Class BinList

java.lang.Object
htsjdk.samtools.BinList
All Implemented Interfaces:
Iterable<Bin>

public class BinList extends Object implements Iterable<Bin>
Provides a list of all bins which could exist in the BAM file. Allows the user to iterate over all bins, selecting ones of interest for later inspection.
  • Constructor Details

    • BinList

      protected BinList(int referenceSequence, BitSet bins)
      Create a new BinList over sequenceCount sequences, consisting of the given bins.
      Parameters:
      referenceSequence - Reference sequence to which these bins are relevant.
      bins - The given bins to include.
  • Method Details

    • iterator

      public Iterator<Bin> iterator()
      Gets an iterator over all selected bins.
      Specified by:
      iterator in interface Iterable<Bin>
      Returns:
      An iterator over all selected bins.
    • getReferenceSequence

      protected int getReferenceSequence()
      Get the reference sequence to which this bin belongs.
      Returns:
      Integer representing the reference sequence.
    • getBins

      protected BitSet getBins()
      Retrieves the bins stored in this list.
      Returns:
      A bitset where a bin is present in the list if the bit is true.