org.hammerlab.guacamole.reads

MappedRead

case class MappedRead(name: String, sequence: IndexedSeq[Byte], baseQualities: IndexedSeq[Byte], isDuplicate: Boolean, sampleId: SampleId, contigName: ContigName, alignmentQuality: Int, start: Locus, cigar: Cigar, failedVendorQualityChecks: Boolean, isPositiveStrand: Boolean, isPaired: Boolean) extends Read with ReferenceRegion with Product with Serializable

A mapped read. See the Read trait for some of the field descriptions.

contigName

the contig name (e.g. "chr12") that this read was mapped to.

alignmentQuality

the mapping quality, phred scaled.

start

the (0-based) reference locus that the first base in this read aligns to.

cigar

parsed samtools CIGAR object.

Linear Supertypes
Serializable, Serializable, Product, Equals, ReferenceRegion, Interval, Ordered[Interval], Comparable[Interval], HasContig, Read, HasSampleId, AnyRef, Any
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Inherited
  1. MappedRead
  2. Serializable
  3. Serializable
  4. Product
  5. Equals
  6. ReferenceRegion
  7. Interval
  8. Ordered
  9. Comparable
  10. HasContig
  11. Read
  12. HasSampleId
  13. AnyRef
  14. Any
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Instance Constructors

  1. new MappedRead(name: String, sequence: IndexedSeq[Byte], baseQualities: IndexedSeq[Byte], isDuplicate: Boolean, sampleId: SampleId, contigName: ContigName, alignmentQuality: Int, start: Locus, cigar: Cigar, failedVendorQualityChecks: Boolean, isPositiveStrand: Boolean, isPaired: Boolean)

    contigName

    the contig name (e.g. "chr12") that this read was mapped to.

    alignmentQuality

    the mapping quality, phred scaled.

    start

    the (0-based) reference locus that the first base in this read aligns to.

    cigar

    parsed samtools CIGAR object.

Value Members

  1. final def !=(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  2. final def !=(arg0: Any): Boolean

    Definition Classes
    Any

  3. final def ##(): Int

    Definition Classes
    AnyRef → Any

  4. def <(that: Interval): Boolean

    Definition Classes
    Ordered

  5. def <=(that: Interval): Boolean

    Definition Classes
    Ordered

  6. final def ==(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  7. final def ==(arg0: Any): Boolean

    Definition Classes
    Any

  8. def >(that: Interval): Boolean

    Definition Classes
    Ordered

  9. def >=(that: Interval): Boolean

    Definition Classes
    Ordered

  10. lazy val alignmentLikelihood: Double

  11. val alignmentQuality: Int

    the mapping quality, phred scaled.

  12. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  13. def asMappedRead: Some[MappedRead]

    Definition Classes
    MappedRead → Read

  14. val baseQualities: IndexedSeq[Byte]

    The base qualities, phred scaled.

    The base qualities, phred scaled. These are numbers, and are NOT character encoded.

    Definition Classes
    MappedRead → Read

  15. val cigar: Cigar

    parsed samtools CIGAR object.

  16. val cigarElements: Buffer[CigarElement]

    Individual components of the CIGAR string (e.

    Individual components of the CIGAR string (e.g. "10M"), parsed, and as a Scala buffer.

  17. def clone(): AnyRef

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  18. def compare(other: Interval): Int

    Comparisons between ranges.

    Comparisons between ranges. Order is DESCENDING (i.e. reversed) from by start.

    Definition Classes
    Interval → Ordered

  19. def compareTo(that: Interval): Int

    Definition Classes
    Ordered → Comparable

  20. def contains(locus: Locus): Boolean

    Definition Classes
    Interval

  21. val contigName: ContigName

    the contig name (e.

    the contig name (e.g. "chr12") that this read was mapped to.

    Definition Classes
    MappedRead → ReferenceRegion → HasContig

  22. def countOfMismatches(contigSequence: ContigSequence): Int

  23. val end: Long

    The end of the alignment, exclusive.

