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