Type Members

1.  case class RunInfo (run_barcode: String, flowcell_barcode: String, instrument_name: String, run_date: Iso8601Date, read_structure: ReadStructure, num_lanes: Int) extends Metric with Product with Serializable

   Stores the result of parsing the run info (RunInfo.xml) file from an Illumina run folder.

   Stores the result of parsing the run info (RunInfo.xml) file from an Illumina run folder.

   run_barcode

   the unique identifier for the sequencing run and flowcell, stored as "<instrument-name>_<flowcell-barcode>".

   flowcell_barcode

   the flowcell barcode.

   instrument_name

   the instrument name.

   run_date

   the date of the sequencing run.

   read_structure

   the description of the logical structure of cycles within the sequencing run. This will only contain template and sample barcode segments, as the RunInfo.xml does not contain information about other segments (i.e. molecular barcodes and skips).

   num_lanes

   the number of lanes in the flowcell.

2.  case class Sample (sampleOrdinal: Int, sampleId: String, sampleName: String, libraryId: String, project: Option[String] = None, description: Option[String] = None, lane: Option[Int] = None, i7IndexBases: Option[String] = None, i5IndexBases: Option[String] = None, extendedAttributes: Map[String, String] = Map.empty) extends Product with Serializable

   Represents information about a sample within an Illumina Experiment Manager sample sheet.

   Represents information about a sample within an Illumina Experiment Manager sample sheet.

   Optionally contains information about dual indexes: i7 and i5.

   sampleOrdinal

   the sample ordinal if this sample belongs to a sample set.

   sampleId

   the unique sample identifier.

   sampleName

   the sample name.

   libraryId

   the library identifier.

   project

   the project identifier.

   description

   the sample description.

   lane

   the lane number for the sample.

   i7IndexBases

   the sample barcode bases in the i7 read.

   i5IndexBases

   the sample barcode bases in the i5 read.

   extendedAttributes

   a map of non-standard or site-specific extended attributes. Keys should be upper-case.

3.  class SampleSheet extends Iterable[Sample]

   Stores information about samples from an Illumina Experiment Manager Sample Sheet (typically a MiSeq).

   Stores information about samples from an Illumina Experiment Manager Sample Sheet (typically a MiSeq). The samples may also include derived information.

   Optional fields include support for specifying the expected sample barcode for each sample. The sample barcode can be present as a sub-sequence (or sub-sequences) in the i7 or i5 read. If additional bases are found in the i7 or i5 read, such as molecular barcodes, the should be included as Ns. It is up to the developer to obtain the correct read structure elsewhere to infer which bases are sample barcode and which bases are not (ex. molecular identifiers).

   The sample identifier should be unique across samples within the sample sheet, and the combination of sample name and library identifier should also be unique across samples within the sample sheet.