0.1.4-alpha

Bug fixes

• Fixes a bug in the assembler which could cause segmentation faults and memory corruption.
• Fixes problem in VCF output where multiple overlapping records could have inconsistent genotypes.
• Fixes bug in cancer caller which could result in arithmetic error resulting in Phred exception.
• Fixes bug in haplotype generator which could result in only one haplotype being generated.

New features

• Adds command line options --num-assembler-fallbacks and --assembler-fallback-interval.
• Allows --debug and --trace to take arguments, specifying the paths of the debug and trace logs respectively.

0.1.3-alpha

Bug fixes

• Fixes a bug in the assembler which could cause segmentation faults and memory corruption.

New features

• Removes command line options --disable-reference-base-capitalisation and --disable-read-base-capitalisation added in previous release. On reflection there is no foreseeable use-case for them. All reference and read bases are now capitalised.
• Adds a new command line --assembler-bin-size that controls the region size used for local re-assembley. Most users will never need to set this option.

0.1.2-alpha

This is a bug-fix patch.

Bug fixes

• Fixes an issue where mixed case bases cause a very high number of candidate variants, causing massive slow-down in variant calling. Capitalisation is now applied to all reference and read bases by default, and must be explicitly disabled by the user.
• Corrects a typo in one of the search paths used in FindHTSlib.cmake.

New features

• Command line options --disable-reference-base-capitalisation and --disable-read-base-capitalisation to disable reference and read base capitalisation respectively.

0.1.1-alpha

This is a bug-fix patch. There are no new features.

Bug fixes

• Fixes an arithmetic overflow issues in the cancer calling model that could cause an exception to be thrown. This may also cause a multithreaded run to stall forever.

Testing

• Travis is now working for OSX/Clang.

First alpha release

The first public release: not feature complete and may be unstable (expect some bugs). It is intended for potential users to get a feel for the software, and give feedback which may then be integrated into the first official release.