0.2.1-alpha

This release includes a new de novo mutation model that improves trio calling.

New features

• A new de novo mutation model that includes context dependent indel gap open and extension penalties, calculates using an exponential model. There are now two options that parametrise the model; snv-denovo-mutation-rate and indel-denovo-mutation-rate. Gap open and extension penalties are weighted based on context.

Bug fixes

• Fixes a bug that could prevent a legacy VCF being made.
• Corrects a region difference method that sometimes resulted in incorrect 'skip region' deduction, which could lead to an exception being thrown.
• Fixes a bug that resulted in an incorrect trio model posterior probability.
• Fixes some numerical overflow/underflow bugs that resulted in undefined behaviour.

Other changes

• Increases max-joint-genotypes to 1,000,00.