0.6.0-beta

This release improves calling accuracy, includes more flexible error modelling, and adds annotations to filtered VCF and realigned BAM files.

Interface changes

• The --training-annotations option is replaced with --annotations, with has slightly different behaviour (see below).
• The --split-bamout option is removed as --bamout realignments now include tags.
• Adds the option --full-bamout. [1147e8f]
• Adds the option --refcall-block-merge-threshold for controlling recall blocks.
• Renames --extract-filtered-source-candidates to --use-filtered-source-candidates. [6972ffa]

Improvements

• Indel error models now include variable gap extension penalties and account for tetra-nucleotide tandem repeats. [8f40fc3]
• More built-in sequence error models to choose from, and custom error models (see wiki). [8f40fc3]
• Annotations can now be requested for filtered VCF files using the new --annotations option. [c75cbac]
• Reference calling now outputs calls in adaptive blocks using the new --refcall-block-merge-threshold option. [9127cf3]
• Better handling of temporary BCF files in multithreaded mode helps prevent system errors due to too many open files (addresses issue #52). [42fa364]
• Adds annotations to realigned evidence BAMs (see wiki). [c047e96]