added code to pass test for setting custom type via commandline in fl…

…atfile-to-json.pl
Arabidopsis-Information-Portal · Jul 16, 2013 · ec94f45 · ec94f45
1 parent 30581f2
commit ec94f45
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Showing 2 changed files with 4 additions and 1 deletion.
diff --git a/src/perl5/Bio/JBrowse/Cmd/FlatFileToJson.pm b/src/perl5/Bio/JBrowse/Cmd/FlatFileToJson.pm
@@ -35,6 +35,7 @@ sub option_definitions {
         "bam=s",
         "out=s",
         "trackLabel=s",
+        "trackType=s",
         "key=s",
         "cssClass|className=s",
         "autocomplete=s",
@@ -89,6 +90,7 @@ sub run {
 
     my %config = (
         type         => $self->opt('getType') || $self->opt('type') ? 1 : 0,
+        csstype      => $self->{'opt'}->{'trackType'},
         phase        => $self->opt('getPhase'),
         subfeatures  => $self->opt('getSubs'),
         style          => {

diff --git a/src/perl5/GenomeDB.pm b/src/perl5/GenomeDB.pm
@@ -104,8 +104,9 @@ sub writeTrackEntry {
                                      %{ $track->config || {} },
                                      label => $track->label,
                                      key => $track->key,
-                                     type => $track->type,
+                                     type => $track->{'config'}->{'csstype'} || $track->type,
                                     };
+
         return $trackData;
     };