@Override
public void performOperation() throws OperationFailedException {
if (verbose) {
System.out.println("TestOperator is performing operation");
}
inputFile = inputBuffers.get(0).getFile();
try {
BufferedReader reader = new BufferedReader(new FileReader(inputFile));
FileBuffer output = outputBuffers.get(0);
String line = reader.readLine();
BufferedWriter writer = new BufferedWriter(new FileWriter(output.getFile()));
writer.write("Top of the new output buffer!\n");
int count = 0;
while (line != null) {
System.out.println("Read this line from input file : " + line);
writer.write(count + "\t " + line + "\n");
count++;
line = reader.readLine();
}
reader.close();
writer.close();
} catch (FileNotFoundException e) {
throw new OperationFailedException(e.getCause() + "\t" + e.getMessage(), this);
} catch (IOException e) {
throw new OperationFailedException(e.getCause() + "\t" + e.getMessage(), this);
}
}
@Override
protected String[] getCommand(FileBuffer inputBuffer) throws OperationFailedException {
if (cutAdaptPath == null) {
cutAdaptPath = this.getPipelineProperty(CUTADAPT_PATH);
if (cutAdaptPath == null)
throw new OperationFailedException("No path to cutadapt found", this);
}
if (!(inputBuffer instanceof FastQFile)) {
return null;
}
if (adapterString == null) {
try {
FileBuffer adapterBuf = this.getInputBufferForClass(TextBuffer.class);
if (adapterBuf == null)
throw new OperationFailedException(
"No adapter file specified, cannot cut adapters", this);
BufferedReader reader = new BufferedReader(new FileReader(adapterBuf.getFile()));
StringBuffer adapterStr = new StringBuffer();
String line = reader.readLine();
while (line != null) {
adapterStr.append(" -a " + line.trim());
line = reader.readLine();
}
reader.close();
adapterString = adapterStr.toString();
} catch (IOException ex) {
throw new OperationFailedException(
"Error reading adapter sequences : " + ex.getMessage(), this);
}
}
String outputFilename = "adaptercut-" + inputBuffer.getFilename();
FastQFile outputFile = new FastQFile(new File(getProjectHome() + outputFilename));
super.addOutputFile(outputFile);
String command =
cutAdaptPath
+ adapterString
+ " -o "
+ outputFile.getAbsolutePath()
+ " "
+ inputBuffer.getAbsolutePath();
return new String[] {command};
}