public StyledHTMLEditorPane() {
this.setContentType("text/html");
this.document = (HTMLDocument) this.getDocument();
this.setDocument(document);
Constants.loadSimpleStyle(document.getStyleSheet());
}
public static void main(String[] args) throws Exception {
if (args.length != 2) {
System.err.println("USAGE: java -jar SAMSort.jar <BWA PAIRED SAM file> <configFile>");
} else {
System.err.println("Running: java -jar SAMSort.jar " + args[0] + " " + args[1]);
// args[1]: conf file
Constants.loadConstants(args[1], false);
StringBuffer headers = new StringBuffer();
ArrayList<SAM> list = new ArrayList<SAM>();
BufferedReader br = new BufferedReader(new FileReader(args[0]));
int i = 0;
int count = 0;
String curline = null;
String curline2 = null;
SAM s1 = null;
SAM s2 = null;
boolean done = false;
// int cordantCount = 0;
// int discordantCount = 0;
int totalPairCount = 0;
int discordantPairCount = 0;
int singleEndMappedPairCount = 0;
int unmappedPairCount = 0;
BufferedWriter unmapped_bw = null;
BufferedWriter se_bw = null;
while (!done) {
curline = br.readLine();
if (curline == null) break;
else if (!curline.startsWith("@")) {
s1 = new SAM(curline);
// skip secondary. Load until primary
while (s1.isSecondary()) {
curline = br.readLine();
if (curline == null) {
done = true;
break;
}
s1 = new SAM(curline);
}
if (done) break;
curline2 = br.readLine();
s2 = new SAM(curline2);
// skip secondary. Load until primary
while (s2.isSecondary()) {
curline = br.readLine();
if (curline == null) {
done = true;
break;
}
s2 = new SAM(curline);
}
if (done) break;
totalPairCount++;
// only collect discordant
SAMPair tmppair = new SAMPair(s1, s2);
if (tmppair.isDiscordant()) {
discordantPairCount++;
list.add(s1);
list.add(s2);
s1 = null;
s2 = null;
if (list.size() == 200000) {
Collections.sort(list);
BufferedWriter bw = new BufferedWriter(new FileWriter(args[0] + ".part_" + i));
for (SAM s : list) {
bw.write(s.getSamline() + "\n");
}
bw.close();
bw = null;
i++;
list = new ArrayList<SAM>();
}
} else if (!tmppair.isBothUnmapped()) { // single-end mapped
if (se_bw == null) {
se_bw = new BufferedWriter(new FileWriter(args[0] + ".singleEndMapped"));
se_bw.write(headers.toString());
}
singleEndMappedPairCount++;
se_bw.write(s1.getSamline() + "\n");
se_bw.write(s2.getSamline() + "\n");
s1 = null;
s2 = null;
} else { // both unmapped
if (unmapped_bw == null) {
unmapped_bw = new BufferedWriter(new FileWriter(args[0] + ".unmapped"));
unmapped_bw.write(headers.toString());
}
unmappedPairCount++;
unmapped_bw.write(s1.getSamline() + "\n");
unmapped_bw.write(s2.getSamline() + "\n");
s1 = null;
s2 = null;
}
} else {
headers.append(curline + "\n");
}
}
br.close();
br = null;
if (se_bw != null) se_bw.close();
if (unmapped_bw != null) unmapped_bw.close();
if (list.size() > 0) {
Collections.sort(list);
BufferedWriter bw = new BufferedWriter(new FileWriter(args[0] + ".part_" + i));
// System.err.println(count + "\t" + set.size());
for (SAM s : list) {
bw.write(s.getSamline() + "\n");
}
bw.close();
bw = null;
i++;
list = null;
}
Map<SAM, Queue<SAM>> map = new TreeMap<SAM, Queue<SAM>>();
// Set<SAM> set = new TreeSet<SAM>();
// System.err.println("openning " + i + " files");
BufferedReader[] brArr = new BufferedReader[i];
for (int j = 0; j < i; j++) {
brArr[j] = new BufferedReader(new FileReader(args[0] + ".part_" + j));
String tmpline = brArr[j].readLine();
SAM tmp = new SAM(tmpline, j);
if (!map.containsKey(tmp)) map.put(tmp, new LinkedList<SAM>());
else {
// System.err.println("here");
map.get(tmp).add(tmp); // brArr[j].pushBack(tmpline);
}
// System.err.println(map.get(tmp).size());
}
// System.err.println(map.size());
BufferedWriter bw = new BufferedWriter(new FileWriter(args[0] + ".discordant.midsorted"));
bw.write(headers.toString());
SAM s = null;
// int counter = 0;
Queue<SAM> q = null;
while (!map.isEmpty()) {
s = map.keySet().iterator().next();
q = map.get(s);
// map.remove(s);
bw.write(s.getSamline());
bw.write("\n");
if (q.size() == 0) {
map.remove(s);
int tmpIndex = s.getIndex();
String tmpline = brArr[tmpIndex].readLine();
if (tmpline != null) {
s = new SAM(tmpline, tmpIndex);
if (!map.containsKey(s)) {
// System.err.print("put b4: " + map.size());
map.put(s, new LinkedList<SAM>());
// System.err.println("\ta4: " + map.size());
} else {
// System.err.print("here2: ");
map.get(s).add(s);
// System.err.println(map.size());
}
} // else{
// System.err.println("reader[" + tmpIndex + "] : NULL");
// }
} else {
// System.err.print("B4 Q size: " + q.size() + " map size: " + map.size() );
map.remove(s);
map.put(q.remove(), q);
// System.err.println("\tA4 Q size: " + q.size() + " map size: " + map.size() );
int tmpIndex = s.getIndex();
String tmpline = brArr[tmpIndex].readLine();
if (tmpline != null) {
s = new SAM(tmpline, tmpIndex);
if (!map.containsKey(s)) {
// System.err.print("put b4: " + map.size());
map.put(s, new LinkedList<SAM>());
// System.err.println("\ta4: " + map.size());
} else {
// System.err.print("here2: ");
map.get(s).add(s);
// System.err.println(map.size());
}
} // else{
// System.err.println("reader[" + tmpIndex + "] : NULL");
// }
}
// counter++;
}
// System.err.println(counter);
bw.close();
for (int j = 0; j < brArr.length; j++) {
brArr[j].close();
new File(args[0] + ".part_" + j).delete();
}
// int totalPairCount = 0;
// int discordantPairCount = 0;
System.out.println("------ DONE WITH REMOVAL OF CONCORDANT & UNMAPPED PAIRS ---------");
System.out.println("------ Processed a total of\t" + totalPairCount + " read-pairs");
System.out.println(
"------ Retained a total of\t"
+ discordantPairCount
+ " read-pairs writtend out to "
+ args[0]
+ ".discordant.midsorted");
System.out.println(
"------ Single-end mapped :\t"
+ singleEndMappedPairCount
+ " read-pairs written out to "
+ args[0]
+ ".singleEndMapped");
System.out.println(
"------ Unmapped (both ends) : \t"
+ unmappedPairCount
+ " read-pairs written out to "
+ args[0]
+ ".unmapped");
}
}
