Class AlignmentSpan


  • public class AlignmentSpan
    extends Object
    A span of reads on a single reference.
    • Field Detail

      • UNMAPPED_SPAN

        public static final AlignmentSpan UNMAPPED_SPAN
        A constant to represent an unmapped span.
    • Constructor Detail

      • AlignmentSpan

        public AlignmentSpan​(int start,
                             int span)
        Create a new span with a single read in it.
        Parameters:
        start - alignment start of the span
        span - alignment span
      • AlignmentSpan

        public AlignmentSpan​(int start,
                             int span,
                             int count)
        Create a new span with a multiple reads in it.
        Parameters:
        start - alignment start of the span
        span - alignment span
        count - number of reads in the span
    • Method Detail

      • add

        public void add​(int start,
                        int span,
                        int count)
        Add multiple reads to the span.
        Parameters:
        start - alignment start
        span - alignment span
        count - number of reads to add
      • addSingle

        public void addSingle​(int start,
                              int span)
        Add a single read to the span
        Parameters:
        start - alignment start
        span - read span on the reference
      • getStart

        public int getStart()
      • setStart

        public void setStart​(int start)
      • getSpan

        public int getSpan()
      • setSpan

        public void setSpan​(int span)
      • getCount

        public int getCount()
      • hashCode

        public int hashCode()
        Overrides:
        hashCode in class Object