Package picard.analysis
Class ChimeraUtil
- java.lang.Object
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- picard.analysis.ChimeraUtil
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public class ChimeraUtil extends Object
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Field Summary
Fields Modifier and Type Field Description static Set<htsjdk.samtools.SamPairUtil.PairOrientation>
DEFAULT_EXPECTED_ORIENTATIONS
static int
DEFAULT_INSERT_SIZE_LIMIT
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Constructor Summary
Constructors Constructor Description ChimeraUtil()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static boolean
isChimeric(htsjdk.samtools.SAMRecord rec, int maxInsertSize, 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, Set<htsjdk.samtools.SamPairUtil.PairOrientation> expectedOrientations)
Checks whether the given read is part of a chimeric pair.
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Field Detail
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DEFAULT_INSERT_SIZE_LIMIT
public static int DEFAULT_INSERT_SIZE_LIMIT
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DEFAULT_EXPECTED_ORIENTATIONS
public static Set<htsjdk.samtools.SamPairUtil.PairOrientation> DEFAULT_EXPECTED_ORIENTATIONS
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Method Detail
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isChimeric
public static boolean isChimeric(htsjdk.samtools.SAMRecord rec, int maxInsertSize, 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 readmaxInsertSize
- max insert size to be considered non-chimericexpectedOrientations
- 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
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isChimeric
public static boolean isChimeric(htsjdk.samtools.SAMRecord r1, htsjdk.samtools.SAMRecord r2, int maxInsertSize, 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 pairr2
- second read of the pairmaxInsertSize
- max insert size to be considered non-chimericexpectedOrientations
- set of orientations that are not chimeric- Returns:
- true if this pair is chimeric, false otherwise
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