skip lc for empty check. comment why hash lookup is separate

bystrogenomics · Aug 7, 2018 · 7883b7f · 7883b7f
1 parent a7d3aa2
commit 7883b7f
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Showing 2 changed files with 10 additions and 3 deletions.
diff --git a/lib/Seq/Tracks/Build.pm b/lib/Seq/Tracks/Build.pm
@@ -457,14 +457,21 @@ sub _stripAndCoerceUndef {
   # This modifies the caller's version
   StripLTSpace($_[1]);
 
+  if($_[1] eq '') {
+    $_[1] = undef;
+    return $_[1];
+  }
+
   my $v = lc($_[1]);
 
-  # These always get coerced to undef
-  if($v eq '' || $v eq '.' || $v eq 'na' || $v eq $_[0]->{_missChar}){
+  # These will always get coerced to undef
+  # TODO: we may want to force only the missChar comparison
+  if($v eq '.' || $v eq 'na' || $v eq $_[0]->{_missChar}){
     $_[1] = undef;
     return $_[1];
   }
 
+  # This will be configurable
   if(exists $cl->{$v}) {
     $_[1] = undef;
     return $_[1];

diff --git a/t/utils/filterCadd.yml b/t/utils/filterCadd.yml
@@ -22,7 +22,7 @@ tracks:
     - chr22
     - chr1
     - chr2
-    filterCadd_completed: 2018-08-07T21:24:00
+    filterCadd_completed: 2018-08-07T21:28:00
     filterCadd_date: 2017-09-12T19:18:00
     local_files:
     - test.filterCadd.cadd.chr22.chr22.filtered.txt