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 Description: String
5.  val HeaderNames: Set[String]

   The header names that are standard fields in upper case.

6.  val I5Bases: String
7.  val I7Bases: String
8.  val Lane: String
9.  val LibraryId: String
10.  val SampleId: String

    Required header names for standard fields in the Illumina Experiment Manager Sample Sheet.

11.  val SampleName: String
12.  val SampleProject: String

    Optional header names for standard fields in the Illumina Experiment Manager Sample Sheet.

13.  val SplitRegex: String

    Attributes

    protected[com.fulcrumgenomics.illumina]

14.  def apply(lines: Iterator[String], lane: Option[Int]): SampleSheet

    Parses an Illumina Experiment Manager Sample Sheet (typically a MiSeq).

    Parses an Illumina Experiment Manager Sample Sheet (typically a MiSeq).

    If library id is not found, it will be set to the sample identifier.

    If the lane number is given, returns only the samples that have that lane specified.

    NB: the lookup in the columns in the Sample Sheet is case insensitive.

15.  def apply(sampleSheet: Path, lane: Option[Int] = None): SampleSheet

    Parses an Illumina Experiment Manager Sample Sheet (typically a MiSeq).

    Parses an Illumina Experiment Manager Sample Sheet (typically a MiSeq).

    If library id is not found, it will be set to the sample identifier.

    If the lane number is given, returns only the samples that have that lane specified.

    NB: the lookup in the columns in the Sample Sheet is case insensitive.

16.  final def asInstanceOf[T0]: T0

    Definition Classes

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17.  def cleanMiseqSampleId(id: String): String

    Attempts to clean special characters from a sample id or name as Illumina's software does.

18.  def clone(): AnyRef

    Attributes

    protected[java.lang]

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

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20.  def equals(arg0: Any): Boolean

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21.  def finalize(): Unit

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    protected[java.lang]

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

22.  final def getClass(): Class[_]

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23.  def getIntField(sampleDatum: Map[String, String], name: String): Option[Int]

    Attributes

    protected

24.  def getStringField(sampleDatum: Map[String, String], name: String): Option[String]

    Gets the trimmed value of the given key (name) from the map.

    Gets the trimmed value of the given key (name) from the map. If empty or not found, returns None

    Attributes

    protected

25.  def hashCode(): Int

    Definition Classes

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26.  final def isInstanceOf[T0]: Boolean

    Definition Classes

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27.  def makeSample(sampleOrdinal: Int, sampleDatum: Map[String, String]): Sample

    Creates a sample from the given row data.

    Creates a sample from the given row data.

    Attributes

    protected

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

    Definition Classes

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29.  final def notify(): Unit

    Definition Classes

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30.  final def notifyAll(): Unit

    Definition Classes

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31.  def parseSampleData(lines: Iterator[String], lane: Option[Int] = None): List[Map[String, String]]

    Reads in the sample data from an Illumina Experiment Manager sample sheet.

    Reads in the sample data from an Illumina Experiment Manager sample sheet. For each sample, a map of column name to value is returned. If the lane number is given, returns only the samples that have that lane specified.

    Attributes

    protected

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

    Definition Classes

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33.  def toString(): String

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34.  final def wait(): Unit

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

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

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