- Changed SWH prefix to an assignable prefix. the default is VAK_, for vArmyKnife. Can be changed with the --universalTagPrefix parameter
- Added execution time stats to the successfulCompletionFile. Allows easy calculation of runtime.
- added --duplicatesTag option. Counts duplicates and adds counts and indices.
- Added several more tagVariantsExpression modes and documented them: GTTAGCOPY, GTFILT, GTrecodeMultAlle, GTTAGANDCOUNT
- Added tallyFile option. Will make a table with counts for warnings, notices, and tallies
- Added more documentation/help text
- Fixed leftAlignAndTrim to ignore fasta upper/lower case status.
- Fixed dropSpanIndels option
- Changed SnpSift parser to extract MODIFIER variant types and include them with LOW. You can specify the subtypes using the usual params.
- experimented with keepInfo and keepFormat regexes. Function is not yet externally accessable.
- added an option to tagVariantsExpression to add a FORMAT field based on a genotype expression, rather than an INFO field.
- added --thirdAlleleChar option to be used with --convertToStandardVcf or alone. Removes the star-allele multiallelic convention and maps other alt alleles to the supplied string. Recommended values are "." and "0".
- Added --dropSpanIndels option
- Added tally function. Counts various stats and events.
- Improvements to VcfGtExpressionTag walker
- Fixed makeFirstBaseMatch option
- Changed convertToStandardVcf option to edit genotypes better and to avoid tag name collisions
- Improvements to VcfGtExpressionTag walker
- Added --makeFirstBaseMatch option, which adjusts indels so that the first base matches. This is necessary to make LAT work properly on some oddly-formatted multiallelic variants from FreeBayes
- Worked on alpha version of amino acid matcher
- Bugfixes.
- Worked on alpha version of amino acid matcher
- Added BinaryMonoToList argument type
- Added additional tagVariantsExpression modes (allowing genotype-level expressions)
- Shifted convertToStandardVcf walker to later in the pipeline