feat(rna_mt): enables mt for rna

Clinical-Genomics · Apr 29, 2021 · a982aea · a982aea
1 parent 5fedd16
commit a982aea
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Showing 2 changed files with 13 additions and 2 deletions.
diff --git a/lib/MIP/Contigs.pm b/lib/MIP/Contigs.pm
@@ -201,7 +201,8 @@ sub delete_non_wes_contig {
     use MIP::List qw{ check_allowed_array_values };
     use MIP::Contigs qw{ delete_contig_elements };
 
-    return @{$contigs_ref} if ( $consensus_analysis_type eq q{wgs} );
+    return @{$contigs_ref}
+      if ( $consensus_analysis_type eq q{wgs} || $consensus_analysis_type eq q{wts} );
 
     ## Removes contig M | chrMT from contigs
     my @contigs = delete_contig_elements(

diff --git a/t/delete_non_wes_contig.t b/t/delete_non_wes_contig.t
@@ -91,6 +91,16 @@ my @has_wes_contigs = delete_non_wes_contig(
 my @expected_wes_contigs = qw{ 1 2 3 4 MT };
 
 ## Then keep the non wes contigs
-is_deeply( \@has_wes_contigs, \@expected_wes_contigs, q{Keept non wes contigs} );
+is_deeply( \@has_wes_contigs, \@expected_wes_contigs, q{Keept non wes contigs for wgs} );
 
+## Given contigs, when a wts consensus type of run
+@has_wes_contigs = delete_non_wes_contig(
+    {
+        consensus_analysis_type => q{wts},
+        contigs_ref             => \@contigs,
+    }
+);
+
+## Then keep the non wes contigs
+is_deeply( \@has_wes_contigs, \@expected_wes_contigs, q{Keept non wes contigs for wts} );
 done_testing();