Vafator

Changes

* When a tumor copy number below one is provided we ensure the expected allele frequency is never greater than one by setting the tumor copy number to a minimum of one.
* Added support for python 3.10

Bugfix

- For deletions the relative position in the read is empty, it uses instead the next position after the deletion. This was causing a cryptic crash: `'<' not supported between instances of 'NoneType' and 'int'`

Bug fix

- When using replicates VAFator was crashing in 2.0.0 and 2.0.1 due to a wrong annotation name in the header.

Changes

- Dependencies are now more flexible + pysam is upgraded to 0.19

Changes

- Implement an approach to calculate the probability of an undetected somatic mutation
- Implement the absolute approach (Carter, 2017) to calculate the power to call a mutation
- Add the median MQ, BQ and relative position metrics
- Implement the rank sum test approach (DePristo, 2011) over MQ, BQ and relative position

Bugfixes

- There was an error in the accumulation of reads between replicates for indels, thus when providing replicates the aggregated coverage annotations for indels contained only the results from one replicate. This is fixed now

Changes

* Fix issue in vafator2decifer
* Add automated integration test for vafator2decifer