def run(self, command, options, pipe=False, get_stdout=False, memscale=None):
        """Run a Picard command with the provided option pairs.
        """
        cl = self.cl_picard(command, options, memscale=memscale)
        if pipe:
            subprocess.Popen(cl)
        elif get_stdout:
            p = subprocess.Popen(cl, stdout=subprocess.PIPE)
            stdout = p.stdout.read()
            p.wait()
            p.stdout.close()
            return stdout
        else:
            do.run(cl, "Picard {0}".format(command), None)
def run ( self , command , options , pipe = False , get_stdout = False , memscale = None ) : cl = self . cl_picard ( command , options , memscale = memscale ) if pipe : subprocess . Popen ( cl ) elif get_stdout : p = subprocess . Popen ( cl , stdout = subprocess . PIPE ) stdout = p . stdout . read ( ) p . wait ( ) p . stdout . close ( ) return stdout else : do . run ( cl , "Picard {0}" . format ( command ) , None )
Run a Picard command with the provided option pairs.