org.broadinstitute.hellbender.utils.read.mergealignment

Class MultiHitAlignedReadIterator

java.lang.Object

org.broadinstitute.hellbender.utils.read.mergealignment.MultiHitAlignedReadIterator

All Implemented Interfaces:

htsjdk.samtools.util.CloseableIterator<HitsForInsert>, java.io.Closeable, java.lang.AutoCloseable, java.util.Iterator<HitsForInsert>

public final class MultiHitAlignedReadIterator
extends java.lang.Object
implements htsjdk.samtools.util.CloseableIterator<HitsForInsert>

Iterate over queryname-sorted SAM, and return each group of reads with the same queryname. Unmapped reads are filtered out, as are alignments that don't seem to match any part of the reference. If there are multiple hits for the same read, and the first and second ends need to be correlated, then they are sorted by hit index. Supplemental alignments are discarded, with a logged message. A set of hits for a single query may then be filtered with a caller-supplied filter, which will remove any alignments that do not pass the filter. If the primary alignment is removed, the best-mapping secondary alignment or alignment pair will be marked as primary.

Method Summary

Modifier and Type	Method and Description
void	close()
boolean	hasNext()
HitsForInsert	next()
void	remove() Unsupported operation.

Methods inherited from class java.lang.Object

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

Methods inherited from interface htsjdk.samtools.util.CloseableIterator

stream, toList

Methods inherited from interface java.util.Iterator

forEachRemaining

Method Detail

close

public void close()

Specified by:

close in interface htsjdk.samtools.util.CloseableIterator<HitsForInsert>

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

hasNext

public boolean hasNext()

Specified by:

hasNext in interface java.util.Iterator<HitsForInsert>

next

public HitsForInsert next()

Specified by:

next in interface java.util.Iterator<HitsForInsert>

Throws:

java.lang.IllegalStateException - if the input is not queryname-sorted.

remove

public void remove()

Unsupported operation.

Specified by:

remove in interface java.util.Iterator<HitsForInsert>