htsjdk.samtools

Class DuplicateSetIterator

java.lang.Object

htsjdk.samtools.DuplicateSetIterator

All Implemented Interfaces:

CloseableIterator<DuplicateSet>, java.io.Closeable, java.lang.AutoCloseable, java.util.Iterator<DuplicateSet>

public class DuplicateSetIterator
extends java.lang.Object
implements CloseableIterator<DuplicateSet>

An iterator of sets of duplicates. Duplicates are defined currently by the ordering in SAMRecordDuplicateComparator.

If the input records are not pre-sorted according to the duplicate ordering, the records will be sorted on-the-fly. This may require extra memory or disk to buffer records, and also computational time to perform the sorting.

Constructor Summary

Constructors

Constructor and Description
DuplicateSetIterator(CloseableIterator<SAMRecord> iterator, SAMFileHeader header)
DuplicateSetIterator(CloseableIterator<SAMRecord> iterator, SAMFileHeader header, boolean preSorted)
DuplicateSetIterator(CloseableIterator<SAMRecord> iterator, SAMFileHeader header, boolean preSorted, SAMRecordDuplicateComparator comparator)
DuplicateSetIterator(CloseableIterator<SAMRecord> iterator, SAMFileHeader header, boolean preSorted, SAMRecordDuplicateComparator comparator, Log log) Allows the user of this iterator to skip the sorting of the input if the input is already sorted.

Method Summary

Modifier and Type	Method and Description
void	close() Should be implemented to close/release any underlying resources.
boolean	hasNext()
DuplicateSet	next()
void	remove()
void	setScoringStrategy(DuplicateScoringStrategy.ScoringStrategy scoringStrategy) Deprecated.

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

Constructor Detail

DuplicateSetIterator

public DuplicateSetIterator(CloseableIterator<SAMRecord> iterator,
                            SAMFileHeader header)

DuplicateSetIterator

public DuplicateSetIterator(CloseableIterator<SAMRecord> iterator,
                            SAMFileHeader header,
                            boolean preSorted)

DuplicateSetIterator

public DuplicateSetIterator(CloseableIterator<SAMRecord> iterator,
                            SAMFileHeader header,
                            boolean preSorted,
                            SAMRecordDuplicateComparator comparator)

DuplicateSetIterator

public DuplicateSetIterator(CloseableIterator<SAMRecord> iterator,
                            SAMFileHeader header,
                            boolean preSorted,
                            SAMRecordDuplicateComparator comparator,
                            Log log)

Allows the user of this iterator to skip the sorting of the input if the input is already sorted. If the records are said to be sorted but not actually sorted in the correct order, an exception during iteration will be thrown. Progress information will be printed for sorting of the input if `log` is provided.

Method Detail

setScoringStrategy

@Deprecated
public void setScoringStrategy(DuplicateScoringStrategy.ScoringStrategy scoringStrategy)

Deprecated.

next

public DuplicateSet next()

Specified by:

next in interface java.util.Iterator<DuplicateSet>

close

public void close()

Description copied from interface: CloseableIterator

Should be implemented to close/release any underlying resources.

Specified by:

close in interface CloseableIterator<DuplicateSet>

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<DuplicateSet>

remove

public void remove()

Specified by:

remove in interface java.util.Iterator<DuplicateSet>