picard.analysis

Class ChimeraUtil

java.lang.Object

picard.analysis.ChimeraUtil

public class ChimeraUtil
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
static java.util.Set<htsjdk.samtools.SamPairUtil.PairOrientation>	DEFAULT_EXPECTED_ORIENTATIONS
static int	DEFAULT_INSERT_SIZE_LIMIT

Constructor Summary

Constructors

Constructor and Description
ChimeraUtil()

Method Summary

Modifier and Type	Method and Description
static boolean	isChimeric(htsjdk.samtools.SAMRecord rec, int maxInsertSize, java.util.Set<htsjdk.samtools.SamPairUtil.PairOrientation> expectedOrientations) Checks whether the given read is part of a chimeric pair.
static boolean	isChimeric(htsjdk.samtools.SAMRecord r1, htsjdk.samtools.SAMRecord r2, int maxInsertSize, java.util.Set<htsjdk.samtools.SamPairUtil.PairOrientation> expectedOrientations) Checks whether the given read is part of a chimeric pair.

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_INSERT_SIZE_LIMIT

public static int DEFAULT_INSERT_SIZE_LIMIT

DEFAULT_EXPECTED_ORIENTATIONS

public static java.util.Set<htsjdk.samtools.SamPairUtil.PairOrientation> DEFAULT_EXPECTED_ORIENTATIONS

Constructor Detail

ChimeraUtil

public ChimeraUtil()

Method Detail

isChimeric

public static boolean isChimeric(htsjdk.samtools.SAMRecord rec,
                                 int maxInsertSize,
                                 java.util.Set<htsjdk.samtools.SamPairUtil.PairOrientation> expectedOrientations)

Checks whether the given read is part of a chimeric pair. Note that this method returns false if the read is unpaired or if either end of the pair is unmapped.

Parameters:

rec - the read

maxInsertSize - max insert size to be considered non-chimeric

expectedOrientations - set of orientations that are not chimeric; must not ne null

Returns:

true if this record is part of a chimeric read pair, false otherwise

isChimeric

public static boolean isChimeric(htsjdk.samtools.SAMRecord r1,
                                 htsjdk.samtools.SAMRecord r2,
                                 int maxInsertSize,
                                 java.util.Set<htsjdk.samtools.SamPairUtil.PairOrientation> expectedOrientations)

Checks whether the given read is part of a chimeric pair. Note that this method returns false if either end of the pair is unmapped.

Parameters:

r1 - first read of the pair

r2 - second read of the pair

maxInsertSize - max insert size to be considered non-chimeric

expectedOrientations - set of orientations that are not chimeric

Returns:

true if this pair is chimeric, false otherwise