--- a/wrapper.sh	Thu Oct 13 10:52:24 2016 -0400
+++ b/wrapper.sh	Tue Oct 25 07:28:43 2016 -0400
@@ -158,13 +158,13 @@
 
 classes="IGA,IGA1,IGA2,IGG,IGG1,IGG2,IGG3,IGG4,IGM,unmatched"
 echo "R mutation analysis"
-Rscript $dir/shm_csr.r $outdir/merged.txt $classes $outdir ${include_fr1} 2>&1
+Rscript $dir/shm_csr.r $outdir/merged.txt $classes $outdir ${empty_region_filter} 2>&1
 
 
 echo "---------------- shm_csr.py ----------------"
 echo "---------------- shm_csr.py ----------------<br />" >> $log
 
-python $dir/shm_csr.py --input $outdir/merged.txt --genes $classes --includefr1 "${include_fr1}" --output $outdir/hotspot_analysis.txt
+python $dir/shm_csr.py --input $outdir/merged.txt --genes $classes --empty_region_filter "${empty_region_filter}" --output $outdir/hotspot_analysis.txt
 
 echo "---------------- aa_histogram.r ----------------"
 echo "---------------- aa_histogram.r ----------------<br />" >> $log
@@ -575,6 +575,9 @@
 
 cd $tmp
 
+echo "Cleaning up *.RData files"
+find $outdir/baseline -name "*.RData" -type f -delete
+
 echo "---------------- naive_output.r ----------------"
 echo "---------------- naive_output.r ----------------<br />" >> $log