public void run ( String [ ] args ) { LOG . info ( "Starting GA4GHPicardRunner" ) ; try { parseCmdLine ( args ) ; buildPicardCommand ( ) ; startProcess ( ) ; pumpInputData ( ) ; waitForProcessEnd ( ) ; } catch ( Exception e ) { System . out . println ( e . getMessage ( ) ) ; e . printStackTrace ( ) ; } }
Sets up required streams and pipes and then spawns the Picard tool