0.1.6-alpha

This release contains numerous new features, enhancements, and bug fixes.

New features

• A prototype population model has been implemented.
• Uniform genotype priors are available with the --use-uniform-genotype-priors command line option.
• Switchable sequence error model (only X10 alternative at the moment).
• Multiple source variant files can now be supplied.

Enhancements

• The holdout mechanism has been improved which results in much fewer skipped regions due to haplotype overflow.
• The runtime performance of the trio caller has been significantly improved.
• The runtime performance of the phaser has been significantly improved.
• Genotype posteriors are now capped at 255 rather than 99.

Bug fixes

• Fixes an issue with active region boundary insertions which could cause missing genotype calls.
• Corrects somatic prior calculation which resulted in many false positive somatic calls.
• Fixes some issues which could result in HaplotypeTree exceptions.