read

Type Members

class ADAMBAMOutputFormat[K] extends KeyIgnoringBAMOutputFormat[K] with Serializable

Wrapper for Hadoop-BAM to work around requirement for no-args constructor.
Wrapper for Hadoop-BAM to work around requirement for no-args constructor.
K
The key type. Keys are not written.
class ADAMBAMOutputFormatHeaderLess[K] extends KeyIgnoringBAMOutputFormat[K] with Serializable

Wrapper for Hadoop-BAM to work around requirement for no-args constructor.
Wrapper for Hadoop-BAM to work around requirement for no-args constructor.
K
The key type. Keys are not written.
class ADAMCRAMOutputFormat[K] extends KeyIgnoringCRAMOutputFormat[K] with Serializable

Wrapper for Hadoop-BAM to work around requirement for no-args constructor.
Wrapper for Hadoop-BAM to work around requirement for no-args constructor.
K
The key type. Keys are not written.
class ADAMCRAMOutputFormatHeaderLess[K] extends KeyIgnoringCRAMOutputFormat[K] with Serializable

Wrapper for Hadoop-BAM to work around requirement for no-args constructor.
Wrapper for Hadoop-BAM to work around requirement for no-args constructor.
K
The key type. Keys are not written.
class ADAMSAMOutputFormat[K] extends KeyIgnoringAnySAMOutputFormat[K] with Serializable
class ADAMSAMOutputFormatHeaderLess[K] extends KeyIgnoringAnySAMOutputFormat[K] with Serializable
case class AlignedReadRDD(rdd: RDD[AlignmentRecord], sequences: SequenceDictionary, recordGroups: RecordGroupDictionary) extends AvroReadGroupGenomicRDD[AlignmentRecord, AlignmentRecordRDD] with AlignmentRecordRDD with Product with Serializable
sealed trait AlignmentRecordRDD extends AvroReadGroupGenomicRDD[AlignmentRecord, AlignmentRecordRDD]
trait AnySAMInFormatter[T <: AnySAMInFormatter[T]] extends InFormatter[AlignmentRecord, AlignmentRecordRDD, T]

A trait that writes reads using an Htsjdk SAMFileWriter.
A trait that writes reads using an Htsjdk SAMFileWriter.
T
The recursive type of the class that implements this trait.
trait AnySAMInFormatterCompanion[T <: AnySAMInFormatter[T]] extends InFormatterCompanion[AlignmentRecord, AlignmentRecordRDD, T]

Companion object that builds an InFormatter that writes data where the metadata is contained in a SAMFileHeaderWritable.
Companion object that builds an InFormatter that writes data where the metadata is contained in a SAMFileHeaderWritable.
T
The type of the underlying InFormatter.
class AnySAMOutFormatter extends OutFormatter[AlignmentRecord]

An OutFormatter that automatically infers whether the piped input is SAM or BAM.
An OutFormatter that automatically infers whether the piped input is SAM or BAM. Autodetecting streamed CRAM is not currently supported.
case class IncorrectMDTagException(read: AlignmentRecord, mdTag: String) extends Exception with Product with Serializable

A class describing an exception where a read's MD tag was recomputed and did not match the MD tag originally attached to the read.
A class describing an exception where a read's MD tag was recomputed and did not match the MD tag originally attached to the read.
read
The read whose MD tag was recomputed, with original MD tag.
mdTag
The recomputed MD tag.
class InstrumentedADAMBAMOutputFormat[K] extends InstrumentedOutputFormat[K, SAMRecordWritable]

Wrapper that adds instrumentation to the BAM output format.
Wrapper that adds instrumentation to the BAM output format.
K
The key type. Keys are not written.
class InstrumentedADAMBAMOutputFormatHeaderLess[K] extends InstrumentedOutputFormat[K, SAMRecordWritable]

Wrapper that adds instrumentation to the SAM output format.
Wrapper that adds instrumentation to the SAM output format.
K
The key type. Keys are not written.
class InstrumentedADAMCRAMOutputFormat[K] extends InstrumentedOutputFormat[K, SAMRecordWritable]

Wrapper that adds instrumentation to the CRAM output format.
Wrapper that adds instrumentation to the CRAM output format.
K
The key type. Keys are not written.
class InstrumentedADAMCRAMOutputFormatHeaderLess[K] extends InstrumentedOutputFormat[K, SAMRecordWritable]

