diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantDataManager.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantDataManager.java
index dfd3c02c1..1e28d2306 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantDataManager.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantDataManager.java
@@ -3,6 +3,31 @@ package org.broadinstitute.sting.playground.gatk.walkers.variantoptimizer;
 import org.broadinstitute.sting.utils.ExpandingArrayList;
 import org.broadinstitute.sting.utils.StingException;
 
+/*
+ * Copyright (c) 2010 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 /**
  * Created by IntelliJ IDEA.
  * User: rpoplin
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantDatum.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantDatum.java
index c856aa092..01f9bd892 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantDatum.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantDatum.java
@@ -1,5 +1,30 @@
 package org.broadinstitute.sting.playground.gatk.walkers.variantoptimizer;
 
+/*
+ * Copyright (c) 2010 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 /**
  * Created by IntelliJ IDEA.
  * User: rpoplin
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantGaussianMixtureModel.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantGaussianMixtureModel.java
index a7a086424..f7ebf8df7 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantGaussianMixtureModel.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantGaussianMixtureModel.java
@@ -2,6 +2,31 @@ package org.broadinstitute.sting.playground.gatk.walkers.variantoptimizer;
 
 import java.util.Random;
 
+/*
+ * Copyright (c) 2010 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 /**
  * Created by IntelliJ IDEA.
  * User: rpoplin
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantNearestNeighborsModel.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantNearestNeighborsModel.java
index fdfcf30be..2ad9c795c 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantNearestNeighborsModel.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantNearestNeighborsModel.java
@@ -1,5 +1,30 @@
 package org.broadinstitute.sting.playground.gatk.walkers.variantoptimizer;
 
+/*
+ * Copyright (c) 2010 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 /**
  * Created by IntelliJ IDEA.
  * User: rpoplin
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantOptimizationInterface.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantOptimizationInterface.java
index 934889a58..a6b4d7415 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantOptimizationInterface.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantOptimizationInterface.java
@@ -1,5 +1,30 @@
 package org.broadinstitute.sting.playground.gatk.walkers.variantoptimizer;
 
+/*
+ * Copyright (c) 2010 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 /**
  * Created by IntelliJ IDEA.
  * User: rpoplin
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantOptimizationModel.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantOptimizationModel.java
index 82853a2fb..184d67019 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantOptimizationModel.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantOptimizationModel.java
@@ -1,5 +1,30 @@
 package org.broadinstitute.sting.playground.gatk.walkers.variantoptimizer;
 
+/*
+ * Copyright (c) 2010 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 /**
  * Created by IntelliJ IDEA.
  * User: rpoplin
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantTree.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantTree.java
index 952a064e3..f86d88af4 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantTree.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantTree.java
@@ -2,6 +2,31 @@ package org.broadinstitute.sting.playground.gatk.walkers.variantoptimizer;
 
 import org.broadinstitute.sting.utils.StingException;
 
+/*
+ * Copyright (c) 2010 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 /**
  * Created by IntelliJ IDEA.
  * User: rpoplin
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantTreeNode.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantTreeNode.java
index b77505934..9f1af1b8f 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantTreeNode.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/VariantTreeNode.java
@@ -1,5 +1,30 @@
 package org.broadinstitute.sting.playground.gatk.walkers.variantoptimizer;
 
+/*
+ * Copyright (c) 2010 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
 /**
  * Created by IntelliJ IDEA.
  * User: rpoplin