Modifier and Type | Method and Description |
---|---|
CramCompressionRecord |
Sam2CramRecordFactory.createCramRecord(SAMRecord record)
Create a CramCompressionRecord.
|
Modifier and Type | Method and Description |
---|---|
java.util.List<CramCompressionRecord> |
ContainerParser.getRecords(Container container,
java.util.ArrayList<CramCompressionRecord> records,
ValidationStringency validationStringency) |
Modifier and Type | Method and Description |
---|---|
static int |
CramNormalizer.computeInsertSize(CramCompressionRecord firstEnd,
CramCompressionRecord secondEnd)
The method is similar in semantics to
computeInsertSize but operates on CRAM native records instead of
SAMRecord objects. |
SAMRecord |
Cram2SamRecordFactory.create(CramCompressionRecord cramRecord) |
Modifier and Type | Method and Description |
---|---|
CompressionHeader |
CompressionHeaderFactory.build(java.util.List<CramCompressionRecord> records,
SubstitutionMatrix substitutionMatrix,
boolean sorted)
Decides on compression methods to use for the given records.
|
Container |
ContainerFactory.buildContainer(java.util.List<CramCompressionRecord> records) |
java.util.List<CramCompressionRecord> |
ContainerParser.getRecords(Container container,
java.util.ArrayList<CramCompressionRecord> records,
ValidationStringency validationStringency) |
void |
CramNormalizer.normalize(java.util.ArrayList<CramCompressionRecord> records,
byte[] ref,
int refOffset_zeroBased,
SubstitutionMatrix substitutionMatrix) |
static void |
CramNormalizer.restoreQualityScores(byte defaultQualityScore,
java.util.List<CramCompressionRecord> records) |
Modifier and Type | Method and Description |
---|---|
void |
ContentDigests.add(CramCompressionRecord record) |
Modifier and Type | Method and Description |
---|---|
void |
ContentDigests.addCramRecords(java.lang.Iterable<CramCompressionRecord> records) |
Modifier and Type | Method and Description |
---|---|
void |
CramRecordReader.read(CramCompressionRecord cramRecord) |
Modifier and Type | Method and Description |
---|---|
void |
Writer.write(CramCompressionRecord r) |
Modifier and Type | Method and Description |
---|---|
void |
QualityScorePreservation.addQualityScores(SAMRecord samRecord,
CramCompressionRecord cramRecord,
ReferenceTracks referenceTracks) |
Modifier and Type | Field and Description |
---|---|
CramCompressionRecord |
CramCompressionRecord.next |
CramCompressionRecord |
CramCompressionRecord.previous |