diff bincalculator.r @ 1:243f75d0ed6e draft default tip

Uploaded. Includes new release 1.0.7 with fixed optional controls.

--- a/bincalculator.r	Wed Dec 17 10:40:23 2014 -0500
+++ b/bincalculator.r	Thu Feb 19 05:39:45 2015 -0500
@@ -1,7 +1,22 @@
-#############################################################
-#### Bin Size Calculator after Shimazaki and Shinomoto 2007
-#### R script		
-#############################################################
+########################################################################
+# JAMMv1.0.7rev1 is a peak finder for joint analysis of NGS replicates.
+# Copyright (C) 2014-2015  Mahmoud Ibrahim
+#
+# 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.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+# Contact: [e-mail]
+########################################################################
 
 
 # ======================= 
@@ -171,9 +186,9 @@
 
 
 
-# ===================== 
-# Shimazaki Procedure
-# =====================
+# ===================================================
+# Shimazaki Procedure (Shimazaki and Shinomoto 2007)
+# ===================================================
 for (i in 1:length(ibed)) {
 	if (frags[i] > rl[i]) {
 		minbin = floor(frags[i] / 2)