--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Bam.py	Wed Dec 21 12:13:04 2016 -0500
@@ -0,0 +1,81 @@
+#!/usr/bin/python
+# -*- coding: utf8 -*-
+
+"""
+Class to handle Bam files to UCSC TrackHub
+"""
+
+import logging
+import os
+import shutil
+
+from Datatype import Datatype
+from Track import Track
+from TrackDb import TrackDb
+from util import subtools
+
+
+class Bam( Datatype ):
+    def __init__(self, input_bam_false_path, data_bam):
+        super(Bam, self).__init__()
+
+        self.track = None
+
+        self.input_bam_false_path = input_bam_false_path
+
+        self.data_bam = data_bam
+        # TODO: Check if it already contains the .bam extension / Do a function in Datatype which check the extension
+        if ".bam" not in self.data_bam["name"]:
+            self.name_bam = self.data_bam["name"] + ".bam"
+        else:
+            self.name_bam = self.data_bam["name"]
+
+        self.priority = self.data_bam["order_index"]
+        self.index_bam = self.data_bam["index"]
+        # TODO: Think about how to avoid repetition of the color treatment
+        self.track_color = self.data_bam["track_color"]
+
+        # TODO: Think about how to avoid repetition of the group_name everywhere
+        self.group_name = self.data_bam["group_name"]
+
+        # First: Add the bam file
+        # Second: Add the bam index file, in the same folder (https://genome.ucsc.edu/goldenpath/help/bam.html)
+
+        bam_file_path = os.path.join(self.myTrackFolderPath, self.name_bam)
+        shutil.copyfile(self.input_bam_false_path, bam_file_path)
+
+        # Create and add the bam index file to the same folder
+        name_index_bam = self.name_bam + ".bai"
+        bam_index_file_path = os.path.join(self.myTrackFolderPath, name_index_bam)
+        shutil.copyfile(self.index_bam, bam_index_file_path)
+
+        # Create the Track Object
+        self.createTrack(file_path=self.name_bam,
+                         track_name=self.name_bam,
+                         long_label=self.name_bam, track_type='bam', visibility='pack', priority=self.priority,
+                         track_file=bam_index_file_path,
+                         track_color=self.track_color,
+                         group_name=self.group_name
+                         )
+        #
+        # dataURL = "tracks/%s" % self.name_bam
+        #
+        # trackDb = TrackDb(
+        #     trackName=self.name_bam,
+        #     longLabel=self.name_bam,
+        #     shortLabel=self.getShortName( self.name_bam ),
+        #     trackDataURL=dataURL,
+        #     trackType='bam',
+        #     visibility='pack',
+        #     priority=self.priority,
+        # )
+        #
+        # # Return the Bam Track Object
+        # self.track = Track(
+        #     trackFile=bam_index_file_path,
+        #     trackDb=trackDb,
+        # )
+
+        print("- Bam %s created" % self.name_bam)
+        #print("- %s created in %s" % (self.name_bam, bam_file_path))
+        #print("- %s created in %s" % (self.index_bam, bam_index_file_path))