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