From 2c0d70c86328519a571ea1a183c8f1f808420095 Mon Sep 17 00:00:00 2001
From: Karthik Gururaj <karthik.gururaj@intel.com>
Date: Mon, 27 Jan 2014 14:52:59 -0800
Subject: [PATCH] Moved vector JNI code to public/c++/VectorPairHMM

---
 {PairHMM_JNI => public/c++/VectorPairHMM}/.gitignore              | 0
 {PairHMM_JNI => public/c++/VectorPairHMM}/JNI_README              | 0
 {PairHMM_JNI => public/c++/VectorPairHMM}/LoadTimeInitializer.cc  | 0
 {PairHMM_JNI => public/c++/VectorPairHMM}/LoadTimeInitializer.h   | 0
 {PairHMM_JNI => public/c++/VectorPairHMM}/Makefile                | 0
 .../c++/VectorPairHMM}/avx_function_instantiations.cc             | 0
 {PairHMM_JNI => public/c++/VectorPairHMM}/baseline.cc             | 0
 {PairHMM_JNI => public/c++/VectorPairHMM}/define-double.h         | 0
 {PairHMM_JNI => public/c++/VectorPairHMM}/define-float.h          | 0
 {PairHMM_JNI => public/c++/VectorPairHMM}/define-sse-double.h     | 0
 {PairHMM_JNI => public/c++/VectorPairHMM}/define-sse-float.h      | 0
 {PairHMM_JNI => public/c++/VectorPairHMM}/headers.h               | 0
 {PairHMM_JNI => public/c++/VectorPairHMM}/jni_common.h            | 0
 {PairHMM_JNI => public/c++/VectorPairHMM}/jnidebug.h              | 0
 ...g_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.cc | 0
 ...rg_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.h | 0
 ...org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.cc | 0
 .../org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.h | 0
 {PairHMM_JNI => public/c++/VectorPairHMM}/pairhmm-1-base.cc       | 0
 .../c++/VectorPairHMM}/pairhmm-template-kernel.cc                 | 0
 .../c++/VectorPairHMM}/pairhmm-template-main.cc                   | 0
 {PairHMM_JNI => public/c++/VectorPairHMM}/run.sh                  | 0
 {PairHMM_JNI => public/c++/VectorPairHMM}/shift_template.c        | 0
 .../c++/VectorPairHMM}/sse_function_instantiations.cc             | 0
 {PairHMM_JNI => public/c++/VectorPairHMM}/template.h              | 0
 {PairHMM_JNI => public/c++/VectorPairHMM}/utils.cc                | 0
 {PairHMM_JNI => public/c++/VectorPairHMM}/utils.h                 | 0
 {PairHMM_JNI => public/c++/VectorPairHMM}/vector_defs.h           | 0
 .../c++/VectorPairHMM}/vector_function_prototypes.h               | 0
 29 files changed, 0 insertions(+), 0 deletions(-)
 rename {PairHMM_JNI => public/c++/VectorPairHMM}/.gitignore (100%)
 rename {PairHMM_JNI => public/c++/VectorPairHMM}/JNI_README (100%)
 rename {PairHMM_JNI => public/c++/VectorPairHMM}/LoadTimeInitializer.cc (100%)
 rename {PairHMM_JNI => public/c++/VectorPairHMM}/LoadTimeInitializer.h (100%)
 rename {PairHMM_JNI => public/c++/VectorPairHMM}/Makefile (100%)
 rename {PairHMM_JNI => public/c++/VectorPairHMM}/avx_function_instantiations.cc (100%)
 rename {PairHMM_JNI => public/c++/VectorPairHMM}/baseline.cc (100%)
 rename {PairHMM_JNI => public/c++/VectorPairHMM}/define-double.h (100%)
 rename {PairHMM_JNI => public/c++/VectorPairHMM}/define-float.h (100%)
 rename {PairHMM_JNI => public/c++/VectorPairHMM}/define-sse-double.h (100%)
 rename {PairHMM_JNI => public/c++/VectorPairHMM}/define-sse-float.h (100%)
 rename {PairHMM_JNI => public/c++/VectorPairHMM}/headers.h (100%)
 rename {PairHMM_JNI => public/c++/VectorPairHMM}/jni_common.h (100%)
 rename {PairHMM_JNI => public/c++/VectorPairHMM}/jnidebug.h (100%)
 rename {PairHMM_JNI => public/c++/VectorPairHMM}/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.cc (100%)
 rename {PairHMM_JNI => public/c++/VectorPairHMM}/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.h (100%)
 rename {PairHMM_JNI => public/c++/VectorPairHMM}/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.cc (100%)
