+
−#!/usr/bin/env python
+
−import os
+
−import json
+
−import logging
+
−
+
−from TrackDb import TrackDb
+
−from util import subtools
+
−from util import santitizer
+
−
+
−
+
−class BamFeatures(TrackDb):
+
−    def __init__(self, trackName, trackLabel, trackDataURL, trackType, dataType, extraSettings=None):
+
−        super(BamFeatures, self).__init__(trackName, trackLabel, trackDataURL, trackType, dataType, extraSettings)
+
− 
+
−    def prepareExtraSetting(self):
+
−        if 'category' not in self.extraSettings or not self.extraSettings['category']:
+
−            self.extraSettings['category'] = "Default group"
+
−        bam_track = dict()
+
−        bam_track['type'] = 'JBrowse/View/Track/Alignments2'
+
−        bam_track['storeClass'] = 'JBrowse/Store/SeqFeature/BAM'
+
−        bam_track['urlTemplate'] = os.path.join('bbi', self.trackName)
+
−        bam_track['baiUrlTemplate'] = os.path.join('bbi', self.extraSettings['index'])
+
−        bam_track['label'] = self.trackLabel
+
−        bam_track['category'] = self.extraSettings['category']
+
−        #extraConfigs = json.dumps(bam_track)
+
−        extraConfigs = bam_track
+
−        return extraConfigs
+
−
+
−