object Bams extends LazyLogging

Utility methods for working with BAMs.

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  1. final def !=(arg0: Any): Boolean
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  2. final def ##(): Int
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  3. final def ==(arg0: Any): Boolean
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  4. val MaxInMemory: Int

    The default maximum # of records to keep and sort in memory.

  5. final def asInstanceOf[T0]: T0
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  6. def clone(): AnyRef
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  7. final def eq(arg0: AnyRef): Boolean
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  8. def equals(arg0: Any): Boolean
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  9. def finalize(): Unit
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  10. final def getClass(): Class[_]
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  11. def hashCode(): Int
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  12. def insertCoordinates(rec: SamRecord): (Int, Int)

    Calculates the coordinates of the insert represented by this record and returns them as a pair of 1-based closed ended coordinates.

    Calculates the coordinates of the insert represented by this record and returns them as a pair of 1-based closed ended coordinates.

    Invalid to call on a read that is not mapped in a pair to the same chromosome as it's mate.

    returns

    the start and end position of the insert as a tuple, always with start <= end

  13. final def isInstanceOf[T0]: Boolean
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  14. lazy val logger: Logger
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  15. final def ne(arg0: AnyRef): Boolean
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  16. final def notify(): Unit
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  17. final def notifyAll(): Unit
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  18. def positionFromOtherEndOfTemplate(rec: SamRecord, genomicPosition: Int): Option[Int]

    If the read is mapped in an FR pair, returns the distance of the position from the other end of the template, other wise returns None.

    If the read is mapped in an FR pair, returns the distance of the position from the other end of the template, other wise returns None.

    rec

    the SamRecord whose insert to calculate the position within

    genomicPosition

    the genomic position of interest (NOT the position within the read)

  19. def queryGroupedIterator(iterator: Iterator[SamRecord], header: SAMFileHeader, maxInMemory: Int, tmpDir: FgBioDef.DirPath): SelfClosingIterator[SamRecord]

    Returns an iterator over the records in the given reader in such a way that all reads with the same query name are adjacent in the iterator.

    Returns an iterator over the records in the given reader in such a way that all reads with the same query name are adjacent in the iterator. Does NOT guarantee a queryname sort, merely a query grouping.

    iterator

    an iterator from which to consume records

    header

    the header associated with the records.

    maxInMemory

    the maximum number of records to keep and sort in memory if sorting is needed

    tmpDir

    an optional temp directory to use for temporary sorting files if needed

    returns

    an Iterator with reads from the same query grouped together

  20. def queryGroupedIterator(in: SamSource, maxInMemory: Int = MaxInMemory, tmpDir: FgBioDef.DirPath = Io.tmpDir): BetterBufferedIterator[SamRecord]

    Returns an iterator over the records in the given reader in such a way that all reads with the same query name are adjacent in the iterator.

    Returns an iterator over the records in the given reader in such a way that all reads with the same query name are adjacent in the iterator. Does NOT guarantee a queryname sort, merely a query grouping.

    in

    a SamReader from which to consume records

    maxInMemory

    the maximum number of records to keep and sort in memory if sorting is needed

    tmpDir

    an optional temp directory to use for temporary sorting files if needed

    returns

    an Iterator with reads from the same query grouped together

  21. def regenerateNmUqMdTags(rec: SamRecord, ref: ReferenceSequenceFileWalker): Unit

    Ensures that any NM/UQ/MD tags on the read are accurate.

    Ensures that any NM/UQ/MD tags on the read are accurate. If the read is unmapped, any existing values are removed. If the read is mapped all three tags will have values regenerated.

    rec

    the SamRecord to update

    ref

    a reference sequence file walker to pull the reference information from

  22. def sorter(order: SamOrder, header: SAMFileHeader, maxRecordsInRam: Int = MaxInMemory, tmpDir: FgBioDef.DirPath = Io.tmpDir): Sorter[SamRecord, A]

    Generates a Sorter for doing disk-backed sorting of objects.

  23. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  24. def templateIterator(iterator: Iterator[SamRecord], header: SAMFileHeader, maxInMemory: Int, tmpDir: FgBioDef.DirPath): Iterator[Template]

    Returns an iterator of Template objects generated from all the reads in the SamReader.

    Returns an iterator of Template objects generated from all the reads in the SamReader. If the SamReader is not query sorted or grouped, a sort to queryname will be performed.

    iterator

    an iterator from which to consume records

    header

    the header associated with the records.

    maxInMemory

    the maximum number of records to keep and sort in memory if sorting is needed

    tmpDir

    an optional temp directory to use for temporary sorting files if needed

    returns

    an Iterator of Template objects

  25. def templateIterator(in: SamSource, maxInMemory: Int = MaxInMemory, tmpDir: FgBioDef.DirPath = Io.tmpDir): Iterator[Template]

    Returns an iterator of Template objects generated from all the reads in the SamReader.

    Returns an iterator of Template objects generated from all the reads in the SamReader. If the SamReader is not query sorted or grouped, a sort to queryname will be performed.

    in

    a SamReader from which to consume records

    maxInMemory

    the maximum number of records to keep and sort in memory if sorting is needed

    tmpDir

    an optional temp directory to use for temporary sorting files if needed

    returns

    an Iterator of Template objects

  26. def toString(): String
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  27. final def wait(): Unit
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  28. final def wait(arg0: Long, arg1: Int): Unit
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  29. final def wait(arg0: Long): Unit
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Inherited from LazyLogging

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