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diff --git a/Makefile b/PairHMM_JNI/Makefile
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diff --git a/convert_char.cc b/PairHMM_JNI/convert_char.cc
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diff --git a/define-double.h b/PairHMM_JNI/define-double.h
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diff --git a/hmm_mask.cc b/PairHMM_JNI/hmm_mask.cc
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diff --git a/org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.cc b/PairHMM_JNI/org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.cc
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diff --git a/org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.h b/PairHMM_JNI/org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.h
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diff --git a/template.h b/PairHMM_JNI/template.h
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