update to 1.0.7.4

mahmoudibrahim · Jun 7, 2016 · 5944021 · 5944021
1 parent ccad620
commit 5944021
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Showing 11 changed files with 21 additions and 18 deletions.
diff --git a/JAMM.sh b/JAMM.sh
@@ -1,5 +1,5 @@
 ########################################################################
-# JAMMv1.0.7rev3 is a peak finder for joint analysis of NGS replicates.
+# JAMMv1.0.7rev4 is a peak finder for joint analysis of NGS replicates.
 # Copyright (C) 2014-2016  Mahmoud Ibrahim
 #
 # This program is free software: you can redistribute it and/or modify
@@ -28,7 +28,7 @@ sPath="`( cd \"$sPath\" && pwd )`"
 usage()
 {
 cat << EOF
-Welcome to JAMM v1.0.7rev3 (GNU GPLv3). Copyright (C) 2014-2016  Mahmoud Ibrahim.
+Welcome to JAMM v1.0.7rev4 (GNU GPLv3). Copyright (C) 2014-2016  Mahmoud Ibrahim.
 
 This program comes with ABSOLUTELY NO WARRANTY; for details visit http://www.gnu.org/licenses/gpl.html. This is free software, and you are welcome to redistribute it under certain conditions; visit http://www.gnu.org/licenses/gpl.html for details.
 
@@ -157,7 +157,7 @@ fi
 # ============================= 
 # Step One: Initial Processing
 # =============================
-printf "\n\n============================================\nStarted JAMM Pipeline v1.0.7rev2...Hang on!\n============================================\n\n"
+printf "\n\n============================================\nStarted JAMM Pipeline v1.0.7rev4...Hang on!\n============================================\n\n"
 
 if [ ! -d "$wdir" ]; then
 	mkdir $wdir #make working directory

diff --git a/SignalGenerator.sh b/SignalGenerator.sh
@@ -1,5 +1,5 @@
 ########################################################################
-# JAMMv1.0.7rev3 is a peak finder for joint analysis of NGS replicates.
+# JAMMv1.0.7rev4 is a peak finder for joint analysis of NGS replicates.
 # Copyright (C) 2014-2016  Mahmoud Ibrahim
 #
 # This program is free software: you can redistribute it and/or modify
@@ -27,7 +27,7 @@ sPath="`( cd \"$sPath\" && pwd )`"
 usage()
 {
 cat << EOF
-Welcome to JAMM v1.0.7rev3 Signal Generator Script (GNU GPLv3). Copyright (C) 2014-2016  Mahmoud Ibrahim.
+Welcome to JAMM v1.0.7rev4 Signal Generator Script (GNU GPLv3). Copyright (C) 2014-2016  Mahmoud Ibrahim.
 
 This program comes with ABSOLUTELY NO WARRANTY; for details visit http://www.gnu.org/licenses/gpl.html. This is free software, and you are welcome to redistribute it under certain conditions; visit http://www.gnu.org/licenses/gpl.html for details.
 
@@ -119,7 +119,7 @@ fi
 # ============================= 
 # Step One: Initial Processing
 # =============================
-printf "\n\n==========================================================\nStarted JAMM1.0.7rev2 Signal Generator Pipeline...Hang on!\n==========================================================\n\n"
+printf "\n\n==========================================================\nStarted JAMM1.0.7rev4 Signal Generator Pipeline...Hang on!\n==========================================================\n\n"
 
 if [ ! -d "$wdir" ]; then
 	mkdir $wdir #make working directory

diff --git a/bincalculator.r b/bincalculator.r
@@ -1,5 +1,5 @@
 ########################################################################
-# JAMMv1.0.7rev3 is a peak finder for joint analysis of NGS replicates.
+# JAMMv1.0.7rev4 is a peak finder for joint analysis of NGS replicates.
 # Copyright (C) 2014-2016  Mahmoud Ibrahim
 #
 # This program is free software: you can redistribute it and/or modify

diff --git a/changelog b/changelog
@@ -1,6 +1,5 @@
 ===================
-Version 1.0.7rev3
+Version 1.0.7rev4
 ===================
 
