error

Type Members

1. sealed trait CigarOpsError extends AnyRef

   

   Container for flags related to inconsistencies in BAM-record-candidates' cigar-related fields.

2. case class Counts(tooFewFixedBlockBytes: Long, negativeReadIdx: Long, tooLargeReadIdx: Long, negativeReadPos: Long, tooLargeReadPos: Long, negativeNextReadIdx: Long, tooLargeNextReadIdx: Long, negativeNextReadPos: Long, tooLargeNextReadPos: Long, tooFewBytesForReadName: Long, nonNullTerminatedReadName: Long, nonASCIIReadName: Long, noReadName: Long, emptyReadName: Long, tooFewBytesForCigarOps: Long, invalidCigarOp: Long, emptyMappedCigar: Long, emptyMappedSeq: Long, tooFewRemainingBytesImplied: Long, readsBeforeError: Map[Int, Long]) extends Error[Long] with Product with Serializable

   

3. case class EmptyMapped(emptyMappedCigar: Boolean, emptyMappedSeq: Boolean) extends CigarOpsError with Product with Serializable

   

4. trait Error[T] extends AnyRef

   

   Bag of fields with information related to various inconsistencies in BAM-record-candidates.

   Bag of fields with information related to various inconsistencies in BAM-record-candidates.

   T

   field type: Boolean for individual positions Flags, Long for aggregate Counts.

5. case class Flags(tooFewFixedBlockBytes: Boolean, negativeReadIdx: Boolean, tooLargeReadIdx: Boolean, negativeReadPos: Boolean, tooLargeReadPos: Boolean, negativeNextReadIdx: Boolean, tooLargeNextReadIdx: Boolean, negativeNextReadPos: Boolean, tooLargeNextReadPos: Boolean, tooFewBytesForReadName: Boolean, nonNullTerminatedReadName: Boolean, nonASCIIReadName: Boolean, noReadName: Boolean, emptyReadName: Boolean, tooFewBytesForCigarOps: Boolean, invalidCigarOp: Boolean, emptyMappedCigar: Boolean, emptyMappedSeq: Boolean, tooFewRemainingBytesImplied: Boolean, readsBeforeError: Int) extends Error[Boolean] with Result with Product with Serializable

   

   Information about BAM-record checks at a org.hammerlab.bgzf.Pos.

6. class FlagsSerializer extends Serializer[Flags]

   

   Serialize a Flags as a BitSet to save IO.

7. sealed trait NegativeRefIdx extends RefPosError

   

8. sealed trait NegativeRefPos extends RefPosError

   

9. sealed trait ReadNameError extends AnyRef

   

   Container for flags related to inconsistencies in BAM-record-candidates' read-name-length and read-name fields.

10. sealed trait ReadNameLengthError extends ReadNameError

    

11. sealed trait RefPosError extends AnyRef

    

    Container for flags related to inconsistencies in BAM-records' "reference-sequence-index", "reference position", and analogous "mate-" fields.

12. class Registrar extends kryo.spark.Registrar

    

13. sealed trait Result extends AnyRef

    

14. case class Success(readsParsed: Int) extends Result with Product with Serializable

    

15. sealed trait TooLargeRefIdx extends RefPosError