Class ReadStructure

java.lang.Object
picard.illumina.parser.ReadStructure

public class ReadStructure extends Object
Describes the intended logical output structure of clusters of an Illumina run. (e.g. If the input data consists of 80 base clusters and we provide a read structure of "28T8M8B8S28T" then those bases should be split into 4 reads: read one should be 28 cycles of template, read two should be 8 cycles of molecular barcode, read three should be 8 cycles of sample barcode, 8 cycles are skipped, read four should be another 36 cycle template read.) Note: In future releases, ReadStructures will be specified by clients of IlluminaDataProvider(currently read structures are detected by IlluminaDataProviderFactory via the structure of QSeq files). When working with QSeq formats, while the individual reads need not fall on QSeq end file boundaries the total number of cycles should equal the total number of cycles found in all end files for one tile. (e.g. if I have 80 reads and 3 end files per tile, those end files should have a total of 80 reads in them regardless of how many reads appear in each individual file)
  • Field Details

  • Constructor Details

    • ReadStructure

      public ReadStructure(List<ReadDescriptor> collection)
      Copies collection into descriptors (making descriptors unmodifiable) and then calculates relevant statistics about descriptors.
      Parameters:
      collection - A collection of ReadDescriptors that describes this ReadStructure
    • ReadStructure

      public ReadStructure(String readStructureString)
      Converts readStructureString into a List and calls the primary constructor using this List as it's argument.
      Parameters:
      readStructureString - A string of the format ... describing this read structure
  • Method Details

    • getNumDescriptors

      public int getNumDescriptors()
    • toString

      public String toString()
      Converts this object into a String using rules complementary to the single string constructor above.
      Overrides:
      toString in class Object
      Returns:
      A string of the form ... with one per ReadDescriptor in descriptors.
    • equals

      public boolean equals(Object thatObj)
      Overrides:
      equals in class Object
    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object
    • hasSampleBarcode

      public boolean hasSampleBarcode()