Logger initialization in vase.py now adds debug messages to log file only, not to stdout, if --debug is set
Resolves #87 Check for BAM indexes in paramchecker
BAM and VCF indices are now both checked during argparse file type checking
Resolves #82 Variant filtering is wonky
Not sure why this was a bug in the first place, but it should be fixed now that alleles are checked and filtering is reworked.
Resolves #72 Utils: Use variant context file to subset VCF/BCF
VCF records for variant spike-ins are output in P and A (formerly D) modes in BuildSpikeIns
Still need to add VCF output for AssembleValidationSet and BuildValidationSet, but these should also have the option to add the VCF spike-ins into an acceptor VCF.
Resolves #71 Implement filter based on specified column and value for variant filter list (mvl)
Filtering and prioritization has been reworked
Any valid header in the filtering list / MVL can be used to subset by values in that column or to set prioritization by values in that column
Multiple subsets can be specified and follow AND logic
Multiple prioritizations can be specified high-to-low, with values for each also specified high-to-low
Two built-in filter possibilities:
"type" is automatically calculated and can be used to subset/prioritize "indel" or "snp"
"size" is automatically calculated and can be used to subset, with special formatting
Issues: