public class LibraryIdGenerator
extends java.lang.Object
Constructor and Description |
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LibraryIdGenerator(htsjdk.samtools.SAMFileHeader header) |
Modifier and Type | Method and Description |
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void |
addMetricsByLibrary(java.lang.String library,
DuplicationMetrics metrics) |
short |
getLibraryId(htsjdk.samtools.SAMRecord rec)
Get the library ID for the given SAM record.
|
java.util.Map<java.lang.String,java.lang.Short> |
getLibraryIdsMap() |
static java.lang.String |
getLibraryName(htsjdk.samtools.SAMFileHeader header,
htsjdk.samtools.SAMRecord rec)
Gets the library name from the header for the record.
|
DuplicationMetrics |
getMetricsByLibrary(java.lang.String library) |
java.util.Map<java.lang.String,DuplicationMetrics> |
getMetricsByLibraryMap() |
long |
getNumberOfOpticalDuplicateClusters() |
htsjdk.samtools.util.Histogram<java.lang.Short> |
getOpticalDuplicatesByLibraryIdMap() |
static java.lang.String |
getReadGroupLibraryName(htsjdk.samtools.SAMReadGroupRecord readGroup) |
public LibraryIdGenerator(htsjdk.samtools.SAMFileHeader header)
public java.util.Map<java.lang.String,java.lang.Short> getLibraryIdsMap()
public java.util.Map<java.lang.String,DuplicationMetrics> getMetricsByLibraryMap()
public htsjdk.samtools.util.Histogram<java.lang.Short> getOpticalDuplicatesByLibraryIdMap()
public static java.lang.String getReadGroupLibraryName(htsjdk.samtools.SAMReadGroupRecord readGroup)
public static java.lang.String getLibraryName(htsjdk.samtools.SAMFileHeader header, htsjdk.samtools.SAMRecord rec)
public short getLibraryId(htsjdk.samtools.SAMRecord rec)
public DuplicationMetrics getMetricsByLibrary(java.lang.String library)
public void addMetricsByLibrary(java.lang.String library, DuplicationMetrics metrics)
public long getNumberOfOpticalDuplicateClusters()