File: CHANGELOG

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qcumber 2.3.0-2
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## [Unreleased] 

Activation of new file input comming in 2.4
Fix for kraken will be in 2.3.1

## [2.3.0] - 2018-16-05

### Added 
-  Support for continous integration
-  Sample sheet generation (not used)

#### Test script: 
- Verbosity Option
- intoduced diffrent run levels for tests (low to high spec) (CI Node friendly)  
- remote data support

### Fixes
- SE MODE abort because of regex issue #19
- TrimBetter regex issue caused it to trim everything

## [2.2.1] - 2018-20-03

### Added

#### Test script:
- bash completion
- regex testing
- mapping
- local real data tests (no validation yet) 

### Changes
- touch ups
- zipped reference input works consistently 
- reexecution of rules is now based on their parameters 

#### Test script:
- utility functions for manipulation of goldstandard 


### Fixes
- matplotlib issue with long filenames (tight_layout() does not like them)
- 

 
## [2.2.0] - 2018-24-01

### Added

- An extended test suite is introduced. For more information please see the readme, which you will find in the test folder (soon: see #15) #4
- Insert size estimation: Distribution plots in mapping folder for each sample and text files with average, min and max fragment length. In batch report: boxplot with fragment length distribution

### Changed

- When using the option - - save for the Illumina Sequence Analysis Viewer, now all standard generated .xml files are required, as well as the InterOp folder. #14 
- “Couldn’t rename sample files” warnings are not displayed anymore.
- In single end data the plots in the batch report are now colored.
- In the kraken plots the top 10 taxonomies are displayed, instead of all over 5%. The taxanomy “root” is silenced. #7 

## [2.1.1] 

## [2.1.0] - 2017-31-12

### Added

- unclassified out option for kraken

### Changed

- report generation and format of output. Fixes #6 and concurrency issue
- Permission Updates

## [2.0.4] - 2017-17-11