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package align2;
import java.util.ArrayList;
import fileIO.TextFile;
public class ReformatBatchOutput2 {
// Elapsed: 31.7
//
// Mapping Statistics for 0s_default.sam:
// mapped: 100.00%
// retained: 96.06%
// discarded: 0.00%
// ambiguous: 3.94%
//
// Strict correctness (both ends exactly correct):
// true positive: 96.06%
// false positive: 0.00%
//
// Loose correctness (one end approximately correct):
// true positive: 96.06%
// false positive: 0.00%
//
// false negative: 0.00%
// Elapsed: 2.34
// Elapsed: 20.51
public static void main(String[] args){
TextFile tf=new TextFile(args[0], false);
String[] lines=tf.toStringLines();
ArrayList<String> list=new ArrayList<String>();
int mode=0;
System.out.println(header());
for(String s : lines){
if(s.startsWith("Elapsed:")){mode++;}
if(mode>1){
mode=0;
}else{
// list.add(s);
if(s.startsWith("Mapping Statistics for ")){
System.out.println(s.replace("Mapping Statistics for ", "").replace(".sam:", "")+"\t");
}else if(s.startsWith("Mapping:")){
s=s.replace("Mapping:", "").replace("seconds.", "").trim();
System.out.print(s+"\t");
}
}
}
}
public static String header() {
return("name\tcount\ttime\tmapTime\tmapped\tretained\tdiscarded\tambiguous\ttruePositive\t" +
"falsePositive\ttruePositiveL\tfalsePositiveL\tfalseNegative");
}
}
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