 rename {PairHMM_JNI => public/c++/VectorPairHMM}/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.h (100%)
 rename {PairHMM_JNI => public/c++/VectorPairHMM}/pairhmm-1-base.cc (100%)
 rename {PairHMM_JNI => public/c++/VectorPairHMM}/pairhmm-template-kernel.cc (100%)
 rename {PairHMM_JNI => public/c++/VectorPairHMM}/pairhmm-template-main.cc (100%)
 rename {PairHMM_JNI => public/c++/VectorPairHMM}/run.sh (100%)
 rename {PairHMM_JNI => public/c++/VectorPairHMM}/shift_template.c (100%)
 rename {PairHMM_JNI => public/c++/VectorPairHMM}/sse_function_instantiations.cc (100%)
 rename {PairHMM_JNI => public/c++/VectorPairHMM}/template.h (100%)
 rename {PairHMM_JNI => public/c++/VectorPairHMM}/utils.cc (100%)
 rename {PairHMM_JNI => public/c++/VectorPairHMM}/utils.h (100%)
 rename {PairHMM_JNI => public/c++/VectorPairHMM}/vector_defs.h (100%)
 rename {PairHMM_JNI => public/c++/VectorPairHMM}/vector_function_prototypes.h (100%)

diff --git a/PairHMM_JNI/.gitignore b/public/c++/VectorPairHMM/.gitignore
similarity index 100%
rename from PairHMM_JNI/.gitignore
rename to public/c++/VectorPairHMM/.gitignore
diff --git a/PairHMM_JNI/JNI_README b/public/c++/VectorPairHMM/JNI_README
similarity index 100%
rename from PairHMM_JNI/JNI_README
rename to public/c++/VectorPairHMM/JNI_README
diff --git a/PairHMM_JNI/LoadTimeInitializer.cc b/public/c++/VectorPairHMM/LoadTimeInitializer.cc
similarity index 100%
rename from PairHMM_JNI/LoadTimeInitializer.cc
rename to public/c++/VectorPairHMM/LoadTimeInitializer.cc
diff --git a/PairHMM_JNI/LoadTimeInitializer.h b/public/c++/VectorPairHMM/LoadTimeInitializer.h
similarity index 100%
rename from PairHMM_JNI/LoadTimeInitializer.h
rename to public/c++/VectorPairHMM/LoadTimeInitializer.h
diff --git a/PairHMM_JNI/Makefile b/public/c++/VectorPairHMM/Makefile
similarity index 100%
rename from PairHMM_JNI/Makefile
rename to public/c++/VectorPairHMM/Makefile
diff --git a/PairHMM_JNI/avx_function_instantiations.cc b/public/c++/VectorPairHMM/avx_function_instantiations.cc
similarity index 100%
rename from PairHMM_JNI/avx_function_instantiations.cc
rename to public/c++/VectorPairHMM/avx_function_instantiations.cc
diff --git a/PairHMM_JNI/baseline.cc b/public/c++/VectorPairHMM/baseline.cc
similarity index 100%
rename from PairHMM_JNI/baseline.cc
rename to public/c++/VectorPairHMM/baseline.cc
diff --git a/PairHMM_JNI/define-double.h b/public/c++/VectorPairHMM/define-double.h
similarity index 100%
rename from PairHMM_JNI/define-double.h
rename to public/c++/VectorPairHMM/define-double.h
diff --git a/PairHMM_JNI/define-float.h b/public/c++/VectorPairHMM/define-float.h
similarity index 100%
rename from PairHMM_JNI/define-float.h
rename to public/c++/VectorPairHMM/define-float.h
diff --git a/PairHMM_JNI/define-sse-double.h b/public/c++/VectorPairHMM/define-sse-double.h
similarity index 100%
rename from PairHMM_JNI/define-sse-double.h
rename to public/c++/VectorPairHMM/define-sse-double.h
diff --git a/PairHMM_JNI/define-sse-float.h b/public/c++/VectorPairHMM/define-sse-float.h
similarity index 100%
rename from PairHMM_JNI/define-sse-float.h
rename to public/c++/VectorPairHMM/define-sse-float.h
diff --git a/PairHMM_JNI/headers.h b/public/c++/VectorPairHMM/headers.h
similarity index 100%
rename from PairHMM_JNI/headers.h
rename to public/c++/VectorPairHMM/headers.h
diff --git a/PairHMM_JNI/jni_common.h b/public/c++/VectorPairHMM/jni_common.h
similarity index 100%
rename from PairHMM_JNI/jni_common.h
rename to public/c++/VectorPairHMM/jni_common.h
diff --git a/PairHMM_JNI/jnidebug.h b/public/c++/VectorPairHMM/jnidebug.h
similarity index 100%
rename from PairHMM_JNI/jnidebug.h
rename to public/c++/VectorPairHMM/jnidebug.h
