During precleaning step for problem files, remove ref reads which do not match expected reference sequence
Memoize access to sequence dictionaries and reference to avoid repeated hits to disk
Include validation category as subsettable variable in metrics
Handle metrics retrieval from VCF files lacking likelihoods
Release v0.0.8
Update to next snapshot version 0.0.9
Update normalization heuristic for sorting variants to avoid out of order variants following MNP splitting
Handle selecting and subsetting VCF files with single samples that differ from configured sample name
Ensure reference dictionary created for Picard sequence retrieval. Provide more useful exception if reference and variant files mismatch. Thanks to David Mittelman and Jason Wang
Provide flag to variant-prep argument to avoid removing reference and no-call inputs. Re-use existing remove-refcalls flag for this instead of prep-sv-genotype specific flag. Thanks to Jason Wang
Provide flag to variant-prep argument to avoid removing reference and no-call inputs. Re-use existing remove-refcalls flag for this instead of prep-sv-genotype specific flag. Thanks to Jason Wang
Explicitly separate structural variation fixes from other prep activities: no call/partial call removal and sample header fixing.
Document new generalized arguments for prep functionality. Use in multiple comparison tests
Ensure padding of previous mapping bases respects hg19/GRCh37 name remapping. Thanks to Jason Wang.
Provide test to ensure consistent preparation of indel case
Remove unused alternative alleles from VariantContexts when stripping indels, since these can prevent reduction of indels. Thanks to Jason Wang
Improve readme introduction including links to writeups and other resources. Add history to track changes between versions
Update API documentation to latest version
Update GATK dependency to 2.5-2, using only the MIT licensed framework code. Add in used walkers and annotators from GATK 2.3 lite
Build fai FASTA indexes with samtools if not present: equivalent java functionality removed from GATK and Picard