Vafator

Bugfixes:

* Issue 18
* Issue 19

Changes:

* Nextflow workflow now has a more flexible input to allow using multiple samples

Fixes

* VCFs with MNVs were crashing, this is fixed now. No annotation is added for MNVs

Non functional features

* Nextfllow workflow automated tests do not rely now on conda and hence work

Fixes

* Fix error when `--bam` parameter is not provided

Non functional features

* Added automated integration tests that install vafator and run some different command line configurations

Changes:

* Add script vafator2decifer
* Add parameter `--bam sample_name bam_file` to replace difficult to use `--prefix`

Changes:
* Support for the annotation of indels
* Added better unit testing using data from GIAB
* Changed the thresholds `--mapping-quality` and `--base-call-quality` to filter all reads below the thresholds as opposed to previous behaviour filtering all reads equal or below the threshold. This was cause of a lot of confusion and pysam uses this thresholds
* Use pysam filtering of reads to avoid reading qualities manually, this increases performance around 60%