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()

• equals

  public boolean equals​(Object o)

  Overrides:

  equals in class Object

• hashCode

  public int hashCode()

  Overrides:

  hashCode in class Object