org.broadinstitute.gatk.nativebindings.smithwaterman.SWAlignerNativeBinding Maven / Gradle / Ivy

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package org.broadinstitute.gatk.nativebindings.smithwaterman;


import org.broadinstitute.gatk.nativebindings.NativeLibrary;

/**
 * Provides access to the native kernel of the Smith-Waterman computation.
 * GATK will call {@link #initialize(SWAlignerArguments)} to set the
 * parameter values and will call {@link #align(byte[], byte[])} to perform
 * an alignment.
 *
 * Only one thread will call methods on any given object of classes that implement this interface.
 */
public interface SWAlignerNativeBinding extends NativeLibrary {

    /**
     * Initialize the native Smith-Waterman
     *
     * @param args arguments used for Smith-Waterman
     */
    void initialize(SWAlignerArguments args);

    /**
     * Perform a Smith-Waterman alignment and return the result
     *
     * @param ref reference sequence
     * @param alt alternate sequence
     * @return alignment result
     */
    SWAlignmentResult align(byte[] ref, byte[] alt);

}