Value Members

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 FilterInsufficientSupport: String

   Filter reason for when there are too few reads to form a consensus.

5.  val FilterLowQuality: String

   Filter reason for when reads are rejected due to low quality.

6.  val FilterMinorityAlignment: String

   Filter reason for when reads are rejected for having a minority CIGAR.

7.  val FilterOrphan: String

   Filter reason for when reads are rejected due creation of orphaned consensus (i.e.

   Filter reason for when reads are rejected due creation of orphaned consensus (i.e. R1 or R2 failed).

8.  final def asInstanceOf[T0]: T0

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9.  def checkSortOrder(header: SAMFileHeader, source: Any, warn: (String) ⇒ Unit, error: (String) ⇒ Unit): Unit

   Helper method to check that the input BAM is in the correct order for consensus calling.

   Helper method to check that the input BAM is in the correct order for consensus calling. Will call the warn function if the sort order looks like it's probably compatible but it's not 100% sure. Will invoke the error function in cases where the sort order is definitely incompatible.

   header

   the header of the BAM file to be used for consensus calling

   source

   a path or string representing the source of the header

   warn

   a function to be called when any warnings are detected/emitted

   error

   a function to be called when any errors are encountered; should probably throw an exception!

10.  def clone(): AnyRef

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    @throws( ... ) @native()

11.  final def eq(arg0: AnyRef): Boolean

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12.  def equals(arg0: Any): Boolean

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13.  def finalize(): Unit

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    @throws( classOf[java.lang.Throwable] )

14.  final def getClass(): Class[_]

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    @native()

15.  def hashCode(): Int

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16.  final def isInstanceOf[T0]: Boolean

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17.  def makePrefixFromSamHeader(header: SAMFileHeader): String

    Attempts to construct a String that can be used as a prefix for consensus read names based on the contents of the incoming SAMFileHeader.

18.  final def ne(arg0: AnyRef): Boolean

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19.  final def notify(): Unit

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20.  final def notifyAll(): Unit

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    @native()

21.  def outputHeader(in: SAMFileHeader, readGroupId: String, sortOrder: Option[SamOrder] = None): SAMFileHeader

    Constructs an output header with a single read group for the a BAM.

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

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23.  def toString(): String

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24.  final def wait(): Unit

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    @throws( ... )

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

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    @throws( ... )

26.  final def wait(arg0: Long): Unit

    Definition Classes

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27.  object ReadType extends Enumeration

    The type of consensus read to output.