chapmanb/bcbio-nextgen — pull request #144 by lbeltrame (2013-10-14 13:57:47+00:00)
Title: De-generify VarScan tumor/normal sample renaming

This patch makes the sample renaming needed for VarScan adjustment
exclusive for paired tumor/normal calling ("VarScan somatic"). Instead,
a dictionary is used to map NORMAL and TUMOR to the right sample names.

The rationale for the change is as follows:

- This function is only used in paired mode (no breakage of other calls);
- The change removes needless samtools calls for sample names (the
helper function called during VarScan invokation already does the job);
- Reduces the risk of BAMs provided in a different order than [normal,
tumor] which may cause incorrect results later on.