An extended Contig class used by filter parser that keeps an Option(contigName) updated under And and Or operations and provides other required functionalities
An extended 1-based Interval class used by filter parser that keeps an Option(SimpleInterval) updated under And and Or operations and provides other required functionalities
Converts internal rows with the provided schema into HTSJDK variant context.
An input formatter that writes rows as VCF records.
This internal row -> variant context stream writer maintains a header that is set exactly once.
Converts an HTSJDK variant context into a SparkSQL row with the provided schema.
Contains filter parsing tools and other tools used to apply tabix index
Infers the schema of a VCF file from its headers.
This internal row -> variant context stream writer maintains a header that is set exactly once. The sample IDs are set by sampleIdInfo if predetermined, or inferred from the first written row otherwise.
If missing sample IDs were used to set the header, sample IDs in all rows to be written will be replaced with those from the header. If all sample IDs are present when setting the header, sample IDs in written rows will not be replaced. Mixed missing/present sample IDs are not permitted.