0.1.8-alpha

This release contains some significant performance improvements, and a few bug fixes.

New features

• Adds more options for --phasing-level which control the length of haplotypes.

Improvements

• The Phasing algorithm has been overhauled; it is now approximately 5x faster.
• The downsampling procedure has significantly improved; it is now orders of magnitude faster.
• The read likelihood calculation flank score adjustment has been improved, which gives minor calling improvements.
• Minor improvements to BAM/CRAM reading.

Bug fixes

• A bug introduced in the phasing algorithm in v0.1.6-alpha, which resulted in wrong phasing in many cases has been fixed.
• Fixes a floating point overflow error in HaplotypeGenerator which could result in huge memory spikes.
• Fixes a bug in CoverageTracker which could cause segmentation faults.