sanger-pathogens/vr-codebase — pull request #132 by CraigPorter (2012-09-06 13:13:05+00:00)
Title: Coverage from bamcheck

Changes for getting coverage by bamcheck.
- Added module and tests
- Made change to Fastq QC
- Made change to Mapping.

This replaces the calculation of coverage from mpileup and should just slot in with without having to shutdown the pipelines.