/* DO NOT EDIT THIS FILE - it is machine generated */
#include <jni.h>
/* Header for class org_broadinstitute_sting_alignment_bwa_c_BWACAligner */

#ifndef _Included_org_broadinstitute_sting_alignment_bwa_c_BWACAligner
#define _Included_org_broadinstitute_sting_alignment_bwa_c_BWACAligner
#ifdef __cplusplus
extern "C" {
#endif
/*
 * Class:     org_broadinstitute_sting_alignment_bwa_c_BWACAligner
 * Method:    create
 * Signature: (Lorg/broadinstitute/sting/alignment/bwa/BWTFiles;Lorg/broadinstitute/sting/alignment/bwa/BWAConfiguration;)J
 */
JNIEXPORT jlong JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner_create
  (JNIEnv *, jobject, jobject, jobject);

/*
 * Class:     org_broadinstitute_sting_alignment_bwa_c_BWACAligner
 * Method:    updateConfiguration
 * Signature: (JLorg/broadinstitute/sting/alignment/bwa/BWAConfiguration;)V
 */
JNIEXPORT void JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner_updateConfiguration
  (JNIEnv *, jobject, jlong, jobject);

/*
 * Class:     org_broadinstitute_sting_alignment_bwa_c_BWACAligner
 * Method:    destroy
 * Signature: (J)V
 */
JNIEXPORT void JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner_destroy
  (JNIEnv *, jobject, jlong);

/*
 * Class:     org_broadinstitute_sting_alignment_bwa_c_BWACAligner
 * Method:    getPaths
 * Signature: (J[B)[Lorg/broadinstitute/sting/alignment/bwa/c/BWAPath;
 */
JNIEXPORT jobjectArray JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner_getPaths
  (JNIEnv *, jobject, jlong, jbyteArray);

/*
 * Class:     org_broadinstitute_sting_alignment_bwa_c_BWACAligner
 * Method:    convertPathsToAlignments
 * Signature: (J[B[Lorg/broadinstitute/sting/alignment/bwa/c/BWAPath;)[Lorg/broadinstitute/sting/alignment/Alignment;
 */
JNIEXPORT jobjectArray JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner_convertPathsToAlignments
  (JNIEnv *, jobject, jlong, jbyteArray, jobjectArray);

/*
 * Class:     org_broadinstitute_sting_alignment_bwa_c_BWACAligner
 * Method:    getBestAlignment
 * Signature: (J[B)Lorg/broadinstitute/sting/alignment/Alignment;
 */
JNIEXPORT jobject JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner_getBestAlignment
  (JNIEnv *, jobject, jlong, jbyteArray);

#ifdef __cplusplus
}
#endif
#endif
