0.1.12-alpha

This release contains some bug fixes and performance improvements:

Improvements

• Thread management has been improved; there is now a dedicated VCF writing thread, and tasks can be run as soon as they are created, rather than having to wait for all tasks on a contig to be made.
• A new de novo mutation model has been introduced which reduces false positive indels.
• Haplotype generation now recognises regions which are likely to contain 'interacting' variation - basically non-independent indels - and groups them together when possible.
• Some minor efficiency improvements to the trio model should see it run slightly faster.
• Regions which contain massive amounts of variation are now automatically excluded from lagging. This can stop runtimes exploding in very difficult regions.

Bug fixes

• Resolves a bug which could cause VCF records to contain a single alt '*' allele.
• Closed an infinite loop in the assembler.
• Fixes a bug in VCF reading which could drop a record.

Other changes

• There is now a --very-fast option in addition to --fast.
• The default read memory footprint has been increased to 6GB.