# HG changeset patch
# User zzhou
# Date 1353956214 18000
# Node ID 0e5d77e4d9bf50732d26b75ef6d397ee4e96887e
# Parent  d913c7afea82c6fb296546947b169f906b1755ff
Uploaded

diff -r d913c7afea82 -r 0e5d77e4d9bf bamedit.py
--- a/bamedit.py	Mon Nov 26 13:56:48 2012 -0500
+++ b/bamedit.py	Mon Nov 26 13:56:54 2012 -0500
@@ -11,23 +11,20 @@
 CHUNK_SIZE = 1024
 
 def main():
-    options = simplejson.load( open( sys.argv[1] ) )
+   options = simplejson.load( open( sys.argv[1] ) )
 
-    asdf = options['asdf']
-    print "asdf %s" % asdf
 
-    shscript = sys.argv[2]
-    print shscript
-
-    test1 = sys.argv[3]
-
-    plscript = "%s/pileup.pl" % os.environ.get('SCRIPT_PATH')
-    if(options['action'] == "merge"):
+   shscript = "%s/pileup.pl" % os.environ.get('SCRIPT_PATH')
+   plscript = "%s/pileup.pl" % os.environ.get('SCRIPT_PATH')
+   print plscript 
+   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'] )
     elif (options['action'] == "split"):
 	#cmdline = "bash /mnt/galaxyTools/galaxy-central/tools/modENCODE_DCC/bamedit/split.sh %s %s %s" % ( options['bamout'], options['bamout2'], options['input1'] )
+        asdf = options['asdf']
+        print asdf
 	cmdline = "bash %s %s %s %s" % ( shscript, options['bamout'], options['bamout2'], options['input1'] )
     elif (options['action'] == "pileup"):
 	#cmdline = "perl /mnt/galaxyTools/galaxy-central/tools/modENCODE_DCC/bamedit/pileup.pl %s %s %s %s %s" % ( options['input1'], options['input2'], options['bamout'], options['bamname'], options['refname'] )