From d30a4c6364d6338915a49085e696a7a7c555f1c1 Mon Sep 17 00:00:00 2001
From: mpmeers <mpmeers@gmail.com>
Date: Mon, 4 Nov 2019 16:38:26 -0800
Subject: [PATCH 1/2] Update SEACR_1.2.sh

Added calls to SEACR_1.2.R on lines 122, 126, and 129
---
 SEACR_1.2.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/SEACR_1.2.sh b/SEACR_1.2.sh
index e27f034..6651339 100755
--- a/SEACR_1.2.sh
+++ b/SEACR_1.2.sh
@@ -119,14 +119,14 @@ path=`dirname $0`
 if [[ -f $2 ]] && [[ $norm == "norm" ]]
 then
 	echo "Calculating threshold using normalized control: $(date)"
-	Rscript $path/SEACR_1.1.R --exp=$password.auc --ctrl=$password2.auc --norm=yes --output=$password
+	Rscript $path/SEACR_1.2.R --exp=$password.auc --ctrl=$password2.auc --norm=yes --output=$password
 elif [[ -f $2 ]]
 then
 	echo "Calculating threshold using non-normalized control: $(date)"
-	Rscript $path/SEACR_1.1.R --exp=$password.auc --ctrl=$password2.auc --norm=no --output=$password
+	Rscript $path/SEACR_1.2.R --exp=$password.auc --ctrl=$password2.auc --norm=no --output=$password
 else
 	echo "Using user-provided threshold: $(date)"
-	Rscript $path/SEACR_1.1.R --exp=$password.auc --ctrl=$2 --norm=no --output=$password
+	Rscript $path/SEACR_1.2.R --exp=$password.auc --ctrl=$2 --norm=no --output=$password
 fi
 	
 fdr=`cat $password.fdr.txt | sed -n '1p'`			## Added 5/15/19 for SEACR_1.1

From 169c97f1c7e0c39a7b0751b63ed498fb8474477c Mon Sep 17 00:00:00 2001
From: mpmeers <mpmeers@gmail.com>
Date: Mon, 4 Nov 2019 16:39:39 -0800
Subject: [PATCH 2/2] Update SEACR_1.2.R

Added a d0 term to percentile threshold part of loop so that write.table on line 144 does not fail due to an unspecified d0
---
 SEACR_1.2.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/SEACR_1.2.R b/SEACR_1.2.R
index f013939..9648f81 100644
--- a/SEACR_1.2.R
+++ b/SEACR_1.2.R
@@ -137,6 +137,7 @@ if(is.na(numtest)){ ## If 2nd field is a bedgraph, calculate empirical threshold
 	ctrl<-as.vector(as.numeric(paste(0,argsL$ctrl,sep="")))
 	x0<-min(frame$values[frame$percentile <= ctrl[1]])
 	z0<-min(frame2$values[frame2$percentile <= ctrl[1]])
+	d0<-0
 	fdr<-ctrl[1] ## New for SEACR_1.1
 }
 invis <- gc(verbose=FALSE)