-- fixed bugs in paired-end handling
-- fixed bugs in automated threshold that slowed it down when input was present
+- fixed a bug in window finding
diff --git a/peakfilter.pl b/peakfilter.pl
@@ -1,5 +1,5 @@
 ########################################################################
-# JAMMv1.0.7rev3 is a peak finder for joint analysis of NGS replicates.
+# JAMMv1.0.7rev4 is a peak finder for joint analysis of NGS replicates.
 # Copyright (C) 2014-2016  Mahmoud Ibrahim
 #
 # This program is free software: you can redistribute it and/or modify

diff --git a/peakfinder.r b/peakfinder.r
@@ -1,5 +1,5 @@
 ########################################################################
-# JAMMv1.0.7rev3 is a peak finder for joint analysis of NGS replicates.
+# JAMMv1.0.7rev4 is a peak finder for joint analysis of NGS replicates.
 # Copyright (C) 2014-2016  Mahmoud Ibrahim
 #
 # This program is free software: you can redistribute it and/or modify
@@ -900,7 +900,11 @@ coffeeshop = as.numeric(unlist(coffeeshop))
 coffeeshop[coffeeshop != numdup] = 0
 
 if (sum(coffeeshop) != 0) { #Any enriched bins?
-coffeeshop = c(0, diff(coffeeshop))
+if (coffeeshop[1] == numdup) {
+	coffeeshop = c(numdup, diff(coffeeshop))
+} else {
+	coffeeshop = c(0, diff(coffeeshop))
+}
 coffeeshop = cbind(coffeeshop, bins)
 coffeeshopNord = coffeeshop[coffeeshop[,1] == numdup,,drop=FALSE]
 coffeeshopSud = coffeeshop[coffeeshop[,1] == -numdup,,drop=FALSE]

diff --git a/peakhelper.r b/peakhelper.r
@@ -1,5 +1,5 @@
 ########################################################################
-# JAMMv1.0.7rev3 is a peak finder for joint analysis of NGS replicates.
+# JAMMv1.0.7rev4 is a peak finder for joint analysis of NGS replicates.
 # Copyright (C) 2014-2016  Mahmoud Ibrahim
 #
 # This program is free software: you can redistribute it and/or modify

diff --git a/readshifter.pl b/readshifter.pl
@@ -1,5 +1,5 @@
 ########################################################################
-# JAMMv1.0.7rev3 is a peak finder for joint analysis of NGS replicates.
+# JAMMv1.0.7rev4 is a peak finder for joint analysis of NGS replicates.
 # Copyright (C) 2014-2016  Mahmoud Ibrahim
 #
 # This program is free software: you can redistribute it and/or modify

diff --git a/signalmaker.r b/signalmaker.r
@@ -1,5 +1,5 @@
 ########################################################################
-# JAMMv1.0.7rev3 is a peak finder for joint analysis of NGS replicates.
+# JAMMv1.0.7rev4 is a peak finder for joint analysis of NGS replicates.
 # Copyright (C) 2014-2016  Mahmoud Ibrahim
 #
 # This program is free software: you can redistribute it and/or modify

diff --git a/xcorr.r b/xcorr.r
@@ -1,5 +1,5 @@
 ########################################################################
-# JAMMv1.0.7rev3 is a peak finder for joint analysis of NGS replicates.
+# JAMMv1.0.7rev4 is a peak finder for joint analysis of NGS replicates.
 # Copyright (C) 2014-2016  Mahmoud Ibrahim
 #
 # This program is free software: you can redistribute it and/or modify

diff --git a/xcorrhelper.r b/xcorrhelper.r
@@ -1,5 +1,5 @@
 ########################################################################
-# JAMMv1.0.7rev3 is a peak finder for joint analysis of NGS replicates.
+# JAMMv1.0.7rev4 is a peak finder for joint analysis of NGS replicates.
 # Copyright (C) 2014-2016  Mahmoud Ibrahim
 #
 # This program is free software: you can redistribute it and/or modify