# HG changeset patch
# User davidvanzessen
# Date 1463064715 14400
# Node ID a4c2ddeadec0e3264b6afaf59f99fa92b3ce63bb
# Parent  0513b46178c45c5469a60cee02307dee7a873087
Uploaded

diff -r 0513b46178c4 -r a4c2ddeadec0 naive_output.r
--- a/naive_output.r	Thu May 12 07:35:07 2016 -0400
+++ b/naive_output.r	Thu May 12 10:51:55 2016 -0400
@@ -17,9 +17,9 @@
 final.numeric[is.na(final.numeric)] = 0
 final[,sapply(final, is.numeric)] = final.numeric
 
-final.ca = final[grepl("ca", final$Sample),]
-final.cg = final[grepl("cg", final$Sample),]
-final.cm = final[grepl("cm", final$Sample),]
+final.ca = final[grepl("^ca", final$Sample),]
+final.cg = final[grepl("^cg", final$Sample),]
+final.cm = final[grepl("^cm", final$Sample),]
 
 if(nrow(final.ca) > 0){
 	final.ca$Replicate = 1
diff -r 0513b46178c4 -r a4c2ddeadec0 wrapper.sh
--- a/wrapper.sh	Thu May 12 07:35:07 2016 -0400
+++ b/wrapper.sh	Thu May 12 10:51:55 2016 -0400
@@ -227,9 +227,9 @@
 then
 	echo "---------------- imgt_loader.r ----------------"
 	#python $dir/imgt_loader.py --summ $PWD/summary.txt --aa $PWD/aa.txt --junction $PWD/junction.txt --output $naive_output
-	Rscript --verbose $dir/imgt_loader.r $PWD/summary.txt $PWD/aa.txt $PWD/junction.txt ${naive_output_ca} 2>&1
+	Rscript --verbose $dir/imgt_loader.r $PWD/summary.txt $PWD/aa.txt $PWD/junction.txt $outdir/loader_output.txt 2>&1
 	echo "---------------- naive_output.r ----------------"
-	Rscript $dir/naive_output.r $naive_output_ca $outdir/merged.txt $naive_output_ca $naive_output_cg $naive_output_cm 2>&1
+	Rscript $dir/naive_output.r $outdir/loader_output.txt $outdir/merged.txt ${naive_output_ca} ${naive_output_cg} ${naive_output_cm} 2>&1
 fi
 
 echo "---------------- sequence_overview.r ----------------"