object SampleSheet
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!=(arg0: Any): Boolean
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final
def
##(): Int
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- val Description: String
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val
HeaderNames: Set[String]
The header names that are standard fields in upper case.
- val I5Bases: String
- val I7Bases: String
- val Lane: String
- val LibraryId: String
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val
SampleId: String
Required header names for standard fields in the Illumina Experiment Manager Sample Sheet.
- val SampleName: String
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val
SampleProject: String
Optional header names for standard fields in the Illumina Experiment Manager Sample Sheet.
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val
SplitRegex: String
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- protected[com.fulcrumgenomics.illumina]
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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.
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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.
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final
def
asInstanceOf[T0]: T0
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def
cleanMiseqSampleId(id: String): String
Attempts to clean special characters from a sample id or name as Illumina's software does.
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def
clone(): AnyRef
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eq(arg0: AnyRef): Boolean
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equals(arg0: Any): Boolean
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finalize(): Unit
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final
def
getClass(): Class[_]
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def
getIntField(sampleDatum: Map[String, String], name: String): Option[Int]
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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
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def
hashCode(): Int
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final
def
isInstanceOf[T0]: Boolean
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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.
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ne(arg0: AnyRef): Boolean
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final
def
notify(): Unit
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final
def
notifyAll(): Unit
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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.
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synchronized[T0](arg0: ⇒ T0): T0
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def
toString(): String
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def
wait(): Unit
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def
wait(arg0: Long, arg1: Int): Unit
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wait(arg0: Long): Unit
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