Package htsjdk.samtools

Class SecondaryOrSupplementarySkippingIterator

java.lang.Object

htsjdk.samtools.SecondaryOrSupplementarySkippingIterator

public class SecondaryOrSupplementarySkippingIterator
extends Object

Wrapper around SAMRecord iterator that skips over secondary and supplementary elements. This iterator conflates a filtering iterator and a peekable iterator. It would be cleaner to handle those concerns separately. This class should be viewed as a replacement for SecondaryAlignmentSkippingIterator, in that we did not want to change the functionality of NPSI to no longer match its name

Constructor Summary

Constructors

Constructor	Description
SecondaryOrSupplementarySkippingIterator(CloseableIterator<SAMRecord> underlyingIt)

Method Summary

Modifier and Type	Method	Description
boolean	advance()
SAMRecord	getCurrent()
boolean	hasCurrent()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

SecondaryOrSupplementarySkippingIterator

public SecondaryOrSupplementarySkippingIterator(CloseableIterator<SAMRecord> underlyingIt)

Method Details

hasCurrent

public boolean hasCurrent()

getCurrent

public SAMRecord getCurrent()

advance

public boolean advance()