/** {@inheritDoc} */
@Override
public void initialize(final int readMaxLength, final int haplotypeMaxLength) {
super.initialize(readMaxLength, haplotypeMaxLength);
transition = PairHMMModel.createTransitionMatrix(maxReadLength);
prior = new double[paddedMaxReadLength][paddedMaxHaplotypeLength];
// Initialize all arrays
// Final Cell of array is a padding cell, initialized to zero.
currentMatchArray = new double[paddedMaxReadLength];
currentDeleteArray = new double[paddedMaxReadLength];
currentInsertArray = new double[paddedMaxReadLength];
parentMatchArray = new double[paddedMaxReadLength];
parentDeleteArray = new double[paddedMaxReadLength];
parentInsertArray = new double[paddedMaxReadLength];
grandparentMatchArray = new double[paddedMaxReadLength];
grandparentDeleteArray = new double[paddedMaxReadLength];
grandparentInsertArray = new double[paddedMaxReadLength];
// Initialize the special arrays used for caching when successive haplotypes have a common
// prefix
matchCacheArray = new double[paddedMaxReadLength];
deleteCacheArray = new double[paddedMaxReadLength];
insertCacheArray = new double[paddedMaxReadLength];
nextMatchCacheArray = new double[paddedMaxReadLength];
nextDeleteCacheArray = new double[paddedMaxReadLength];
nextInsertCacheArray = new double[paddedMaxReadLength];
}
/**
* Initializes the matrix that holds all the constants related to quality scores.
*
* @param insertionGOP insertion quality scores of the read
* @param deletionGOP deletion quality scores of the read
* @param overallGCP overall gap continuation penalty
*/
@Requires({"insertionGOP != null", "deletionGOP != null", "overallGCP != null"})
@Ensures("constantsAreInitialized")
protected static void initializeProbabilities(
final double[][] transition,
final byte[] insertionGOP,
final byte[] deletionGOP,
final byte[] overallGCP) {
PairHMMModel.qualToTransProbs(transition, insertionGOP, deletionGOP, overallGCP);
}