sensitive

cobilab · Dec 9, 2022 · 9b754cb · 9b754cb
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commit 9b754cb
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diff --git a/cassava/SensitiveCassava.sh b/cassava/SensitiveCassava.sh
@@ -0,0 +1,17 @@
+#!/bin/bash
+#
+THRESHOLD=" 1.0 ";
+#
+# ------------------------------------------------------------------------------
+#
+for((x=1;x<=18;++x));
+  do
+  echo "Running $x ...";
+  echo "[H1] ...";
+  ./AlcoR mapper -v --hide --threshold $THRESHOLD --ignore 5 --dna -w 10 -m 14:50:0:1:10:0.9/3:10:0.9 -m 13:50:5000:1:10:0.9/3:10:0.9 -k -o masked-H1_C$x.fa H1_C$x.fa > positions-h1-$x.txt
+  echo "[H2] ...";
+  ./AlcoR mapper -v --hide --threshold $THRESHOLD --ignore 5 --dna -w 10 -m 14:50:0:1:10:0.9/3:10:0.9 -m 13:50:5000:1:10:0.9/3:10:0.9 -k -o masked-H2_C$x.fa H2_C$x.fa > positions-h2-$x.txt
+  done
+#
+# ------------------------------------------------------------------------------
+#