0.1.13-alpha

This release contains bug fixes and minor performance improvements, it also switches on the assembler by default.

Bug fixes

• Fixes a bug which could cause very large regions to be considered, resulting in memory overflow due to too many reads being read.
• A bug causing incorrect de novo haplotype priors due to overflow in the simd alignment routine has been resolved by capping the de novo mutation probability.
• Fixes a few suitable bugs in haplotype generation.

Improvements

• The assembler now removes more false positive bubbles due to cycles.
• De novo mutations which cause reversion to the reference are flagged as REVERSION in the INFO field.
• Candidates from raw cigar alignments are now filtered depending on a calculated probability or read misalignment.

Other changes

• The assembler is now on be default.
• The penalty for matching to an 'N' has been set to 2.
• More informative debug logging.
• Unmapped reference contigs can now be ignored with the --ignore-unmapped-contigs option.