org.bdgenomics.adam.converters

AlignmentRecordConverter

class AlignmentRecordConverter extends Serializable

Linear Supertypes
Serializable, Serializable, AnyRef, Any
Ordering
  1. Alphabetic
  2. By inheritance
Inherited
  1. AlignmentRecordConverter
  2. Serializable
  3. Serializable
  4. AnyRef
  5. Any
  1. Hide All
  2. Show all
Learn more about member selection
Visibility
  1. Public
  2. All

Instance Constructors

  1. new AlignmentRecordConverter()

Value Members

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

    Definition Classes
    AnyRef → Any
  2. final def ##(): Int

    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any
  4. final def asInstanceOf[T0]: T0

    Definition Classes
    Any
  5. def clone(): AnyRef

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  6. def convert(adamRecord: AlignmentRecord, header: SAMFileHeaderWritable): SAMRecord

    Converts a single ADAM record into a SAM record.

    Converts a single ADAM record into a SAM record.

    adamRecord

    ADAM formatted alignment record to convert.

    header

    SAM file header to use.

    returns

    Returns the record converted to SAMtools format. Can be used for output to SAM/BAM.

  7. def convertFragment(fragment: Fragment): Iterable[AlignmentRecord]

    Converts a fragment to a set of reads.

    Converts a fragment to a set of reads.

    fragment

    Fragment to convert.

    returns

    The collection of alignments described by the fragment. If the fragment doesn't contain any alignments, this method will return one unaligned AlignmentRecord per sequence in the Fragment.

  8. def convertToFastq(adamRecord: AlignmentRecord, maybeAddSuffix: Boolean = false, outputOriginalBaseQualities: Boolean = false): String

    Converts a single record to FASTQ.

    Converts a single record to FASTQ. FASTQ format is:

    @readName
    sequence
    +<optional readname>
    ASCII quality scores
    adamRecord

    Read to convert to FASTQ.

    returns

    Returns this read in string form.

  9. def createSAMHeader(sd: SequenceDictionary, rgd: RecordGroupDictionary): SAMFileHeader

    Creates a SAM formatted header.

    Creates a SAM formatted header. This can be used with SAM or BAM files.

    sd

    Reference sequence dictionary to use for conversion.

    rgd

    Dictionary containing record groups.

    returns

    Converted SAM formatted record.

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

    Definition Classes
    AnyRef
  11. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any
  12. def finalize(): Unit

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  13. final def getClass(): Class[_]

    Definition Classes
    AnyRef → Any
  14. def hashCode(): Int

    Definition Classes
    AnyRef → Any
  15. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any
  16. final def ne(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef
  17. final def notify(): Unit

    Definition Classes
    AnyRef
  18. final def notifyAll(): Unit

    Definition Classes
    AnyRef
  19. final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes
    AnyRef
  20. def toString(): String

    Definition Classes
    AnyRef → Any
  21. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  22. final def wait(arg0: Long, arg1: Int): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  23. final def wait(arg0: Long): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

Ungrouped