@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};
}
protected void parseOptions() {
FileBuffer inputBEDfb = this.getInputBufferForClass(BEDFile.class);
if (inputBEDfb != null) {
inputBED = (BEDFile) inputBEDfb;
bedFileOpt = " -t " + inputBED.getAbsolutePath();
} else {
bedFileOpt = "";
}
List<FileBuffer> inputBAMBuffers = this.getAllInputBuffersForClass(BAMFile.class);
for (FileBuffer bamBuffer : inputBAMBuffers) {
inputBAMs = inputBAMs + " -b " + bamBuffer.getAbsolutePath();
}
if (extraOptions == null || extraOptions.equals("null")) {
extraOptions = "";
}
inputBuffers = this.getAllInputBuffersForClass(BAMFile.class);
refBuf = (ReferenceFile) this.getInputBufferForClass(ReferenceFile.class);
outputVCF = (VCFFile) this.getOutputBufferForClass(VCFFile.class);
}