added --tracks option to generate-names.pl, updated release notes

bin/generate-names.pl

@@ -19,6 +19,11 @@ =head1 OPTIONS
 
 Data directory to process.  Default 'data/'.
 
+=item --tracks <trackname>[,...]
+
+Comma-separated list of which tracks to include in the names index.  If
+not passed, all tracks are indexed.
+
 =item --thresh <threshold>
 
 Optional LazyPatricia chunking threshold.  Default 200.  See
@@ -59,6 +64,7 @@ =head1 OPTIONS
 $Data::Dumper::Indent = 1;
 
 my %trackHash;
+my @includedTrackNames;
 my @tracksWithNames;
 
 my $outDir = "data";
@@ -68,8 +74,11 @@ =head1 OPTIONS
 GetOptions("dir|out=s" => \$outDir,
            "thresh=i" => \$thresh,
            "verbose+" => \$verbose,
+           'tracks=s' => \@includedTrackNames,
            "help|h|?" => \$help) or pod2usage();
 
+my %includedTrackNames = map { $_ => 1 } @includedTrackNames;
+
 pod2usage( -verbose => 2 ) if $help;
 
 unless (-d $outDir) {
@@ -86,7 +95,8 @@ =head1 OPTIONS
 mkdir($nameDir) unless (-d $nameDir);
 
 my @refSeqs  = @{ $gdb->refSeqs   };
-my @tracks   = @{ $gdb->trackList };
+my @tracks   = grep { !%includedTrackNames || $includedTrackNames{ $_->{label} } }
+               @{ $gdb->trackList };
 
 # open the root file; we lock this file while we're
 # reading the name lists, deleting all the old lazy-*

release-notes.txt

@@ -1,5 +1,11 @@
 {{$NEXT}}
 
+ * Added a `--tracks` option to `generate-names.pl` that allows users
+   to manually specify which tracks will be indexed to enable
+   autocompletion and searching for their feature names in the JBrowse
+   location box.  Thanks to Steffi Geisen for her ongoing help in
+   enhancing the scalability of name indexing.
+
  * Fixed off-by-one error in Wiggle track display code: wiggle data
    was incorrectly displayed shifted one base to the left of its
    proper position.  Thanks to Steffi Geisen for noticing this.

tests/perl_tests/generate-names.pl.t

@@ -16,4 +16,11 @@ system $^X, 'bin/generate-names.pl', (
     );
 ok( ! $?, 'generate-names.pl also ran ok on volvox test data' );
 
+
+system $^X, 'bin/generate-names.pl', (
+    '--out'   => "$tempdir",
+    '--tracks' => 'ExampleFeatures,NameTest'
+    );
+ok( ! $?, 'generate-names.pl also ran ok with the --tracks option' );
+
 done_testing;