Bwa

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 BwaExecutableConfigKey: String

   

5. final def asInstanceOf[T0]: T0

   

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6. def asType[T](path: String)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): T

   

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   ConfigurationLike

7. def bwaMemStreamed(unmappedBam: PathToBam, mappedBam: PathToBam, ref: PathToFasta, sortOrder: SortOrder = SortOrder.coordinate, minThreads: Int = 1, maxThreads: Int = 32, samToFastqCores: Double = 0.5, bwaMemMemory: String = "8G", samToFastqMem: String = "512M", mergeBamAlignmentMem: String = "2G", fifoBufferMem: String = "512M", processAltMappings: Boolean = false, orientation: PairOrientation = PairOrientation.FR): Pipe[SamOrBam, SamOrBam]

   

   Constructs a piped task that pipes from an unmapped SAM or BAM in queryname order through bwa-mem, optionally through bwa.kit's alt contig re-mapping process, and then through MergeBamAlignment to create a well-formed aligned BAM.

   Constructs a piped task that pipes from an unmapped SAM or BAM in queryname order through bwa-mem, optionally through bwa.kit's alt contig re-mapping process, and then through MergeBamAlignment to create a well-formed aligned BAM.

   unmappedBam

   the BAM in which to read unmapped data.

   mappedBam

   the BAM in which to store mapped data

   ref

   the reference FASTA file, with BWA indexes pre-built

   sortOrder

   the desired sort order of the output BAM file

   minThreads

   the minimum number of threads to allocate to bwa-mem

   maxThreads

   the maximum number of threads to allocate to bwa-mem

   bwaMemMemory

   the amount of memory based on the referenceFasta

   samToFastqMem

   the amount of memory for SamToFastq

   mergeBamAlignmentMem

   the amount of memory for MergeBamAlignment

   fifoBufferMem

   the amount of memory for each FifoBuffer

8. def clone(): AnyRef

   

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9. def commandLineName(name: String): String

   

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   ConfigurationLike

10. def config: Config

    

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    Configuration → ConfigurationLike

11. def configure[T](path: String, defaultValue: T)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): T

    

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    ConfigurationLike

12. def configure[T](path: String)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): T

    

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13. def configureExecutable(path: String, executable: String): Path

    

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14. def configureExecutableFromBinDirectory(binPath: String, executable: String, subDir: Option[Path]): Path

    

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

    

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16. def equals(arg0: Any): Boolean

    

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17. def finalize(): Unit

    

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    protected[java.lang]

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

18. def findBwa: Path

    

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

    

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20. def hashCode(): Int

    

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21. final def isInstanceOf[T0]: Boolean

    

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22. lazy val logger: Logger

    

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

    

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24. final def notify(): Unit

    

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25. final def notifyAll(): Unit

    

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26. def optionallyConfigure[T](path: String)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): Option[T]

    

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

    

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28. def systemPath: Seq[Path]

    

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29. def toString(): String

    

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30. final def wait(): Unit

    

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

    

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

    

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