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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.  final def asInstanceOf[T0]: T0

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5.  def bamFileFrom(output: FgBioDef.DirPath, sample: Sample, lane: Int): FgBioDef.PathToBam

   Produces the path to the BAM file for the given sample and lane.

   Produces the path to the BAM file for the given sample and lane.

   The BAM file name will <sample-name>.<barcode-seq>.<lane>.bam. The resulting file name will be sanitized to remove problematic characters.

   output

   the base output directory.

   sample

   the sample.

   lane

   the lane number.

   returns

   the path to the BAM file for the given sample and lane.

6.  def barcodeFileFrom(output: FgBioDef.DirPath, lane: Int): FgBioDef.FilePath

   The lane-specific file containing information necessary to run Picard's ExtractIlluminaBarcodes and CollectIlluminaBasecallingMetrics.

   The lane-specific file containing information necessary to run Picard's ExtractIlluminaBarcodes and CollectIlluminaBasecallingMetrics.

   output

   the base output directory.

   lane

   the lane number.

   returns

   the path to the barcode file, named "barcode_data.<lane>.txt".

7.  def clone(): AnyRef

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

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9.  def equals(arg0: Any): Boolean

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10.  def finalize(): Unit

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11.  def from(sampleSheet: SampleSheet, lanes: Seq[Int], output: FgBioDef.DirPath, bamOutput: Option[FgBioDef.DirPath] = None): Seq[BasecallingParams]

    Extracts sample and library information from an sample sheet for a given lane.

    Extracts sample and library information from an sample sheet for a given lane. The resulting files are used to run Picard's ExtractIlluminaBarcodes, CollectIlluminaBasecallingMetrics, and IlluminaBasecallsToSam. See ExtractBasecallingParamsForPicard for more information.

    sampleSheet

    the Illumina Experiment Manager sample sheet.

    lanes

    the lane number(s) (1-based).

    output

    the output directory where the barcode, library param, and BAM files should be written.

    bamOutput

    the optional output directory to where per-lane BAM files will be written, otherwise use output.

12.  final def getClass(): Class[_]

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13.  def hashCode(): Int

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14.  final def isInstanceOf[T0]: Boolean

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15.  def libraryParamsFileFrom(output: FgBioDef.DirPath, lane: Int): FgBioDef.FilePath

    The lane-specific file containing information necessary to run Picard's IlluminaBasecallsToSam.

    The lane-specific file containing information necessary to run Picard's IlluminaBasecallsToSam.

    output

    the base output directory.

    lane

    the lane number.

    returns

    the path to the library params file, named "library_params.<lane>.txt".

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

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17.  final def notify(): Unit

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18.  final def notifyAll(): Unit

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

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20.  def toString(): String

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21.  final def wait(): Unit

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

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

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