Wrapper that adds instrumentation to the CRAM output format.
Wrapper that adds instrumentation to the CRAM output format.
K
The key type. Keys are not written.
class InstrumentedADAMSAMOutputFormat[K] extends InstrumentedOutputFormat[K, SAMRecordWritable]
class InstrumentedADAMSAMOutputFormatHeaderLess[K] extends InstrumentedOutputFormat[K, SAMRecordWritable]
class ReferencePositionPairSerializer extends Serializer[ReferencePositionPair]
class SingleReadBucketSerializer extends Serializer[SingleReadBucket]
case class UnalignedReadRDD(rdd: RDD[AlignmentRecord], recordGroups: RecordGroupDictionary) extends AvroReadGroupGenomicRDD[AlignmentRecord, AlignmentRecordRDD] with AlignmentRecordRDD with Unaligned with Product with Serializable

Value Members

object BAMInFormatter extends AnySAMInFormatterCompanion[BAMInFormatter] with Serializable

InFormatter companion for building an InFormatter that streams BAM.
object SAMInFormatter extends AnySAMInFormatterCompanion[SAMInFormatter] with Serializable

InFormatter companion for building an InFormatter that streams SAM.
object UnalignedReadRDD extends Serializable
package recalibration

package read

Type Members

class ADAMBAMOutputFormat[K] extends KeyIgnoringBAMOutputFormat[K] with Serializable

class ADAMBAMOutputFormatHeaderLess[K] extends KeyIgnoringBAMOutputFormat[K] with Serializable

class ADAMCRAMOutputFormat[K] extends KeyIgnoringCRAMOutputFormat[K] with Serializable

class ADAMCRAMOutputFormatHeaderLess[K] extends KeyIgnoringCRAMOutputFormat[K] with Serializable

class ADAMSAMOutputFormat[K] extends KeyIgnoringAnySAMOutputFormat[K] with Serializable

class ADAMSAMOutputFormatHeaderLess[K] extends KeyIgnoringAnySAMOutputFormat[K] with Serializable

case class AlignedReadRDD(rdd: RDD[AlignmentRecord], sequences: SequenceDictionary, recordGroups: RecordGroupDictionary) extends AvroReadGroupGenomicRDD[AlignmentRecord, AlignmentRecordRDD] with AlignmentRecordRDD with Product with Serializable

sealed trait AlignmentRecordRDD extends AvroReadGroupGenomicRDD[AlignmentRecord, AlignmentRecordRDD]

trait AnySAMInFormatter[T <: AnySAMInFormatter[T]] extends InFormatter[AlignmentRecord, AlignmentRecordRDD, T]

trait AnySAMInFormatterCompanion[T <: AnySAMInFormatter[T]] extends InFormatterCompanion[AlignmentRecord, AlignmentRecordRDD, T]

class AnySAMOutFormatter extends OutFormatter[AlignmentRecord]

case class IncorrectMDTagException(read: AlignmentRecord, mdTag: String) extends Exception with Product with Serializable

class InstrumentedADAMBAMOutputFormat[K] extends InstrumentedOutputFormat[K, SAMRecordWritable]

class InstrumentedADAMBAMOutputFormatHeaderLess[K] extends InstrumentedOutputFormat[K, SAMRecordWritable]

class InstrumentedADAMCRAMOutputFormat[K] extends InstrumentedOutputFormat[K, SAMRecordWritable]

class InstrumentedADAMCRAMOutputFormatHeaderLess[K] extends InstrumentedOutputFormat[K, SAMRecordWritable]

class InstrumentedADAMSAMOutputFormat[K] extends InstrumentedOutputFormat[K, SAMRecordWritable]

class InstrumentedADAMSAMOutputFormatHeaderLess[K] extends InstrumentedOutputFormat[K, SAMRecordWritable]

class ReferencePositionPairSerializer extends Serializer[ReferencePositionPair]

class SingleReadBucketSerializer extends Serializer[SingleReadBucket]

case class UnalignedReadRDD(rdd: RDD[AlignmentRecord], recordGroups: RecordGroupDictionary) extends AvroReadGroupGenomicRDD[AlignmentRecord, AlignmentRecordRDD] with AlignmentRecordRDD with Unaligned with Product with Serializable

Value Members

object BAMInFormatter extends AnySAMInFormatterCompanion[BAMInFormatter] with Serializable

object SAMInFormatter extends AnySAMInFormatterCompanion[SAMInFormatter] with Serializable

object UnalignedReadRDD extends Serializable

package recalibration

Ungrouped