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()