0.1.5-alpha

This release contains numerous bug fixes and enhancements:

Bug fixes

• Fixes bug in assembler which could cause segmentation faults.
• Fixes bug in haplotype generation which could cause exceptions.
• Fixes bad VCF genotype output for somatic variants (e.g. 2|0).
• Prevents spurious "Not a BGZF file" warning.
• Building fixes.

Key improvements

• Many improvements have been made to the cancer calling model. In particular specificity has been significantly improved. A model posterior is now reported by default which can be used to hard filter calls. Runtime has been improved, but still needs much work.
• The assembler can now selectively extracts bubbles of a minimum weight, increasing both specificity and sensitivity.

Other changes

• Command line options have been added for the new features.
• The command line options --debug and --trace can now take arguments (file paths) to write the respective logs to.
• Downsampling limits have been increased.
• Some other command line option names and default values have changed.