--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Bam.py	Wed Jul 13 13:36:37 2016 -0400
@@ -0,0 +1,68 @@
+#!/usr/bin/python
+# -*- coding: utf8 -*-
+
+"""
+Class to handle Bam files to UCSC TrackHub
+"""
+
+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 ,
+                 inputFastaFile, extra_files_path, tool_directory ):
+        super(Bam, self).__init__( input_fasta_file=inputFastaFile,
+                                   extra_files_path=extra_files_path,
+                                   tool_directory=tool_directory,
+                                   )
+
+        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
+        self.name_bam = self.data_bam["name"] + ".bam"
+        self.priority = self.data_bam["order_index"]
+        self.index_bam = self.data_bam["index"]
+
+        print "Creating TrackHub BAM from (falsePath: %s; name: %s)" % ( self.input_bam_false_path, self.name_bam)
+
+        # 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
+        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("- %s created in %s" % (self.name_bam, bam_file_path))
+        print("- %s created in %s" % (self.index_bam, bam_index_file_path))