Package | Description |
---|---|
htsjdk.samtools | |
htsjdk.samtools.cram.build | |
htsjdk.samtools.cram.encoding.reader | |
htsjdk.samtools.cram.structure | |
htsjdk.samtools.sra |
Modifier and Type | Field and Description |
---|---|
static ValidationStringency |
ValidationStringency.DEFAULT_STRINGENCY |
Modifier and Type | Method and Description |
---|---|
static ValidationStringency |
SAMFileReader.getDefaultValidationStringency()
Deprecated.
|
ValidationStringency |
SamReader.PrimitiveSamReader.getValidationStringency() |
ValidationStringency |
SAMLineParser.getValidationStringency()
Get validation stringency.
|
ValidationStringency |
CRAMIterator.getValidationStringency() |
ValidationStringency |
SRAFileReader.getValidationStringency() |
ValidationStringency |
CRAMFileReader.getValidationStringency() |
ValidationStringency |
SAMRecord.getValidationStringency() |
abstract ValidationStringency |
SamReaderFactory.validationStringency() |
static ValidationStringency |
ValidationStringency.valueOf(String name)
Returns the enum constant of this type with the specified name.
|
static ValidationStringency[] |
ValidationStringency.values()
Returns an array containing the constants of this enum type, in
the order they are declared.
|
Modifier and Type | Method and Description |
---|---|
static void |
CRAMIndexer.createIndex(SeekableStream stream,
File output,
Log log,
ValidationStringency validationStringency)
Generates a BAI index file from an input CRAM stream
|
void |
CRAMIndexer.processContainer(Container container,
ValidationStringency validationStringency)
Index a container, any of mapped, unmapped and multiple references are allowed.
|
static void |
SAMUtils.processValidationError(SAMValidationError validationError,
ValidationStringency validationStringency) |
static void |
SAMUtils.processValidationErrors(List<SAMValidationError> validationErrors,
long samRecordIndex,
ValidationStringency validationStringency)
Handle a list of validation errors according to the validation stringency.
|
static SAMBinaryTagAndValue |
BinaryTagCodec.readTags(byte[] binaryRep,
int offset,
int length,
ValidationStringency validationStringency)
Convert tags from little-endian disk representation to in-memory representation.
|
static void |
SAMFileReader.setDefaultValidationStringency(ValidationStringency defaultValidationStringency)
Deprecated.
Set validation stringency for all subsequently-created SAMFileReaders.
|
static void |
SamReaderFactory.setDefaultValidationStringency(ValidationStringency defaultValidationStringency) |
void |
SAMFileReader.setValidationStringency(ValidationStringency validationStringency)
Deprecated.
Control validation of SAMRecords as they are read from file.
|
void |
CRAMIterator.setValidationStringency(ValidationStringency validationStringency) |
void |
SRAIterator.setValidationStringency(ValidationStringency validationStringency) |
void |
SAMTextHeaderCodec.setValidationStringency(ValidationStringency validationStringency) |
void |
SAMRecord.setValidationStringency(ValidationStringency validationStringency)
Control validation of lazily-decoded elements.
|
abstract SamReaderFactory |
SamReaderFactory.validationStringency(ValidationStringency validationStringency)
Set this factory's
ValidationStringency to the provided one, then returns itself. |
Constructor and Description |
---|
CRAMFileReader(File cramFile,
File indexFile,
ReferenceSource referenceSource,
ValidationStringency validationStringency)
Create a CRAMFileReader from a CRAM file and optional index file using the supplied reference
source and validation stringency.
|
CRAMFileReader(InputStream stream,
File indexFile,
ReferenceSource referenceSource,
ValidationStringency validationStringency)
Create a CRAMFileReader from an input stream and optional index file using the supplied reference
source and validation stringency.
|
CRAMFileReader(InputStream inputStream,
SeekableStream indexInputStream,
ReferenceSource referenceSource,
ValidationStringency validationStringency)
Create a CRAMFileReader from an input stream and optional index stream using the supplied reference
source and validation stringency.
|
CRAMIterator(InputStream inputStream,
ReferenceSource referenceSource,
ValidationStringency validationStringency) |
CRAMIterator(SeekableStream seekableStream,
ReferenceSource referenceSource,
long[] coordinates,
ValidationStringency validationStringency) |
SAMLineParser(SAMRecordFactory samRecordFactory,
ValidationStringency validationStringency,
SAMFileHeader samFileHeader,
SamReader samFileReader,
File samFile)
Public constructor.
|
Modifier and Type | Method and Description |
---|---|
List<CramCompressionRecord> |
ContainerParser.getRecords(Container container,
ArrayList<CramCompressionRecord> records,
ValidationStringency validationStringency) |
Map<Integer,AlignmentSpan> |
ContainerParser.getReferences(Container container,
ValidationStringency validationStringency) |
Constructor and Description |
---|
CramRecordReader(ValidationStringency validationStringency) |
RefSeqIdReader(int seqId,
int alignmentStart,
ValidationStringency validationStringency) |
Modifier and Type | Method and Description |
---|---|
static Object |
ReadTag.readSingleValue(byte tagType,
ByteBuffer byteBuffer,
ValidationStringency validationStringency) |
Constructor and Description |
---|
ReadTag(int id,
byte[] dataAsByteArray,
ValidationStringency validationStringency) |
Modifier and Type | Method and Description |
---|---|
void |
SRAAlignmentIterator.setValidationStringency(ValidationStringency validationStringency) |
void |
SRAUnalignmentIterator.setValidationStringency(ValidationStringency validationStringency) |