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package pacbio;
import fileIO.ReadWrite;
import fileIO.TextFile;
import fileIO.TextStreamWriter;
import shared.Timer;
/**
* @author Brian Bushnell
* @date Jul 10, 2012
*
*/
public class PartitionFastaFile {
public static void main(String[] args){
Timer t=new Timer();
String infile=args[0];
String outfile=args[1];
assert(!infile.equalsIgnoreCase(outfile));
assert(outfile.contains("#"));
long partition=Integer.parseInt(args[2]);
if(args.length>4){maxDataOut=Long.parseLong(args[4]);}
if(ReadWrite.ZIPLEVEL<2){ReadWrite.ZIPLEVEL=2;}
TextFile tf=new TextFile(infile, false);
split(tf, outfile, partition);
t.stop();
System.out.println("Time:\t"+t);
}
public static void split(TextFile tf, String outfile, long partition) {
long currentBases=0;
int pnum=1;
TextStreamWriter tsw=new TextStreamWriter(outfile.replace("#", ""+pnum), true, false, false);
tsw.start();
String s;
for(s=tf.nextLine(); s!=null && dataOut<maxDataOut; s=tf.nextLine()){
if(s.charAt(0)=='>'){
if(currentBases>=partition){
System.out.println("Ended partition "+pnum+" at "+currentBases);
currentBases=0;
pnum++;
tsw.poison();
tsw=new TextStreamWriter(outfile.replace("#", ""+pnum), true, false, false);
tsw.start();
}
}else{
int x=s.length();
currentBases+=x;
dataOut+=x;
}
tsw.println(s);
}
System.out.println("Ended partition "+pnum+" at "+currentBases);
System.out.println("Total: "+dataOut);
System.out.println("Avg: "+(dataOut)/pnum);
// System.out.println("\n"+s+"\n"+dataOut+"\n"+maxDataOut);
try {
synchronized(tsw){
tsw.wait(100);
}
} catch (InterruptedException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
tsw.poison();
}
public static int MIN_CONTIG_TO_ADD=150; //Not currently used
public static long MAX_OUTPUT_LEN=200000000000L;
public static long maxDataOut=Long.MAX_VALUE;
private static long dataOut=0;
}
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