Merge pull request #91 from dufeiyu/docm_filter

Reset filter column with "." if no set_filter_flag
genome · Jun 17, 2019 · 99ca7ed · 99ca7ed
2 parents d787165 + 917a839
commit 99ca7ed
Showing 1 changed file with 7 additions and 3 deletions.
diff --git a/docm_filter.pl b/docm_filter.pl
@@ -59,14 +59,18 @@
         next unless $AD;
         my @AD = split /,/, $AD;
         shift @AD; #the first one is ref count
-        if ($set_filter_flag) {
-            $columns[6] = 'DOCM_ONLY';
-        }
+
         for my $ad (@AD) {
             if ($ad > 5 and $ad/$DP > 0.01) {
                 my ($normal_col, $tumor_col) = map{$columns[$_]}($normal_index, $tumor_index);
                 $columns[9]  = $normal_col;
                 $columns[10] = $tumor_col;
+                if ($set_filter_flag) {
+                    $columns[6] = 'DOCM_ONLY';
+                }
+                else {
+                    $columns[6] = '.';
+                }
                 my $new_line = join "\t", @columns;
                 say $docm_out_fh $new_line;
                 last;