Executor executor = BashExecutor.getInstance(); commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc")); if (!commandOutput.getStdout().toString().contains("Total runtime")) { if (!commandOutput.getStdout().toString().contains("reads were filtered out")) {
Executor executor = BashExecutor.getInstance(); commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc")); if (!commandOutput.getStdout().toString().contains("Total runtime")) { if (!commandOutput.getStdout().toString().contains("reads were filtered out")) {
Executor executor = BashExecutor.getInstance(); commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc")); if (!commandOutput.getStdout().toString().contains("Total runtime")) { if (!commandOutput.getStdout().toString().contains("reads were filtered out")) {
Executor executor = BashExecutor.getInstance(); commandOutput = executor.execute(commandInput, new File(System.getProperty("user.home"), ".mapseqrc")); if (!commandOutput.getStdout().toString().contains("Total runtime")) { if (!commandOutput.getStdout().toString().contains("reads were filtered out")) {
BufferedReader stdout = new BufferedReader(new StringReader(commandOutput.getStdout().toString())); ArrayList<BufferedWriter> fileOutputs = new ArrayList<BufferedWriter>();
commandOutput = executor.execute(ci, mapseqrc); logger.info("commandOutput.getExitCode(): {}", commandOutput.getExitCode()); logger.debug("commandOutput.getStdout(): {}", commandOutput.getStdout()); } catch (ExecutorException e) { if (commandOutput != null) {
commandOutput = executor.execute(ci, mapseqrc); logger.info("commandOutput.getExitCode(): {}", commandOutput.getExitCode()); logger.debug("commandOutput.getStdout(): {}", commandOutput.getStdout()); } catch (ExecutorException e) { if (commandOutput != null) {
commandOutput = executor.execute(ci, mapseqrc); logger.info("commandOutput.getExitCode(): {}", commandOutput.getExitCode()); logger.debug("commandOutput.getStdout(): {}", commandOutput.getStdout()); } catch (ExecutorException e) { if (commandOutput != null) {
commandOutput = executor.execute(ci, mapseqrc); logger.info("commandOutput.getExitCode(): {}", commandOutput.getExitCode()); logger.debug("commandOutput.getStdout(): {}", commandOutput.getStdout()); } catch (ExecutorException e) { if (commandOutput != null) {