Mercurial > repos > zzhou > bamedit

diff bamedit.py @ 73:0d3c69699f0a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author zzhou
date Mon, 26 Nov 2012 15:03:15 -0500
parents ec59db4dc58e
children 500d54c2edf9
line wrap: on
line diff
--- a/bamedit.py	Mon Nov 26 15:00:07 2012 -0500
+++ b/bamedit.py	Mon Nov 26 15:03:15 2012 -0500
@@ -21,7 +21,7 @@
 		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'] )
-	cmdline = "bash %s %s %s %s" % ( shscript, options['bamout'], options['bamout2'], options['input1'] )
+	cmdline = "bash split.sh %s %s %s" % ( 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'] )
     elif (options['action'] == "filter"):