org.broadinstitute.hellbender.utils.read

Class ArtificialReadQueryIterator

java.lang.Object

org.broadinstitute.hellbender.utils.read.ArtificialReadIterator

org.broadinstitute.hellbender.utils.read.ArtificialReadQueryIterator

All Implemented Interfaces:

java.lang.Iterable<GATKRead>, java.util.Iterator<GATKRead>

public final class ArtificialReadQueryIterator
extends ArtificialReadIterator

Field Summary

Fields

Modifier and Type	Field and Description
protected int	contigIndex
protected int	finalPos
protected boolean	overlapping
protected boolean	seeked
protected int	startingChr
protected int	startPos

Fields inherited from class org.broadinstitute.hellbender.utils.read.ArtificialReadIterator

currentChromo, currentRead, done, eChromosomeCount, header, next, open, rCount, sChr, totalReadCount, unmappedReadCount, unmappedRemaining

Method Summary

Modifier and Type	Method and Description
void	ensureUntouched() make sure we haven't been used as an iterator yet; this is to miror the MergingSamIterator2 action.
boolean	hasNext() override the hasNext, to incorportate our limiting factor
boolean	matches(GATKRead rec) given a read and the query type, check if it matches our regions
void	query(java.lang.String contig, int start, int stop, boolean contained)
void	queryContained(java.lang.String contig, int start, int stop) query containing - get reads contained by the specified interval
void	queryOverlapping(java.lang.String contig, int start, int stop) query containing - get reads contained by the specified interval
protected void	reset()

Methods inherited from class org.broadinstitute.hellbender.utils.read.ArtificialReadIterator

close, createNextRead, getHeader, iterator, next, peek, readsTaken, remove

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.Iterator

forEachRemaining

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Field Detail

finalPos

protected int finalPos

startPos

protected int startPos

contigIndex

protected int contigIndex

overlapping

protected boolean overlapping

startingChr

protected int startingChr

seeked

protected boolean seeked

Method Detail

reset

protected void reset()

Overrides:

reset in class ArtificialReadIterator

queryContained

public void queryContained(java.lang.String contig,
                           int start,
                           int stop)

query containing - get reads contained by the specified interval

Parameters:

contig - the contig index string

start - the start position

stop - the stop position

queryOverlapping

public void queryOverlapping(java.lang.String contig,
                             int start,
                             int stop)

query containing - get reads contained by the specified interval

Parameters:

contig - the contig index string

start - the start position

stop - the stop position

query

public void query(java.lang.String contig,
                  int start,
                  int stop,
                  boolean contained)

matches

public boolean matches(GATKRead rec)

given a read and the query type, check if it matches our regions

Parameters:

rec - the read

Returns:

true if it belongs in our region

hasNext

public boolean hasNext()

override the hasNext, to incorportate our limiting factor

Specified by:

hasNext in interface java.util.Iterator<GATKRead>

Overrides:

hasNext in class ArtificialReadIterator

Returns:

ensureUntouched

public void ensureUntouched()

make sure we haven't been used as an iterator yet; this is to miror the MergingSamIterator2 action.