diff bamedit.py @ 53:19dfa6847218 draft

Uploaded

--- a/bamedit.py	Mon Nov 26 13:59:12 2012 -0500
+++ b/bamedit.py	Mon Nov 26 14:01:06 2012 -0500
@@ -11,14 +11,14 @@
 CHUNK_SIZE = 1024
 
 def main():
-   options = simplejson.load( open( sys.argv[1] ) )
+    options = simplejson.load( open( sys.argv[1] ) )
 
 
-   shscript = "%s/split.sh" % os.environ.get('SCRIPT_PATH')
-   print shscript
-   testing = sys.argv[2]
-   print testing
-   if(options['action'] == "merge"):
+    shscript = "%s/split.sh" % os.environ.get('SCRIPT_PATH')
+    print shscript
+    testing = sys.argv[2]
+    print testing
+    if(options['action'] == "merge"):
 	cmdline = "samtools merge  %s %s %s" % ( options['bamout'], options['input1'], options['input2'] )
 	if('input3' in options):
 		cmdline = "samtools merge  %s %s %s %s" % ( options['bamout'], options['input1'], options['input2'], options['input3'] )