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

#ifndef _Included_org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM
#define _Included_org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM
#ifdef __cplusplus
extern "C" {
#endif
#undef org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_TRISTATE_CORRECTION
#define org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_TRISTATE_CORRECTION 3.0
#undef org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_matchToMatch
#define org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_matchToMatch 0L
#undef org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_indelToMatch
#define org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_indelToMatch 1L
#undef org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_matchToInsertion
#define org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_matchToInsertion 2L
#undef org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_insertionToInsertion
#define org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_insertionToInsertion 3L
#undef org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_matchToDeletion
#define org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_matchToDeletion 4L
#undef org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_deletionToDeletion
#define org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_deletionToDeletion 5L
/*
 * Class:     org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM
 * Method:    jniInitialize
 * Signature: (II)V
 */
JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_jniInitialize
  (JNIEnv *, jobject, jint, jint);

/*
 * Class:     org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM
 * Method:    jniInitializeProbabilities
 * Signature: ([[D[B[B[B)V
 */
JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_jniInitializeProbabilities
  (JNIEnv *, jclass, jobjectArray, jbyteArray, jbyteArray, jbyteArray);

/*
 * Class:     org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM
 * Method:    jniInitializePriorsAndUpdateCells
 * Signature: (ZII[B[B[BI)D
 */
JNIEXPORT jdouble JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_jniInitializePriorsAndUpdateCells
  (JNIEnv *, jobject, jboolean, jint, jint, jbyteArray, jbyteArray, jbyteArray, jint);


/*
 * Class:     org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM
 * Method:    jniSubComputeReadLikelihoodGivenHaplotypeLog10
 * Signature: (II[B[B[B[B[B[BI)D
 */
JNIEXPORT jdouble JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_jniSubComputeReadLikelihoodGivenHaplotypeLog10
    (JNIEnv *, jobject, jint, jint, jbyteArray, jbyteArray, jbyteArray, jbyteArray, jbyteArray, jbyteArray, jint);

/*
 * Class:     org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM
 * Method:    jniGlobalInit
 * Signature: (Ljava/lang/Class;Ljava/lang/Class;)V
 */
JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_jniGlobalInit
  (JNIEnv *, jobject, jclass, jclass);

/*
 * Class:     org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM
 * Method:    jniComputeLikelihoods
 * Signature: ([Lorg/broadinstitute/sting/utils/pairhmm/JNILoglessPairHMM/JNIReadDataHolderClass;[Lorg/broadinstitute/sting/utils/pairhmm/JNILoglessPairHMM/JNIHaplotypeDataHolderClass;[D)V
 */
JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_jniComputeLikelihoods
  (JNIEnv *, jobject, jint, jint, jobjectArray, jobjectArray, jdoubleArray, jint);

#ifdef __cplusplus
}
#endif
#endif