Class AlignmentBlock

  • All Implemented Interfaces:
    Serializable

    public class AlignmentBlock
    extends Object
    implements Serializable
    Represents the contiguous alignment of a subset of read bases to a reference sequence. Simply put an alignment block tells you that read bases from readStart are aligned to the reference (matching or mismatching) from referenceStart for length bases.
    See Also:
    Serialized Form
    • Method Detail

      • getReadStart

        public int getReadStart()
        The first, 1-based, base in the read that is aligned to the reference reference.
      • getReferenceStart

        public int getReferenceStart()
        The first, 1-based, position in the reference to which the read is aligned.
      • getLength

        public int getLength()
        The number of contiguous bases aligned to the reference.