Class ReadStructure.Substructure

java.lang.Object
picard.illumina.parser.ReadStructure.Substructure
All Implemented Interfaces:
Iterable<ReadDescriptor>
Enclosing class:
ReadStructure

public class ReadStructure.Substructure extends Object implements Iterable<ReadDescriptor>
Represents a subset of ReadDescriptors in the containing ReadStructure, they ARE NOT necessarily contiguous in the containing ReadStructure but they ARE in the order they appear in the containing ReadStructure
  • Constructor Details

    • Substructure

      public Substructure(List<Integer> descriptorIndices, List<Range> allRanges)
      Indices into the ReadStructure.descriptors for this specific substructure, indices must be in the order they appear in the descriptors list (but the indices do NOT have to be continuous)
      Parameters:
      descriptorIndices - A list of indices into ReadStructure.descriptors of the enclosing ReadStructure
      allRanges - A list of ranges for all reads (not just those in this substructure) in the same order as ReadStructure.descriptors
  • Method Details

    • get

      public ReadDescriptor get(int index)
    • isEmpty

      public boolean isEmpty()
    • length

      public int length()
    • getTotalCycles

      public int getTotalCycles()
    • getIndices

      public int[] getIndices()
    • getDescriptorLengths

      public int[] getDescriptorLengths()
    • getCycleIndexRanges

      public Range[] getCycleIndexRanges()
    • iterator

      public Iterator<ReadDescriptor> iterator()
      Specified by:
      iterator in interface Iterable<ReadDescriptor>
    • getCycles

      public int[] getCycles()
    • toReadStructure

      public ReadStructure toReadStructure()
      Create a ReadStructure from this substructure composed of only the descriptors contained in this substructure, Any ReadDescriptors not in this substructure are treated as if they don't exist (e.g. if you have a readStructure (36T8S8B36T) and this substructure consists of all the non-skipped reads than toReadStructure would return (36T8B36T) in ReadStructure form