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@@ -114,10 +114,9 @@ function tripal_jbrowse_mgmt_cmd_add_track($track) {
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case 'Alignment':
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case 'Alignment':
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$json = tripal_jbrowse_mgmt_get_json($instance);
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$json = tripal_jbrowse_mgmt_get_json($instance);
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$directory = 'bam';
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$directory = 'bam';
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- $file_name = $track->file;
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if (is_dir($track->file)) {
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if (is_dir($track->file)) {
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- $file_name = glob($track->file . '/' . '*.bam')[0];
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- if (!$file_name) { $file_name = glob($track->file . '/' . '*.cram')[0]; }
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+ $file_name = glob($track->file . '/' . '*.[bam][cram]')[0];
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+ $index_file_name = glob($track->file . '/' . '*.[bai][csi][crai]')[0];
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}
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}
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$track_in_json = [
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$track_in_json = [
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@@ -126,7 +125,16 @@ function tripal_jbrowse_mgmt_cmd_add_track($track) {
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'urlTemplate' => $directory . '/' . pathinfo($file_name)['basename'],
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'urlTemplate' => $directory . '/' . pathinfo($file_name)['basename'],
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'type' => 'JBrowse/View/Track/Alignments2',
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'type' => 'JBrowse/View/Track/Alignments2',
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];
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];
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-
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+ $index_path_info = pathinfo($index_file_name);
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+ switch($index_path_info['extension']){
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+ case "bai":
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+ $track_in_json['baiUrlTemplate'] = $directory . '/' . $index_path_info['basename'];
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+ break;
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+
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+ case "csi":
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+ $track_in_json['csiUrlTemplate'] = $directory . '/' . $index_path_info['basename'];
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+ break;
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+ }
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$extension = pathinfo($file_name)['extension'];
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$extension = pathinfo($file_name)['extension'];
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switch($extension){
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switch($extension){
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case 'bam':
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case 'bam':
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