ReferenceSequenceMask.java

/*
 * The MIT License
 *
 * Copyright (c) 2010 The Broad Institute
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
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 * The above copyright notice and this permission notice shall be included in
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 *
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package htsjdk.samtools.util;

/**
 * Interface for specifying loci of interest for genotype calling and other operations.
 * It is a requirement that the sequences be probed in ascending order.
 *
 * @author alecw at broadinstitute dot oh are gee
 */
public interface ReferenceSequenceMask {

    /**
     * It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.
     * @return true if the mask is set for the given sequence and position
     */
    boolean get(int sequenceIndex, int position);

    /**
     * It is required that sequenceIndex is >= any previous sequenceIndex passed to this class.
     * @return the next pos on the given sequence >= position that is set, or -1 if there are no more set positions
     */
    int nextPosition(int sequenceIndex, int position);

    /**
     * @return Largest sequence index for which there are set bits.
     */
    int getMaxSequenceIndex();

    /**
     * @return the largest position on the last sequence index
     */
    int getMaxPosition();
}