requests:**

- Change default QC percent identities to 80 [\#22](https://github.com/sanger-pathogens/iva/pull/22) ([martinghunt](https://github.com/martinghunt))
- Die gracefully if cannot find reference [\#21](https://github.com/sanger-pathogens/iva/pull/21) ([martinghunt](https://github.com/martinghunt))
- Add test embl files [\#20](https://github.com/sanger-pathogens/iva/pull/20) ([martinghunt](https://github.com/martinghunt))
- merge tidy\_up\_for\_v0.4.0 [\#19](https://github.com/sanger-pathogens/iva/pull/19) ([martinghunt](https://github.com/martinghunt))
- merge add\_custom\_ref\_to\_db [\#18](https://github.com/sanger-pathogens/iva/pull/18) ([martinghunt](https://github.com/martinghunt))
- Tidy up checking external programs OK [\#17](https://github.com/sanger-pathogens/iva/pull/17) ([martinghunt](https://github.com/martinghunt))
- Add citation for adapter sequences [\#16](https://github.com/sanger-pathogens/iva/pull/16) ([martinghunt](https://github.com/martinghunt))
- Don't write final ORFs file [\#15](https://github.com/sanger-pathogens/iva/pull/15) ([martinghunt](https://github.com/martinghunt))
- Delete gage-validation.tar.gz [\#14](https://github.com/sanger-pathogens/iva/pull/14) ([martinghunt](https://github.com/martinghunt))
- Keep gage and ratt code and adapters.fasta files when installing [\#13](https://github.com/sanger-pathogens/iva/pull/13) ([martinghunt](https://github.com/martinghunt))
- Add checks for external programs in qc scripts [\#12](https://github.com/sanger-pathogens/iva/pull/12) ([martinghunt](https://github.com/martinghunt))
- Run kraken on reads sampled uniformly across assembly [\#11](https://github.com/sanger-pathogens/iva/pull/11) ([martinghunt](https://github.com/martinghunt))
- Add QC info and citations [\#10](https://github.com/sanger-pathogens/iva/pull/10) ([martinghunt](https://github.com/martinghunt))
- Use same function for all syscalls, so stdout/err only printed when some... [\#9](https://github.com/sanger-pathogens/iva/pull/9) ([martinghunt](https://github.com/martinghunt))
- Add default adapters file [\#8](https://github.com/sanger-pathogens/iva/pull/8) ([martinghunt](https://github.com/martinghunt))
- Add gage code, make gage defaults more permissive [\#7](https://github.com/sanger-pathogens/iva/pull/7) ([martinghunt](https://github.com/martinghunt))
- Catch mpileup lines with no read bases [\#6](https://github.com/sanger-pathogens/iva/pull/6) ([martinghunt](https://github.com/martinghunt))
- Assemble speed increase by using reads more intelligently [\#5](https://github.com/sanger-pathogens/iva/pull/5) ([martinghunt](https://github.com/martinghunt))
- Don't initialize sets, dicts etc in function declarations [\#4](https://github.com/sanger-pathogens/iva/pull/4) ([martinghunt](https://github.com/martinghunt))

## [v0.3.0](https://github.com/sanger-pathogens/iva/tree/v0.3.0) (2014-05-02)
[Full Changelog](https://github.com/sanger-pathogens/iva/compare/v0.2.4...v0.3.0)

**Merged pull requests:**

- Fix missing genome parts [\#3](https://github.com/sanger-pathogens/iva/pull/3) ([martinghunt](https://github.com/martinghunt))

## [v0.2.4](https://github.com/sanger-pathogens/iva/tree/v0.2.4) (2014-04-30)
**Merged pull requests:**

- Fix max\_insert typo [\#2](https://github.com/sanger-pathogens/iva/pull/2) ([martinghunt](https://github.com/martinghunt))
- Initial add of files and update readme [\#1](https://github.com/sanger-pathogens/iva/pull/1) ([martinghunt](https://github.com/martinghunt))

