From fae46dd77e55504434c9f55412f1f13056624a7d Mon Sep 17 00:00:00 2001
From: Jonas Maaskola <jonas.maaskola@weizmann.ac.il>
Date: Fri, 26 Aug 2022 18:45:52 +0300
Subject: [PATCH] saturation --bcstat takes a comma-separated list

---
 script/stereoRun_multiLane_v4.1.0.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/script/stereoRun_multiLane_v4.1.0.sh b/script/stereoRun_multiLane_v4.1.0.sh
index a25fec5..3aeca22 100644
--- a/script/stereoRun_multiLane_v4.1.0.sh
+++ b/script/stereoRun_multiLane_v4.1.0.sh
@@ -290,7 +290,7 @@ singularity exec ${visualSif} saturation \
     -i ${saturationFile} \
     --tissue ${result_04tissuecut}/${SNid}.tissue.gef \
     -o ${result_06saturation} \
-    --bcstat ${bcStat} \
+    --bcstat ${bcStatStr} \
     --summary ${result_02count}/${SNid}.Aligned.sortedByCoord.out.merge.q10.dedup.target.bam.summary.stat &&\
 ## organize your outputs (optional)
 if [[ ! -f $result_sn/${SNid}.saturation.bin200.png ]]