public class Sam2CramRecordFactory extends Object
Modifier and Type | Field | Description |
---|---|---|
boolean |
captureAllTags |
|
Set<String> |
captureTags |
|
Set<String> |
ignoreTags |
|
boolean |
preserveReadNames |
Constructor | Description |
---|---|
Sam2CramRecordFactory(byte[] refBases,
SAMFileHeader samFileHeader,
Version version) |
Modifier and Type | Method | Description |
---|---|---|
CramCompressionRecord |
createCramRecord(SAMRecord record) |
Create a CramCompressionRecord.
|
long |
getBaseCount() |
|
long |
getFeatureCount() |
|
Map<String,Integer> |
getReadGroupMap() |
|
byte[] |
getRefBases() |
|
void |
setRefBases(byte[] refBases) |
public boolean captureAllTags
public boolean preserveReadNames
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 long getBaseCount()
public long getFeatureCount()