diff --git a/PairHMM_JNI/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.cc b/public/c++/VectorPairHMM/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.cc
similarity index 100%
rename from PairHMM_JNI/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.cc
rename to public/c++/VectorPairHMM/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.cc
diff --git a/PairHMM_JNI/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.h b/public/c++/VectorPairHMM/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.h
similarity index 100%
rename from PairHMM_JNI/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.h
rename to public/c++/VectorPairHMM/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.h
diff --git a/PairHMM_JNI/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.cc b/public/c++/VectorPairHMM/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.cc
similarity index 100%
rename from PairHMM_JNI/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.cc
rename to public/c++/VectorPairHMM/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.cc
diff --git a/PairHMM_JNI/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.h b/public/c++/VectorPairHMM/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.h
similarity index 100%
rename from PairHMM_JNI/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.h
rename to public/c++/VectorPairHMM/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.h
diff --git a/PairHMM_JNI/pairhmm-1-base.cc b/public/c++/VectorPairHMM/pairhmm-1-base.cc
similarity index 100%
rename from PairHMM_JNI/pairhmm-1-base.cc
rename to public/c++/VectorPairHMM/pairhmm-1-base.cc
diff --git a/PairHMM_JNI/pairhmm-template-kernel.cc b/public/c++/VectorPairHMM/pairhmm-template-kernel.cc
similarity index 100%
rename from PairHMM_JNI/pairhmm-template-kernel.cc
rename to public/c++/VectorPairHMM/pairhmm-template-kernel.cc
diff --git a/PairHMM_JNI/pairhmm-template-main.cc b/public/c++/VectorPairHMM/pairhmm-template-main.cc
similarity index 100%
rename from PairHMM_JNI/pairhmm-template-main.cc
rename to public/c++/VectorPairHMM/pairhmm-template-main.cc
diff --git a/PairHMM_JNI/run.sh b/public/c++/VectorPairHMM/run.sh
similarity index 100%
rename from PairHMM_JNI/run.sh
rename to public/c++/VectorPairHMM/run.sh
diff --git a/PairHMM_JNI/shift_template.c b/public/c++/VectorPairHMM/shift_template.c
similarity index 100%
rename from PairHMM_JNI/shift_template.c
rename to public/c++/VectorPairHMM/shift_template.c
diff --git a/PairHMM_JNI/sse_function_instantiations.cc b/public/c++/VectorPairHMM/sse_function_instantiations.cc
similarity index 100%
rename from PairHMM_JNI/sse_function_instantiations.cc
rename to public/c++/VectorPairHMM/sse_function_instantiations.cc
diff --git a/PairHMM_JNI/template.h b/public/c++/VectorPairHMM/template.h
similarity index 100%
rename from PairHMM_JNI/template.h
rename to public/c++/VectorPairHMM/template.h
diff --git a/PairHMM_JNI/utils.cc b/public/c++/VectorPairHMM/utils.cc
similarity index 100%
rename from PairHMM_JNI/utils.cc
rename to public/c++/VectorPairHMM/utils.cc
diff --git a/PairHMM_JNI/utils.h b/public/c++/VectorPairHMM/utils.h
similarity index 100%
rename from PairHMM_JNI/utils.h
rename to public/c++/VectorPairHMM/utils.h
diff --git a/PairHMM_JNI/vector_defs.h b/public/c++/VectorPairHMM/vector_defs.h
similarity index 100%
rename from PairHMM_JNI/vector_defs.h
rename to public/c++/VectorPairHMM/vector_defs.h
diff --git a/PairHMM_JNI/vector_function_prototypes.h b/public/c++/VectorPairHMM/vector_function_prototypes.h
similarity index 100%
rename from PairHMM_JNI/vector_function_prototypes.h
rename to public/c++/VectorPairHMM/vector_function_prototypes.h