Removing the -C parameter in BUILD

The jellyfish option to use -C parameter (canonical counts) is de-activated, because it caused skewed counting results when the KINDEX is applied on assembled data.
tschmutzer · Jun 5, 2019 · be42c21 · be42c21
1 parent 3a25e2a
commit be42c21
Showing 1 changed file with 5 additions and 4 deletions.
diff --git a/lib/kmasker/kmasker_build.pm b/lib/kmasker/kmasker_build.pm
@@ -94,9 +94,10 @@ sub build_kindex_jelly{
 	}
 
 	#BUILD JELLY index	
-	if($seq_type eq "reads"){
-		$setting .= " -C"
-	}
+	#if($seq_type eq "reads"){
+	#	$setting .= " -C"
+	#}
+
 	print "\n ... start construction of kindex with the following parameters ".$setting." \n";
 	my $FILE_jelly = "KINDEX_".$HASH_info{"kindex name"}.".jf";
 
@@ -731,4 +732,4 @@ sub promptUser {
 
 
 
-1;
+1;