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