moved contamination detected from minor and consensus alleles out of …

…minor alleles output to consensus output
broadinstitute · Nov 14, 2023 · aa07864 · aa07864
1 parent c168a90
commit aa07864
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/bin/visualize_plate_map.R b/bin/visualize_plate_map.R
@@ -139,15 +139,15 @@ if(input_file_type != "isnvs")
 # subsets input file to display consensus-level potential contamination only
 if(input_file_type == "contamination_consensus")
 {
-  input_table <- subset(input_table, appearance_of_potential_contamination == "consensus-level")
+  input_table <- subset(input_table, appearance_of_potential_contamination == "consensus-level"
+                        | appearance_of_potential_contamination == "minor and consensus-level")
   input_file_type <- "contamination"
 }
 
 # subsets input file to display minor allele or minor-consensus mix potential contamination only
 if(input_file_type == "contamination_minor")
 {
-  input_table <- subset(input_table, appearance_of_potential_contamination == "minor alleles"
-                        | appearance_of_potential_contamination == "minor and consensus-level")
+  input_table <- subset(input_table, appearance_of_potential_contamination == "minor alleles")
   input_file_type <- "contamination"
 }