improve help with latest changes

duartemolha · May 23, 2019 · 7f298dc · 7f298dc
1 parent 7e8b928
commit 7f298dc
Showing 1 changed file with 3 additions and 0 deletions.
diff --git a/CoNVaDING.pl b/CoNVaDING.pl
@@ -2961,6 +2961,7 @@ sub usage {
 \t\t\t\t[-regionThreshold, -ratioCutOffLow, -ratioCutOffHigh, -zScoreCutOffLow, -zScoreCutOffHigh, -sampleRatioScore]
 \t\t\t\t[-percentageLessReliableTargets]
 \t\t\t\t[-mosdepth-fast-mode or -fastmode] negatable with [-nomosdepth-fast-mode]
+\t\t\t\t[-mosdepth-median]
 \t\t\t\t[-samtools-depth]
 
 \t\t\tPipelineFromCounts :
@@ -2984,6 +2985,7 @@ sub usage {
 \t\t\t\tOPTIONAL:
 \t\t\t\t[-rmDup ]
 \t\t\t\t[-mosdepth-fast-mode or -fastmode] negatable with [-nomosdepth-fast-mode]
+\t\t\t\t[-mosdepth-median]
 \t\t\t\t[-samtools-depth]
 
 \t\t\tStartWithBam :
@@ -2994,6 +2996,7 @@ sub usage {
 \t\t\t\tOPTIONAL:
 \t\t\t\t[-rmDup, -useSampleAsControl, -ampliconcov]
 \t\t\t\t[-mosdepth-fast-mode or -fastmode] negatable with [-nomosdepth-fast-mode]
+\t\t\t\t[-mosdepth-median]
 \t\t\t\t[-samtools-depth]
 
 \t\t\tStartWithAvgCount :