org.broadinstitute.hellbender.engine

Interface BasicReference

All Known Subinterfaces:

ReferenceSparkSource

All Known Implementing Classes:

ReferenceContext, ReferenceFileSparkSource, ReferenceHadoopSparkSource, ReferenceMultiSparkSource, ReferenceTwoBitSparkSource

public interface BasicReference

A source of reference base calls.

Method Summary

Modifier and Type	Method and Description
byte[]	getBases(SimpleInterval window) Get the reference base calls in the specified window.

Method Detail

getBases

byte[] getBases(SimpleInterval window)

Get the reference base calls in the specified window. The calls are encoded as ASCII characters, 1 per byte. The are no guarantees about upper or lower case, or particular values that may or may not be present.