diff NGSrich_0.5.5/src/datastructures/Read.java @ 0:89ad0a9cca52 default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/NGSrich_0.5.5/src/datastructures/Read.java	Mon Nov 21 08:12:19 2011 -0500
@@ -0,0 +1,96 @@
+package datastructures;
+
+import java.io.File;
+import java.io.IOException;
+import java.lang.InterruptedException;
+import java.util.Scanner;
+import java.util.Vector;
+
+public class Read implements Comparable<Object> {
+
+	String query;
+	int flag;
+	String rname;
+	int pos;
+	int mapq;
+	String cigar;
+	String rnext;
+	int pnext;
+	int tlen;
+	String seq;
+	String qual;
+	Vector<String> optional;
+
+	public Read(String line) {
+		Scanner s = new Scanner(line);
+		query = s.next();
+		flag = s.nextInt();
+		rname = s.next();
+		pos = s.nextInt();
+		mapq = s.nextInt();
+		cigar = s.next();
+		rnext = s.next();
+		pnext = s.nextInt();
+		tlen = s.nextInt();
+		seq = s.next();
+		qual = s.next();
+		if (s.hasNext()) {
+			optional = new Vector<String>();
+			while (s.hasNext()) {
+				optional.add(s.next());
+			}
+		}
+	}
+
+	public String getRname() {
+		return rname;
+	}
+
+	public int getPos() {
+		return pos;
+	}
+
+	@Override
+	public int compareTo(Object o) {
+		return 0;
+	}
+
+	public static void sort(File input) {
+		Runtime rt = Runtime.getRuntime();
+		try {
+			String 	rawOutput = input.getAbsolutePath(), 
+					tmpD = input.getParentFile().getAbsolutePath(), 
+					outputName = input.getName(), 
+					pathname = 	input.getParentFile().getAbsolutePath() + "/" + 
+								outputName + "Sorted";
+			
+			input = new File(pathname);
+			
+			if (!input.exists())
+				input.createNewFile();
+
+			String command = "sort -k3,3 -k4n,4 -T " + tmpD + " " + rawOutput+" > "+pathname;
+			Process p = rt.exec(command);
+			try{p.waitFor();}
+			catch(InterruptedException e){e.printStackTrace();}
+			System.out.println("Fertig");
+			/*			Scanner ps = new Scanner(p.getInputStream());
+			FileWriter fw = new FileWriter(input);
+
+			while (ps.hasNextLine()) {
+				String nextLine = ps.nextLine();
+				fw.write(nextLine + "\r\n");
+			}
+
+			fw.close(); */
+
+			new File(rawOutput).delete();
+			new File(pathname).renameTo(new File(rawOutput));
+			System.out.println("File " + new File(rawOutput).getAbsolutePath()
+					+ " sorted\n");
+
+		} catch (IOException e1) {
+			e1.printStackTrace();
+		}
+	}
+}