From e6c6f8e313525e833c65b913d0fd5031cb855f19 Mon Sep 17 00:00:00 2001
From: Karthik Gururaj <karthik.gururaj@intel.com>
Date: Thu, 16 Jan 2014 20:28:50 -0800
Subject: [PATCH] Renamed directory

---
 .gitignore => PairHMM_JNI/.gitignore                              | 0
 Makefile => PairHMM_JNI/Makefile                                  | 0
 convert_char.cc => PairHMM_JNI/convert_char.cc                    | 0
 define-double.h => PairHMM_JNI/define-double.h                    | 0
 define-float.h => PairHMM_JNI/define-float.h                      | 0
 hmm_mask.cc => PairHMM_JNI/hmm_mask.cc                            | 0
 .../org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.cc   | 0
 .../org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.h    | 0
 pairhmm-1-base.cc => PairHMM_JNI/pairhmm-1-base.cc                | 0
 .../pairhmm-template-kernel.cc                                    | 0
 pairhmm-template-main.cc => PairHMM_JNI/pairhmm-template-main.cc  | 0
 shift_template.c => PairHMM_JNI/shift_template.c                  | 0
 template.h => PairHMM_JNI/template.h                              | 0
 13 files changed, 0 insertions(+), 0 deletions(-)
 rename .gitignore => PairHMM_JNI/.gitignore (100%)
 rename Makefile => PairHMM_JNI/Makefile (100%)
 rename convert_char.cc => PairHMM_JNI/convert_char.cc (100%)
 rename define-double.h => PairHMM_JNI/define-double.h (100%)
 rename define-float.h => PairHMM_JNI/define-float.h (100%)
 rename hmm_mask.cc => PairHMM_JNI/hmm_mask.cc (100%)
 rename org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.cc => PairHMM_JNI/org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.cc (100%)
 rename org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.h => PairHMM_JNI/org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.h (100%)
 rename pairhmm-1-base.cc => PairHMM_JNI/pairhmm-1-base.cc (100%)
 rename pairhmm-template-kernel.cc => PairHMM_JNI/pairhmm-template-kernel.cc (100%)
 rename pairhmm-template-main.cc => PairHMM_JNI/pairhmm-template-main.cc (100%)
 rename shift_template.c => PairHMM_JNI/shift_template.c (100%)
 rename template.h => PairHMM_JNI/template.h (100%)

diff --git a/.gitignore b/PairHMM_JNI/.gitignore
similarity index 100%
rename from .gitignore
rename to PairHMM_JNI/.gitignore
diff --git a/Makefile b/PairHMM_JNI/Makefile
similarity index 100%
rename from Makefile
rename to PairHMM_JNI/Makefile
diff --git a/convert_char.cc b/PairHMM_JNI/convert_char.cc
similarity index 100%
rename from convert_char.cc
rename to PairHMM_JNI/convert_char.cc
diff --git a/define-double.h b/PairHMM_JNI/define-double.h
similarity index 100%
rename from define-double.h
rename to PairHMM_JNI/define-double.h
diff --git a/define-float.h b/PairHMM_JNI/define-float.h
similarity index 100%
rename from define-float.h
rename to PairHMM_JNI/define-float.h
diff --git a/hmm_mask.cc b/PairHMM_JNI/hmm_mask.cc
similarity index 100%
rename from hmm_mask.cc
rename to PairHMM_JNI/hmm_mask.cc
diff --git a/org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.cc b/PairHMM_JNI/org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.cc
similarity index 100%
rename from org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.cc
rename to PairHMM_JNI/org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.cc
diff --git a/org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.h b/PairHMM_JNI/org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.h
similarity index 100%
rename from org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.h
rename to PairHMM_JNI/org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.h
diff --git a/pairhmm-1-base.cc b/PairHMM_JNI/pairhmm-1-base.cc
similarity index 100%
rename from pairhmm-1-base.cc
rename to PairHMM_JNI/pairhmm-1-base.cc
diff --git a/pairhmm-template-kernel.cc b/PairHMM_JNI/pairhmm-template-kernel.cc
similarity index 100%
rename from pairhmm-template-kernel.cc
rename to PairHMM_JNI/pairhmm-template-kernel.cc
diff --git a/pairhmm-template-main.cc b/PairHMM_JNI/pairhmm-template-main.cc
similarity index 100%
rename from pairhmm-template-main.cc
rename to PairHMM_JNI/pairhmm-template-main.cc
diff --git a/shift_template.c b/PairHMM_JNI/shift_template.c
similarity index 100%
rename from shift_template.c
rename to PairHMM_JNI/shift_template.c
diff --git a/template.h b/PairHMM_JNI/template.h
similarity index 100%
rename from template.h
rename to PairHMM_JNI/template.h