/**
* Get all reference bases in this context. The results are cached in this object for future
* queries. Will always return an empty array if there is no backing data source and/or interval
* to query.
*
* <p>Call {@link #setWindow} before calling this method if you want to configure the amount of
* extra reference context to include around the current interval
*
* @return reference bases in this context, as a byte array
*/
public byte[] getBases() {
if (dataSource == null || window == null) {
return new byte[0];
}
// Only perform a query if we haven't fetched the bases in this context previously
if (cachedSequence == null) {
cachedSequence = dataSource.queryAndPrefetch(window);
}
return cachedSequence.getBases();
}
/**
* Determines the stop of the expanded reference window, bounded if necessary by the contig.
*
* @param locus The locus to expand.
* @param windowTrailingBases number of bases to attempt to expand relative to the locus end (>=
* 0)
* @return The end of the expanded window.
*/
private int calculateWindowStop(final SimpleInterval locus, final int windowTrailingBases) {
final int sequenceLength =
dataSource.getSequenceDictionary().getSequence(locus.getContig()).getSequenceLength();
return Math.min(locus.getEnd() + windowTrailingBases, sequenceLength);
}
/**
* Get an iterator over the reference bases in this context. Will return an empty iterator if this
* context has no backing data source and/or interval.
*
* <p>Call {@link #setWindow} before calling this method if you want to configure the amount of
* extra reference context to include around the current interval
*
* @return iterator over the reference bases in this context
*/
@Override
public Iterator<Byte> iterator() {
return dataSource != null && window != null
? dataSource.query(window)
: new ByteArrayIterator(new byte[0]);
}