Class AlignmentSpan


  • public class AlignmentSpan
    extends Object
    A span of over a single reference. Immutable. Holds alignment start and span values as well as counts of how many are mapped vs. unmapped vs unmapped-unplaced.
    • Constructor Detail

      • AlignmentSpan

        public AlignmentSpan​(AlignmentContext alignmentContext,
                             int mappedCount,
                             int unmappedCount,
                             int unmappedUnplacedCount)
        This does not retain the alignmentContext referenceContext state (its just a shorthand for passing the rest of the alignmentContext values in).
        Parameters:
        alignmentContext -
        mappedCount -
        unmappedCount -
        unmappedUnplacedCount -
      • AlignmentSpan

        public AlignmentSpan​(int alignmentStart,
                             int alignmentSpan,
                             int mappedCount,
                             int unmappedCount,
                             int unmappedUnplacedCount)
        Create a new span with a multiple reads in it.
        Parameters:
        alignmentStart - minimum alignment start of the reads represented by this span, using a 1-based coordinate system
        alignmentSpan - span from minimum alignment start to maximum alignment end of the reads represented by this span span = max(end) - min(start) + 1
        mappedCount - number of mapped reads in the span
        unmappedCount - number of unmapped reads in the span
    • Method Detail

      • combine

        public static AlignmentSpan combine​(AlignmentSpan a,
                                            AlignmentSpan b)
        Combine two AlignmentSpans
        Parameters:
        a - the first AlignmentSpan to combine
        b - the second AlignmentSpan to combine
        Returns:
        the new combined AlignmentSpan
      • getAlignmentStart

        public int getAlignmentStart()
      • getAlignmentSpan

        public int getAlignmentSpan()
      • getMappedCount

        public int getMappedCount()
      • getUnmappedCount

        public int getUnmappedCount()
      • getUnmappedUnplacedCount

        public int getUnmappedUnplacedCount()
      • hashCode

        public int hashCode()
        Overrides:
        hashCode in class Object