added --trackLabel and --key options to prepare-refseqs.pl

GMOD · Feb 7, 2013 · c5dc091 · c5dc091
1 parent 0115e09
commit c5dc091
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Showing 3 changed files with 19 additions and 3 deletions.
diff --git a/bin/prepare-refseqs.pl b/bin/prepare-refseqs.pl
@@ -74,6 +74,15 @@ =head1 OPTIONS
 of the new (more scalable) /seq/hash/hash/hash/$seqname-$chunk.txt
 structure.
 
+=item --trackLabel <label>
+
+The unique name of the sequence track, default 'DNA'.
+
+=item --key <string>
+
+The displayed name of the sequence track, defaults to the value of
+C<--trackLabel>.
+
 =back
 
 =head1 AUTHOR

diff --git a/release-notes.txt b/release-notes.txt
@@ -1,5 +1,9 @@
 {{$NEXT}}
 
+ * Added support for `--trackLabel` and `--key` options to
+   `prepare-refseqs.pl`, allowing users to specify the sequence
+   track's label and title.
+
 1.8.0     2013-01-31 14:05:27 America/New_York
 
  * Added new "File -> Open" function that can display BAM, BigWig, and

diff --git a/src/perl5/Bio/JBrowse/Cmd/FormatSequences.pm b/src/perl5/Bio/JBrowse/Cmd/FormatSequences.pm
@@ -24,7 +24,8 @@ use FastaDatabase;
 
 sub option_defaults {(
     out => 'data',
-    chunksize => 20_000
+    chunksize => 20_000,
+    trackLabel => 'DNA'
 )}
 
 sub option_definitions {(
@@ -37,6 +38,8 @@ sub option_definitions {(
     "refs=s",
     "refids=s",
     "compress",
+    "trackLabel=s",
+    "key=s",
     "help|h|?",
     "nohash"
 )}
@@ -246,7 +249,7 @@ sub writeTrackEntry {
 
     my $compress = $self->opt('compress');
 
-    my $seqTrackName = "DNA";
+    my $seqTrackName = $self->opt('trackLabel');
     unless( $self->opt('noseq') ) {
         $self->{storage}->modify( 'trackList.json',
                                        sub {
@@ -268,7 +271,7 @@ sub writeTrackEntry {
                                            $tracks->[$i] =
                                        {
                                            'label' => $seqTrackName,
-                                           'key' => $seqTrackName,
+                                           'key' => $self->opt('key') || $seqTrackName,
                                            'type' => "SequenceTrack",
                                            'chunkSize' => $self->{chunkSize},
                                            'urlTemplate' => $self->seqUrlTemplate,