Class CRAIEntry

  • All Implemented Interfaces:
    Comparable<CRAIEntry>

    public class CRAIEntry
    extends Object
    implements Comparable<CRAIEntry>
    A class representing CRAI index entry: file and alignment offsets for each slice. Created by vadim on 10/08/2015.
    • Constructor Detail

      • CRAIEntry

        public CRAIEntry​(int sequenceId,
                         int alignmentStart,
                         int alignmentSpan,
                         long containerStartByteOffset,
                         int sliceByteOffsetFromCompressionHeaderStart,
                         int sliceByteSize)
      • CRAIEntry

        public CRAIEntry​(String line)
        Create a CRAI Entry from a serialized CRAI index line.
        Parameters:
        line - string formatted as a CRAI index entry
    • Method Detail

      • writeToStream

        public void writeToStream​(OutputStream os)
        Serialize the entry to a CRAI index stream.
        Parameters:
        os - stream to write to
      • compareTo

        public int compareTo​(CRAIEntry other)
        Sort by numerical order of reference sequence ID, except that unmapped-unplaced reads come last For valid reference sequence ID (placed reads): - sort by alignment start - if alignment start is equal, sort by container offset - if alignment start and container offset are equal, sort by slice offset For unmapped-unplaced reads: - ignore (invalid) alignment start value - sort by container offset - if container offset is equal, sort by slice offset
        Specified by:
        compareTo in interface Comparable<CRAIEntry>
        Parameters:
        other - the CRAIEntry to compare against
        Returns:
        int representing the comparison result, suitable for ordering
      • getSequenceId

        public int getSequenceId()
      • getAlignmentStart

        public int getAlignmentStart()
      • getAlignmentSpan

        public int getAlignmentSpan()
      • getContainerStartByteOffset

        public long getContainerStartByteOffset()
      • getSliceByteOffsetFromCompressionHeaderStart

        public int getSliceByteOffsetFromCompressionHeaderStart()
      • getSliceByteSize

        public int getSliceByteSize()
      • hashCode

        public int hashCode()
        Overrides:
        hashCode in class Object