Sort BED input files based on reference genome dictionary. Sort BED files prior to specification as GATK intervals to avoid issues with truncated non-sorted inputs
Correctly handle 1-based region sizes from GATK and Picard tools. Report additional bases of accuracy for comparisons.
Update tests to match fixed coverage counts
Avoid using GATK intersections with identical total and contestant BED inputs
Improve score table based on feedback from X Prize team
Improve logging messages during processing
Test fix for generalized calc-accuracy reporting
Clean up callability checking to handle multiple input BAMs identically to single BAMs. Improves file handle management so all sources can be properly close in with-open blocks
Experimentation with shoreleave library to add additional security to fetch requests
Add documentation text and pointers to scoring web pages. Thanks to Justin Johnson.
Allow transition from compare to finished for large comparison projects
Select complex indel variants for potential splits into individual variant calls
Split complex indel variants with multiple independent variations into components, maintaing phasing
Remove whitespace in INFO fields during preclean step; GATK and VCF spec do not allow
Consistently move gaps to 3' sequence ends when fixing indels to avoid large internal gaps
API for retrieval of variant quality metrics for plotting
Move variant recalling functionality for batched sets to separate namespace. Clean up combine functionality
Provide recalling of no-call variants using GATK UnifiedGenotyper: only no-calls are re-analyzed, producing final set with original called variants and re-analyzed no-calls
During haploid conversion, report unconverted diploid calls to separate output file.
Add recall functionality as top level executable driven by standard configuration file