public class Sam2CramRecordFactory
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
boolean |
captureAllTags |
java.util.Set<java.lang.String> |
captureTags |
java.util.Set<java.lang.String> |
ignoreTags |
boolean |
preserveReadNames |
Constructor and Description |
---|
Sam2CramRecordFactory(byte[] refBases,
SAMFileHeader samFileHeader,
Version version) |
Modifier and Type | Method and Description |
---|---|
CramCompressionRecord |
createCramRecord(SAMRecord record)
Create a CramCompressionRecord.
|
long |
getBaseCount() |
long |
getFeatureCount() |
java.util.Map<java.lang.String,java.lang.Integer> |
getReadGroupMap() |
byte[] |
getRefBases() |
void |
setRefBases(byte[] refBases) |
public boolean captureAllTags
public boolean preserveReadNames
public final java.util.Set<java.lang.String> captureTags
public final java.util.Set<java.lang.String> ignoreTags
public Sam2CramRecordFactory(byte[] refBases, SAMFileHeader samFileHeader, Version version)
public CramCompressionRecord createCramRecord(SAMRecord record)
record
- If the input record does not have an associated SAMFileHeader, it will be updated
with the header used for the factory in order to allow reference indices to be resolved.public byte[] getRefBases()
public void setRefBases(byte[] refBases)
public java.util.Map<java.lang.String,java.lang.Integer> getReadGroupMap()
public long getBaseCount()
public long getFeatureCount()