    The end of the alignment, exclusive. This is the first reference locus AFTER the locus corresponding to the last base in this read.

    Definition Classes
    MappedRead → Interval

  24. final def eq(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  25. val failedVendorQualityChecks: Boolean

    Whether the read failed predefined vendor checks for quality

    Whether the read failed predefined vendor checks for quality

    Definition Classes
    MappedRead → Read

  26. def finalize(): Unit

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )

  27. final def getClass(): Class[_]

    Definition Classes
    AnyRef → Any

  28. val isDuplicate: Boolean

    Is this read a duplicate of another?

    Is this read a duplicate of another?

    Definition Classes
    MappedRead → Read

  29. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  30. val isMapped: Boolean

    Is this read mapped?

    Is this read mapped?

    Definition Classes
    MappedRead → Read

  31. val isPaired: Boolean

    Whether read is from a paired-end library

    Whether read is from a paired-end library

    Definition Classes
    MappedRead → Read

  32. val isPositiveStrand: Boolean

  33. def iterator(): Iterator[Long]

    Iterate through elements in the range.

    Iterate through elements in the range.

    Definition Classes
    Interval

  34. def length: NumLoci

    Number of elements in the range.

    Number of elements in the range.

    Definition Classes
    Interval

  35. val name: String

    Definition Classes
    MappedRead → Read

  36. final def ne(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  37. final def notify(): Unit

    Definition Classes
    AnyRef

  38. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  39. def overlaps(other: ReferenceRegion): Boolean

    Does the region overlap another reference region

    Does the region overlap another reference region

    other

    another region on the genome

    returns

    True if the the regions overlap

    Definition Classes
    ReferenceRegion

  40. def overlapsLocus(locus: Locus, halfWindowSize: Int = 0): Boolean

    Does the region overlap the given locus, with halfWindowSize padding?

    Does the region overlap the given locus, with halfWindowSize padding?

    Definition Classes
    ReferenceRegion

  41. def regionStr: String

    Definition Classes
    ReferenceRegion

  42. val sampleId: SampleId

    Definition Classes
    MappedRead → HasSampleId

  43. val sequence: IndexedSeq[Byte]

    The nucleotide sequence.

    The nucleotide sequence.

    Definition Classes
    MappedRead → Read

  44. def slice(from: Long, until: Long, contigSequence: ContigSequence): Option[MappedRead]

    Take a subsequence or slice of a read [from, until) Returns None if the provided coordinates do not overlap the read

    Take a subsequence or slice of a read [from, until) Returns None if the provided coordinates do not overlap the read

    from

    reference locus to start the new read

    until

    reference locus to slice up to (exclusive end)

    contigSequence

    reference sequence for the read's contig

    returns

    A read which spans [from, until) or None if the provided coordinates do not overlap the read

  45. val start: Locus

    the (0-based) reference locus that the first base in this read aligns to.

    the (0-based) reference locus that the first base in this read aligns to.

    Definition Classes
    MappedRead → Interval

  46. final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes
    AnyRef

  47. def toString(): String

    Definition Classes
    MappedRead → AnyRef → Any

  48. val unclippedEnd: Long

    The end of the read's alignment, including any final clipped bases, exclusive.

  49. val unclippedStart: Locus

    A read can be "clipped", meaning that some prefix or suffix of it did not align.

    A read can be "clipped", meaning that some prefix or suffix of it did not align. This is the start of the whole read's alignment, including any initial clipped bases.

  50. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  51. final def wait(arg0: Long, arg1: Int): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  52. final def wait(arg0: Long): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from ReferenceRegion

Inherited from Interval

Inherited from Ordered[Interval]

Inherited from Comparable[Interval]

Inherited from HasContig

Inherited from Read

Inherited from HasSampleId

Inherited from AnyRef

Inherited from Any

Ungrouped