dhtslib.tabix

Module providing a wrapper, TabixIndexedFile over a line-oriented NGS flat file, such as BED, GFF3, VCF that has been indexed with tabix.

The wrapper provides a list of reference sequence names, as well as iterator over all rows falling within a sequence range, e.g. "chr1:1000-2000"

Members

Structs

RecordReaderRegion
struct RecordReaderRegion(RecType, CoordSystem cs)

Range that allows reading a record based format via tabix. Needs a record type that encompasses only one line of text and a ChromInterval region to use for tabix filtering. Rectype could be GFF3Record, BedRecord ... This is a sister struct to dhtslib.bgzf.RecordReader.

TabixIndexedFile
struct TabixIndexedFile

Encapsulates a position-sorted record-oriented NGS flat file, indexed with Tabix, including BED, GFF3, VCF.

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