Bug fix

Incorporated bug fix to stop the program throwing an error if a VCF is empty (e.g. an NTC sample might be empty quite regularly)

v0.1.1 - small bug fixes

Added some bug fixes identified while testing on PanCancer data (see issue #5):

• The script currently filters out any variants that aren't labelled as PASS in the VCF filter column, this means that some variants are being filtered out when they shouldn't be (e.g. if they are labelled as 'germline_risk')
• When applying BED files, an error is thrown for multi-allelic sites when finding the variant position, because the comma isn't removed from the string before trying to convert to an integer
• BED files aren't being saved within a 'hotspot_variants' folder

Checklist:

• Code review completed by JH
• Tests present and pass
• No changes to documentation required- except comments in code.
• This tool does not require an SOP - only run as part of larger pipeline.
• Validation will be carried out on a pipeline by pipeline basis.

First release for inclusion in SomaticAmplicon panel.

Merge pull request #4 from AWGL/development

Code review before putting into Somatic Amplicon