Class ReferenceTracks


  • public class ReferenceTracks
    extends Object
    • Constructor Detail

      • ReferenceTracks

        public ReferenceTracks​(int sequenceId,
                               String sequenceName,
                               byte[] reference)
    • Method Detail

      • getSequenceId

        public int getSequenceId()
      • getSequenceName

        public String getSequenceName()
      • getWindowPosition

        public int getWindowPosition()
      • getWindowLength

        public int getWindowLength()
      • getReferenceLength

        public int getReferenceLength()
      • ensure

        public void ensure​(int start,
                           int end)
      • ensureRange

        public void ensureRange​(int start,
                                int length)
      • baseAt

        public final byte baseAt​(int pos)
      • coverageAt

        public final short coverageAt​(int pos)
      • mismatchesAt

        public final short mismatchesAt​(int pos)
      • addCoverage

        public final void addCoverage​(int pos,
                                      int amount)
      • addMismatches

        public final void addMismatches​(int pos,
                                        int amount)