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package driver;
import java.io.File;
import java.util.ArrayList;
import fileIO.TextFile;
import fileIO.TextStreamWriter;
import shared.Parser;
import shared.PreParser;
import shared.Tools;
/**
* @author Brian Bushnell
* @date Apr 29, 2015
*
*/
public class SummarizeCoverage {
/**
* Code entrance from the command line.
* @param args Command line arguments
*/
public static void main(String[] args){
//Create a new instance
SummarizeCoverage x=new SummarizeCoverage(args);
///And run it
x.process();
}
public SummarizeCoverage(String[] args){
{//Preparse block for help, config files, and outstream
PreParser pp=new PreParser(args, getClass(), false);
args=pp.args;
//outstream=pp.outstream;
}
ArrayList<String> names=new ArrayList<String>();
Parser parser=new Parser();
/* Parse arguments */
for(int i=0; i<args.length; i++){
final String arg=args[i];
String[] split=arg.split("=");
String a=split[0].toLowerCase();
String b=split.length>1 ? split[1] : null;
if(parser.parse(arg, a, b)){
//do nothing
}else if(!arg.contains("=")){
String[] x=(new File(arg).exists() ? new String[] {arg} : arg.split(","));
for(String x2 : x){names.add(x2);}
}else{
throw new RuntimeException("Unknown parameter "+arg);
}
}
{//Process parser fields
out=(parser.out1==null ? "stdout" : parser.out1);
if(parser.in1!=null){
String[] x=(new File(parser.in1).exists() ? new String[] {parser.in1} : parser.in1.split(","));
for(String x2 : x){names.add(x2);}
}
}
in=new ArrayList<String>();
for(String s : names){
Tools.getFileOrFiles(s, in, false, false, false, true);
}
}
public void process(){
TextStreamWriter tsw=new TextStreamWriter(out, true, false, false);
tsw.start();
tsw.print("#File\tPrimary_Name\tPrimary_Count\tOther_Count\tPrimary_MB\tOther_MB\n");
for(String fname : in){
String pname=null;
long pcount=0, ocount=0;
double pmb=0, omb=0;
TextFile tf=new TextFile(fname);
for(String line=tf.nextLine(); line!=null; line=tf.nextLine()){
if(!line.startsWith("#")){
String[] split=line.split("\t");
long count=Long.parseLong(split[5]);
double mb=Double.parseDouble(split[2]);
if(pcount==0 || mb>pmb || (mb==pmb && count>pcount)){
pname=split[0];
ocount+=pcount;
omb+=pmb;
pcount=count;
pmb=mb;
}else{
ocount+=count;
omb+=mb;
}
}
}
tf.close();
tsw.print(Tools.format("%s\t%s\t%d\t%d\t%.5f\t%.5f\n", fname, pname, pcount, ocount, pmb, omb));
}
tsw.poisonAndWait();
}
final ArrayList<String> in;
final String out;
}
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