Binary file ._loadandplot.R has changed

Binary file ._plotwithscale.R has changed

Binary file ._testandplot.R has changed

--- a/loadandplot.xml	Thu Jun 08 17:40:15 2017 -0400
+++ b/loadandplot.xml	Fri Jun 09 11:57:33 2017 -0400
@@ -18,7 +18,7 @@
     <exit_code range="35" level="fatal" description="Windows in feature files do not cover all regions in region files." />
     <exit_code range="36" level="fatal" description="All windows in a feature file must have the same size." />
     <exit_code range="40" level="fatal" description="An error has occurred smoothing the data. Please try again." />
-    <regex match="Error" level="fatal" description="An error has occurred. Please try again." />
+    <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." />
   </stdio>
 
   <command>

--- a/plotwithscale.xml	Thu Jun 08 17:40:15 2017 -0400
+++ b/plotwithscale.xml	Fri Jun 09 11:57:33 2017 -0400
@@ -12,7 +12,7 @@
     <exit_code range="40" level="fatal" description="Scale threshold too high." />
     <exit_code range="50" level="fatal" description="Group by 'test' but selected features with different resolution." />
     <exit_code range="60" level="fatal" description="Summary plot error. Please try again." />
-    <regex match="Error" level="fatal" description="An error has occurred. Please try again." />
+    <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." />
   </stdio>
 
   <command>

Binary file test-data/._.DS_Store has changed

Binary file test-data/input/._Controls_regions.bed has changed

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Binary file test-data/input/._Elements3_regions.bed has changed

Binary file test-data/input/._Feature1.bed has changed

Binary file test-data/input/._Feature2.bed has changed

Binary file test-data/input/._features.header.bed.txt has changed

Binary file test-data/input/._regions.header.txt has changed

Binary file test-data/output_loadandplot/._iwtomics.loadandplot.RData has changed

Binary file test-data/output_loadandplot/._iwtomics.loadandplot.features.txt has changed

Binary file test-data/output_loadandplot/._iwtomics.loadandplot.pdf has changed

Binary file test-data/output_loadandplot/._iwtomics.loadandplot.regions.txt has changed

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--- a/testandplot.xml	Thu Jun 08 17:40:15 2017 -0400
+++ b/testandplot.xml	Fri Jun 09 11:57:33 2017 -0400
@@ -10,7 +10,7 @@
     <exit_code range="20" level="fatal" description="Wrong feature ids." />
     <exit_code range="30" level="fatal" description="Same test repeated multiple times." />
     <exit_code range="40" level="fatal" description="Testing error." />
-    <regex match="Error" level="fatal" description="An error has occurred. Please try again." />
+    <regex match="Error" source="both" level="fatal" description="An error has occurred. Please try again." />
   </stdio>
 
   <command>