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package driver;
import java.util.ArrayList;
import java.util.LinkedHashMap;
import fileIO.TextFile;
import fileIO.TextStreamWriter;
import jgi.CovStatsLine;
/**
* @author Brian Bushnell
* @date Oct 13, 2014
*
*/
public class MergeCoverageOTU {
public static void main(String[] args){
String a=args[0];
String b=args[1];
String in=null, out=null;
if(a.toLowerCase().startsWith("in=")){
in=a.split("=")[1];
out=b.split("=")[1];
}else if(a.toLowerCase().startsWith("out=")){
in=b.split("=")[1];
out=a.split("=")[1];
}else{
in=a;
out=b;
}
TextFile tf=new TextFile(in);
LinkedHashMap<String, CovStatsLine> map=new LinkedHashMap<String, CovStatsLine>();
int count=0;
ArrayList<String> headers=new ArrayList<String>();
for(String s=tf.nextLine(); s!=null; s=tf.nextLine()){
if(count==0){
assert(s.startsWith("#")) : "Expected a header line starting with #";
CovStatsLine.initializeHeader(s);
}else{
int space=s.indexOf(' ');
String otu=s.substring(space+1, s.indexOf('\t'));
CovStatsLine csl=new CovStatsLine(s);
CovStatsLine old=map.get(otu);
if(old==null){
map.put(otu, csl);
}else{
old.add(csl);
}
}
count++;
}
tf.close();
TextStreamWriter tsw=new TextStreamWriter(out, true, false, false);
tsw.start();
for(String s : headers){tsw.println(s);}
for(String s : map.keySet()){
CovStatsLine csl=map.get(s);
csl.id=s;
tsw.println(csl.toString());
}
tsw.poisonAndWait();
}
}
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