/**
* A method to set the output file name to a series of numbered files, using a pattern like:
*
* <p>fileName = String.format("%s_%03d.%s", fName, fNumber, ext);
*
* <p>When fName includes an extension, it is first removed and saved into ext.
*
* @param fName a file path + name (with or without an extension).
*/
private static void createOutputStream(String fName) throws Exception {
fName = FilenameUtils.normalize(fName);
String name = FilenameUtils.removeExtension(fName);
String ext = FilenameUtils.getExtension(fName);
if (oSerializeFormat.equals("turtle")) {
ext = "ttl";
} else if (oSerializeFormat.equals("Ntriples")) {
ext = "nt";
} else if (ext.equals("")) {
ext = "txt";
}
fName = String.format("%s_%03d.%s", name, ++oFileNumber, ext);
oFile = new File(fName);
try {
oStream.close();
oStream = new PrintStream(new FileOutputStream(oFile));
if (oSerializeFormat.equals("turtle")) {
oStream.println(SparqlPrefixes.ttlMappingPrefix());
oStream.println();
if (oFileNumber == 1) {
oStream.println(loomInfo.ttlSignature());
oStream.println();
}
}
} catch (Exception e) {
log.fatal("Cannot create output file stream: {}", oFile.getAbsolutePath());
throw e;
}
}
private static void readBowtieResults(
String fileName, HashMap<String, ArrayList<MappingInfo>> map) throws Exception {
BufferedReader bf = Utils.getFile(fileName, "bout");
if (bf != null) {
String line = null;
int counter = 0;
while ((line = bf.readLine()) != null) {
if (counter % 1000000 == 0) {
System.err.println("Read " + counter + " mapping records from " + fileName);
}
String[] splitLine = line.trim().split("\\s+");
MappingInfo m = new MappingInfo();
String contigID = splitLine[2];
Boolean isFwd = null;
if (splitLine[1].contains("-")) {
isFwd = false;
} else if (splitLine[1].contains("+")) {
isFwd = true;
}
m.readID = splitLine[0].replaceAll("/", "_");
m.start = 1;
m.end = SUB_LEN;
m.contigStart = Integer.parseInt(splitLine[3]);
if (isFwd) {
m.contigEnd = m.contigStart + splitLine[4].length() - 1;
} else {
m.contigEnd = m.contigStart;
m.contigStart = m.contigEnd + splitLine[4].length() - 1;
}
if (map.get(contigID) == null) {
map.put(contigID, new ArrayList<MappingInfo>(NUM_READS_PER_CTG));
}
map.get(contigID).add(m);
counter++;
}
bf.close();
}
}
