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package driver;
import fileIO.TextFile;
/**
* Summarizes match/sub/ins/del/N rates for consecutive BBMap runs
* @author Brian Bushnell
* @date Jan 8, 2014
*
*/
public class SummarizeMSDIN {
public static void main(String[] args){
String fname=args[0];
boolean M=false;
boolean E=false;
boolean S=true;
boolean D=false;
boolean I=false;
boolean N=false;
boolean B=false;
boolean MS=true;
long mcount=0;
long ecount=0;
long scount=0;
long dcount=0;
long icount=0;
long ncount=0;
long bcount=0;
TextFile tf=new TextFile(fname);
StringBuilder sb=new StringBuilder();
for(String s=tf.nextLine(); s!=null; s=tf.nextLine()){
String[] split=s.split("\t");
if(s.startsWith("Total time:")){
if(B){
if(sb.length()>0){sb.append('\t');}
sb.append(bcount);
}
if(MS){
if(sb.length()>0){sb.append('\t');}
sb.append((mcount+scount));
}
if(M){
if(sb.length()>0){sb.append('\t');}
sb.append(mcount);
}
if(E){
if(sb.length()>0){sb.append('\t');}
sb.append(ecount);
}
if(S){
if(sb.length()>0){sb.append('\t');}
sb.append(scount);
}
if(D){
if(sb.length()>0){sb.append('\t');}
sb.append(dcount);
}
if(I){
if(sb.length()>0){sb.append('\t');}
sb.append(icount);
}
if(N){
if(sb.length()>0){sb.append('\t');}
sb.append(ncount);
}
System.out.println(sb);
sb.setLength(0);
mcount=ecount=scount=dcount=icount=ncount=bcount=0;
}else if(s.startsWith("Match Rate:")){
String x=split[split.length-1];
try{mcount=(Long.parseLong(x));}catch(Exception e){}
}else if(E && s.startsWith("Error Rate:")){
String x=split[split.length-1];
// if(E){
// if(sb.length()>0){sb.append('\t');}
// sb.append(x);
// }
try{ecount=(Long.parseLong(x));}catch(Exception e){}
}else if(s.startsWith("Sub Rate:")){
String x=split[split.length-1];
// if(S){
// if(sb.length()>0){sb.append('\t');}
// sb.append(x);
// }
try{scount=(Long.parseLong(x));}catch(Exception e){}
}else if(s.startsWith("Del Rate:")){
String x=split[split.length-1];
// if(D){
// if(sb.length()>0){sb.append('\t');}
// sb.append(x);
// }
try{dcount=(Long.parseLong(x));}catch(Exception e){}
}else if(s.startsWith("Ins Rate:")){
String x=split[split.length-1];
// if(I){
// if(sb.length()>0){sb.append('\t');}
// sb.append(x);
// }
try{icount=(Long.parseLong(x));}catch(Exception e){}
}else if(s.startsWith("N Rate:")){
String x=split[split.length-1];
// if(N){
// if(sb.length()>0){sb.append('\t');}
// sb.append(x);
// }
try{ncount=(Long.parseLong(x));}catch(Exception e){}
}else if(s.startsWith("Reads Used:")){
String x=split[split.length-1].replace("(", "").replace(" bases)", "");
// if(B){
// if(sb.length()>0){sb.append('\t');}
// sb.append(x);
// }
try{bcount=(Long.parseLong(x));}catch(Exception e){}
}
}
}
}
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