0.6.3-beta

This release reduces runtime in the cancer and polyclone calling models by 20-25%; fixes a bug in the read deduplication algorithm, resulting in fewer false positive calls in PCR data (particularly for somatic calling), adds new read pre-processing options designed to mitigate systematic artefacts in 10X Genomics sequencing, and adds a new way to metric (RFQUAL_ALL) to filter somatic variant calls.

New features / interface changes

• Adds command line options --mask-inverted-soft-clipping and --mask-3prime-shifted-soft-clipped-heads for masking 10X Genomics sequencing artefacts. [0b8fb93, 6566fb2]

Improvements

• Reduces runtime in the VariationalBayesMixtureMixtureModel used in the cancer and polyclone calling models by ~20-25% [d9cbcec]
• Switches multi-precision floating point arithmetic in the cancer calling model to use GMP library, resulting in a small speedup. This change adds a dependency to GMP. [e59be9d]

Bug fixes

• Fixes the read deduplication algorithm so that reads with multiple duplicates are recognised. [01eb88d]
• Fixes a bug in the NC and SMQ measures that could cause an exception to be thrown. [a1262e2, 226b40a]