0.1.11-alpha

This release contains some performance improvements and bug fixes, and also increases the requirement on htslib to version 1.4.

Improvements

• The assembler has been overhauled. It now only tries to assemble regions that look difficult (i.e. those where the alignments are bad). Sensitivity and specificity have also been greatly improved with better pruning and bubble extraction algorithms. The assembler will now also be run in parallel if --threads is used.
• The trio model has been significantly improved, it is now slower, but offers far greater sensitivity and specificity. Overall performance can be adjusted with the --max-joint-genotypes option.
• The holdout mechanism has been improved, and can now deal with much larger holdout depths.
• Haplotype generation has been improved; regions interacting with large indels will be called together if possible.

Bug fixes

• Some bugs which resulted in incorrect VCF output have been fixed.
• Fixes a bug in read extraction which could cause segmentation faults.
• Fixes some bugs in haplotype generation that could cause segmentation faults or exceptions.
• Fixes a bug where a raw VCF source variant file resulted in an exception.

Other changes

• Htslib version 1.4 is now a requirement as this version fixes a bug that was causing octopus to stall.
• The default number of haplotypes (--max-haplotypes) has been increased to 200.
• The default value for --haplotype-extension-threshold has been reduced to 100.
• Mapping quality modelling can be turned off with the --model-mapping-quality option.