|
@@ -111,6 +111,34 @@ function tripal_jbrowse_mgmt_cmd_add_track($track) {
|
|
tripal_jbrowse_mgmt_save_json($instance, $json);
|
|
tripal_jbrowse_mgmt_save_json($instance, $json);
|
|
break;
|
|
break;
|
|
|
|
|
|
|
|
+ case 'Alignment':
|
|
|
|
+ $json = tripal_jbrowse_mgmt_get_json($instance);
|
|
|
|
+ $directory = 'bam';
|
|
|
|
+ $file_name = $track->file;
|
|
|
|
+ if (is_dir($track->file)) {
|
|
|
|
+ $file_name = glob($track->file . '/' . '*.[bam][cram]')[0];
|
|
|
|
+ }
|
|
|
|
+ $file_name = pathinfo($file_name)['basename'];
|
|
|
|
+
|
|
|
|
+ $track_in_json = [
|
|
|
|
+ 'label' => tripal_jbrowse_mgmt_make_slug($track->label),
|
|
|
|
+ 'key' => $track->label,
|
|
|
|
+ 'urlTemplate' => $directory . '/' . $file_name,
|
|
|
|
+ 'type' => 'JBrowse/View/Track/Alignment2',
|
|
|
|
+ ];
|
|
|
|
+
|
|
|
|
+ $extension = pathinfo($file_name)['extension'];
|
|
|
|
+ switch($extension){
|
|
|
|
+ case 'bam':
|
|
|
|
+ $track_in_json['storeClass'] = 'JBrowse/Store/SeqFeature/BAM';
|
|
|
|
+ break;
|
|
|
|
+ case 'cram':
|
|
|
|
+ $track_in_json['storeClass'] = 'JBrowse/Store/SeqFeature/CRAM';
|
|
|
|
+ break;
|
|
|
|
+ }
|
|
|
|
+ tripal_jbrowse_mgmt_save_json($instance, $json);
|
|
|
|
+ break;
|
|
|
|
+
|
|
case 'XYPlot':
|
|
case 'XYPlot':
|
|
$json = tripal_jbrowse_mgmt_get_json($instance);
|
|
$json = tripal_jbrowse_mgmt_get_json($instance);
|
|
$basename = pathinfo($track->file)['basename'];
|
|
$basename = pathinfo($track->file)['basename'];
|