Constructor Detail

• FastaSequenceIndexEntry

  public FastaSequenceIndexEntry​(String contig,
                                 long location,
                                 long size,
                                 int basesPerLine,
                                 int bytesPerLine,
                                 int sequenceIndex)

  Create a new entry with the given parameters.

  Parameters:

  contig - Contig this entry represents.

  location - Location (byte coordinate) in the fasta file.

  size - The number of bases in the contig.

  basesPerLine - How many bases are on each line.

  bytesPerLine - How many bytes are on each line (includes newline characters).

Method Detail

• getContig

  public String getContig()

  Gets the contig associated with this entry.

  Returns:

  String representation of the contig.

• setContig

  protected void setContig​(String contig)

  Sometimes contigs need to be adjusted on-the-fly to match sequence dictionary entries. Provide that capability to other classes w/i the package.

  Parameters:

  contig - New value for the contig.

• getLocation

  public long getLocation()

  Gets the location of this contig within the fasta.

  Returns:

  seek position within the fasta.

• getSize

  public long getSize()

  Gets the size, in bytes, of the data in the contig.

  Returns:

  size of the contig bases in bytes.

• getBasesPerLine

  public int getBasesPerLine()

  Gets the number of bases in a given line.

  Returns:

  Number of bases in the fasta line.

• getBytesPerLine

  public int getBytesPerLine()

  How many bytes (bases + whitespace) are consumed by the given line?

  Returns:

  Number of bytes in a line.

• getSequenceIndex

  public int getSequenceIndex()

• toString

  public String toString()

  For debugging. Emit the contents of each contig line.

  Overrides:

  toString in class Object

  Returns:

  A string representation of the contig line.

• equals

  public boolean equals​(Object other)

  Compare this index entry to another index entry.

  Overrides:

  equals in class Object

  Parameters:

  other - another FastaSequenceIndexEntry

  Returns:

  True if each has the same name, location, size, basesPerLine and bytesPerLine

• hashCode

  public int hashCode()

  In general, we expect one entry per contig, so compute the hash based only on the contig.

  Overrides:

  hashCode in class Object

  Returns:

  A unique hash code representing this object.