public class Sam2CramRecordFactory extends Object
Modifier and Type | Field and Description |
---|---|
boolean |
captureAllTags |
Set<String> |
captureTags |
static byte |
ignorePositionsWithQualityScore |
Set<String> |
ignoreTags |
boolean |
preserveReadNames |
static String |
UNKNOWN_READ_GROUP_ID |
static String |
UNKNOWN_READ_GROUP_SAMPLE |
static byte |
unsetQualityScore |
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() |
long |
getLandedRefMaskScores() |
long |
getLandedTotalScores() |
Map<String,Integer> |
getReadGroupMap() |
byte[] |
getRefBases() |
byte[] |
getRefSNPs() |
void |
setRefBases(byte[] refBases) |
void |
setRefSNPs(byte[] refSNPs) |
public static final String UNKNOWN_READ_GROUP_ID
public static final String UNKNOWN_READ_GROUP_SAMPLE
public static final byte unsetQualityScore
public static final byte ignorePositionsWithQualityScore
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 long getLandedRefMaskScores()
public long getLandedTotalScores()
public byte[] getRefBases()
public void setRefBases(byte[] refBases)
public byte[] getRefSNPs()
public void setRefSNPs(byte[] refSNPs)
public long getBaseCount()
public long getFeatureCount()