62 lines
2.9 KiB
C
62 lines
2.9 KiB
C
/* DO NOT EDIT THIS FILE - it is machine generated */
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#include <jni.h>
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/* Header for class org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM */
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#ifndef _Included_org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM
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#define _Included_org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM
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#ifdef __cplusplus
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extern "C" {
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#endif
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#undef org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_TRISTATE_CORRECTION
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#define org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_TRISTATE_CORRECTION 3.0
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#undef org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_matchToMatch
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#define org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_matchToMatch 0L
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#undef org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_indelToMatch
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#define org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_indelToMatch 1L
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#undef org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_matchToInsertion
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#define org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_matchToInsertion 2L
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#undef org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_insertionToInsertion
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#define org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_insertionToInsertion 3L
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#undef org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_matchToDeletion
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#define org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_matchToDeletion 4L
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#undef org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_deletionToDeletion
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#define org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_deletionToDeletion 5L
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/*
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* Class: org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM
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* Method: jniInitialize
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* Signature: (II)V
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*/
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JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_jniInitialize
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(JNIEnv *, jobject, jint, jint);
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/*
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* Class: org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM
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* Method: jniInitializeProbabilities
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* Signature: ([[D[B[B[B)V
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*/
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JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_jniInitializeProbabilities
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(JNIEnv *, jclass, jobjectArray, jbyteArray, jbyteArray, jbyteArray);
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/*
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* Class: org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM
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* Method: jniInitializePriorsAndUpdateCells
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* Signature: (ZII[B[B[BI)D
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*/
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JNIEXPORT jdouble JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_jniInitializePriorsAndUpdateCells
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(JNIEnv *, jobject, jboolean, jint, jint, jbyteArray, jbyteArray, jbyteArray, jint);
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/*
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* Class: org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM
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* Method: jniSubComputeReadLikelihoodGivenHaplotypeLog10
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* Signature: (II[B[B[B[B[B[BI)D
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*/
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JNIEXPORT jdouble JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_jniSubComputeReadLikelihoodGivenHaplotypeLog10
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(JNIEnv *, jobject, jint, jint, jbyteArray, jbyteArray, jbyteArray, jbyteArray, jbyteArray, jbyteArray, jint);
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#ifdef __cplusplus
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}
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#endif
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#endif
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