Package picard.sam.markduplicates.util
Class LibraryIdGenerator
java.lang.Object
picard.sam.markduplicates.util.LibraryIdGenerator
A class to generate library Ids and keep duplication metrics by library IDs.
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Constructor Summary
ConstructorsConstructorDescriptionLibraryIdGenerator
(htsjdk.samtools.SAMFileHeader header) LibraryIdGenerator
(htsjdk.samtools.SAMFileHeader header, boolean flowMetrics) -
Method Summary
Modifier and TypeMethodDescriptionvoid
addMetricsByLibrary
(String library, DuplicationMetrics metrics) htsjdk.samtools.util.Histogram<Double>
short
getLibraryId
(htsjdk.samtools.SAMRecord rec) Get the library ID for the given SAM record.static String
getLibraryName
(htsjdk.samtools.SAMFileHeader header, htsjdk.samtools.SAMRecord rec) Gets the library name from the header for the record.getMetricsByLibrary
(String library) htsjdk.samtools.util.Histogram<Double>
long
htsjdk.samtools.util.Histogram<Double>
htsjdk.samtools.util.Histogram<Short>
static String
getReadGroupLibraryName
(htsjdk.samtools.SAMReadGroupRecord readGroup)
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Constructor Details
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LibraryIdGenerator
public LibraryIdGenerator(htsjdk.samtools.SAMFileHeader header) -
LibraryIdGenerator
public LibraryIdGenerator(htsjdk.samtools.SAMFileHeader header, boolean flowMetrics)
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Method Details
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getLibraryIdsMap
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getMetricsByLibraryMap
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getOpticalDuplicatesByLibraryIdMap
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getDuplicateCountHist
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getNonOpticalDuplicateCountHist
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getOpticalDuplicateCountHist
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getReadGroupLibraryName
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getLibraryName
public static String getLibraryName(htsjdk.samtools.SAMFileHeader header, htsjdk.samtools.SAMRecord rec) Gets the library name from the header for the record. If the RG tag is not present on the record, or the library isn't denoted on the read group, a constant string is returned. -
getLibraryId
public short getLibraryId(htsjdk.samtools.SAMRecord rec) Get the library ID for the given SAM record. -
getMetricsByLibrary
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addMetricsByLibrary
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getNumberOfOpticalDuplicateClusters
public long getNumberOfOpticalDuplicateClusters()
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