Licensed under GPLv3

gabraham · Dec 18, 2012 · 36eb37d · 36eb37d
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diff --git a/00README.txt b/00README.txt
diff --git a/01LICENSE b/01LICENSE
diff --git a/README.md b/README.md
@@ -24,7 +24,25 @@ memory-efficient analysis of all SNPs for phenotype prediction'', BMC
 Bioinformatics,
 2012, 13:88, [doi:10.1186/1471-2105-13-88](http://www.biomedcentral.com/1471-2105/13/88/)
 
-Copyright (C), Gad Abraham and National ICT Australia (2011-2012), All Rights Reserved. 
+License
+-------
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 3 of the License, or
+(at your option) any later version.
+
+Copyright (C) 2011-2012 Gad Abraham and National ICT Australia (NICTA).
+All rights reserved.
+
+Requirements
+------------
+
+   For the post-analysis scripts:  R packages ggplot2 >=0.9.3, scales, grid, abind, ROCR
+
+   A 64-bit operating system is recommended; we have tested SparSNP on 64-bit
+   OSX and Linux.
+
 
 Quick Start
 -----------

diff --git a/cbind.c b/cbind.c
@@ -1,5 +1,10 @@
 /*
- * Copyright (c) 2011, National ICT Australia (NICTA)
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Copyright (C) 2011-2012 Gad Abraham and National ICT Australia (NICTA).
  * All rights reserved.
  */
 

diff --git a/coder.c b/coder.c
@@ -1,5 +1,10 @@
 /*
- * Copyright (c) 2011, National ICT Australia (NICTA)
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Copyright (C) 2011-2012 Gad Abraham and National ICT Australia (NICTA).
  * All rights reserved.
  */
 

diff --git a/coder.h b/coder.h
@@ -1,3 +1,12 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Copyright (C) 2011-2012 Gad Abraham and National ICT Australia (NICTA).
+ * All rights reserved.
+ */
 
 #define PACK_DENSITY 4
 

diff --git a/common.c b/common.c
@@ -1,5 +1,10 @@
 /*
- * Copyright (c) 2011, National ICT Australia (NICTA)
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Copyright (C) 2011-2012 Gad Abraham and National ICT Australia (NICTA).
  * All rights reserved.
  */
 

diff --git a/common.h b/common.h
@@ -1,5 +1,10 @@
 /*
- * Copyright (c) 2011, National ICT Australia (NICTA)
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Copyright (C) 2011-2012 Gad Abraham and National ICT Australia (NICTA).
  * All rights reserved.
  */
 

diff --git a/covtest.c b/covtest.c
@@ -1,5 +1,10 @@
 /*
- * Copyright (c) 2011, National ICT Australia (NICTA)
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Copyright (C) 2011-2012 Gad Abraham and National ICT Australia (NICTA).
  * All rights reserved.
  */
 

diff --git a/crossval.sh b/crossval.sh
@@ -1,5 +1,15 @@
 #!/bin/bash
 
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 3 of the License, or
+# (at your option) any later version.
+# 
+# Copyright (C) 2011-2012 Gad Abraham and National ICT Australia (NICTA).
+# All rights reserved.
+#
+
 set -e
 
 if [ -z "$1" ] || [ -z "$2" ];

diff --git a/crossvaluni.sh b/crossvaluni.sh
@@ -1,5 +1,15 @@
 #!/bin/bash
 
+# 
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 3 of the License, or
+# (at your option) any later version.
+# 
+# Copyright (C) 2011-2012 Gad Abraham and National ICT Australia (NICTA).
+# All rights reserved.
+# 
+
 # This script MUST be called after crossval.sh has been called
 
 set -e

diff --git a/eval.R b/eval.R
@@ -1,5 +1,15 @@
 #!/usr/bin/env Rscript
 
+# 
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 3 of the License, or
+# (at your option) any later version.
+# 
+# Copyright (C) 2011-2012 Gad Abraham and National ICT Australia (NICTA).
+# All rights reserved.
+# 
+
 usage <- paste("usage: eval.R [title=<title>]",
       "[prev=<K>] [h2l=<V>] [mode=discovery|validation]",
       "(prev must be specified if h2l is specified)")

diff --git a/evalprofile.R b/evalprofile.R
@@ -1,6 +1,17 @@
 #!/usr/bin/env Rscript
 
+# 
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 3 of the License, or
+# (at your option) any later version.
+# 
+# Copyright (C) 2011-2012 Gad Abraham and National ICT Australia (NICTA).
+# All rights reserved.
+# 
+
 usage <- paste("usage: evalprofile.R",
+   "model=<MODEL>",
    "[prev=<PREVALENCE>]",
    "[name=results]",
    "[indir=discovery]",

diff --git a/gennetwork.c b/gennetwork.c
@@ -1,3 +1,13 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Copyright (C) 2011-2012 Gad Abraham and National ICT Australia (NICTA).
+ * All rights reserved.
+ */
+
 #include <math.h>
 #include <stdio.h>
 

diff --git a/gennetwork.h b/gennetwork.h
@@ -1,3 +1,12 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Copyright (C) 2011-2012 Gad Abraham and National ICT Australia (NICTA).
+ * All rights reserved.
+ */
 
 #define CORTYPE_IND 0
 #define CORTYPE_ABS 1

diff --git a/gennetwork_test.R b/gennetwork_test.R
@@ -1,4 +1,14 @@
 
+# 
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 3 of the License, or
+# (at your option) any later version.
+# 
+# Copyright (C) 2011-2012 Gad Abraham and National ICT Australia (NICTA).
+# All rights reserved.
+# 
+
 set.seed(2879)
 
 Y <- round(matrix(rnorm(20 * 5), 20, 5), 2)

diff --git a/gennetwork_test.c b/gennetwork_test.c
@@ -1,3 +1,13 @@
+/*
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * Copyright (C) 2011-2012 Gad Abraham and National ICT Australia (NICTA).
+ * All rights reserved.
+ */
+
 #include <stdlib.h>
 #include <stdio.h>