removes deprecated tiddit option

Clinical-Genomics · Sep 6, 2022 · 89eb717 · 89eb717
1 parent 39e8da9
commit 89eb717
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Showing 3 changed files with 0 additions and 11 deletions.
diff --git a/lib/MIP/Program/Tiddit.pm b/lib/MIP/Program/Tiddit.pm
@@ -41,7 +41,6 @@ sub tiddit_coverage {
 ##          : $infile_path            => Infile path
 ##          : $outfile_path_prefix    => Outfile path prefix
 ##          : $output_wig             => Generate wig instead of bed
-##          : $skip_quality_track     => Skip quality track in output file
 ##          : $stderrfile_path        => Stderrfile path
 ##          : $stderrfile_path_append => Append stderr info to file path
 ##          : $stdoutfile_path        => Stdoutfile path
@@ -123,11 +122,6 @@ sub tiddit_coverage {
         push @commands, q{-w};
     }
 
-    if ($skip_quality_track) {
-
-        push @commands, q{-u};
-    }
-
     push @commands, q{--bam} . $SPACE . $infile_path;
 
     push @commands,

diff --git a/lib/MIP/Recipes/Analysis/Tiddit_coverage.pm b/lib/MIP/Recipes/Analysis/Tiddit_coverage.pm
@@ -209,7 +209,6 @@ sub analysis_tiddit_coverage {
             infile_path         => $infile_path,
             outfile_path_prefix => $outfile_path_prefix,
             output_wig          => 1,
-            skip_quality_track  => 1,
         }
     );
     say {$filehandle} $NEWLINE;

diff --git a/t/tiddit_coverage.t b/t/tiddit_coverage.t
@@ -91,10 +91,6 @@ my %specific_argument = (
         input           => 1,
         expected_output => q{-w},
     },
-    skip_quality_track => {
-        input           => 1,
-        expected_output => q{-u},
-    },
 );
 
 ## Coderef - enables generalized use of generate call