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package driver;
import java.io.File;
import java.io.PrintStream;
import fileIO.FileFormat;
import fileIO.ReadWrite;
import fileIO.TextFile;
import fileIO.TextStreamWriter;
import shared.Parse;
import shared.Parser;
import shared.PreParser;
import shared.Shared;
import shared.Timer;
import shared.Tools;
/**
* @author Brian Bushnell
* @date June 9, 2016
*
*/
public class ParseCrossblockResults {
public static void main(String[] args){
Timer t=new Timer();
ParseCrossblockResults x=new ParseCrossblockResults(args);
x.process(t);
//Close the print stream if it was redirected
Shared.closeStream(x.outstream);
}
public ParseCrossblockResults(String[] args){
{//Preparse block for help, config files, and outstream
PreParser pp=new PreParser(args, getClass(), false);
args=pp.args;
outstream=pp.outstream;
}
ReadWrite.USE_PIGZ=ReadWrite.USE_UNPIGZ=false;
Parser parser=new Parser();
for(int i=0; i<args.length; i++){
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(a.equals("verbose")){
verbose=Parse.parseBoolean(b);
ReadWrite.verbose=verbose;
}else if(parser.in1==null && i==0 && Tools.looksLikeInputStream(arg)){
parser.in1=arg;
}else{
outstream.println("Unknown parameter "+args[i]);
assert(false) : "Unknown parameter "+args[i];
// throw new RuntimeException("Unknown parameter "+args[i]);
}
}
{//Process parser fields
Parser.processQuality();
maxReads=parser.maxReads;
overwrite=parser.overwrite;
append=parser.append;
in1=parser.in1;
out1=parser.out1;
}
if(in1==null){throw new RuntimeException("Error - at least one input file is required.");}
if(out1!=null && out1.equalsIgnoreCase("null")){out1=null;}
if(!Tools.testOutputFiles(overwrite, append, false, out1)){
outstream.println((out1==null)+", "+out1);
throw new RuntimeException("\n\noverwrite="+overwrite+"; Can't write to output files "+out1+"\n");
}
ffout1=FileFormat.testOutput(out1, FileFormat.TEXT, null, true, overwrite, append, false);
ffin1=FileFormat.testInput(in1, FileFormat.TEXT, null, false, false);
}
void process(Timer t){
final TextFile tf;
{
tf=new TextFile(ffin1);
if(verbose){outstream.println("Started tf");}
}
long linesProcessed=0;
long charsProcessed=0;
{
String line;
while((maxReads<0 || linesProcessed<maxReads) && (line=tf.nextLine())!=null){
linesProcessed++;
charsProcessed+=line.length();
if(!line.startsWith("#")){
processLine(line);
}
}
}
errorState|=tf.close();
if(ffout1!=null){
final TextStreamWriter tsw;
{
tsw=new TextStreamWriter(ffout1);
tsw.start();
if(verbose){outstream.println("Started tsw");}
errorState|=tsw.poisonAndWait();
}
}
t.stop();
outstream.println(Tools.timeLinesBytesProcessed(t, linesProcessed, charsProcessed, 8));
if(errorState){
throw new RuntimeException(getClass().getName()+" terminated in an error state; the output may be corrupt.");
}
}
private void processLine(String line){
ResultsLine rl=new ResultsLine(line);
if(rl.removed){
basesDiscarded+=rl.length;
contigsDiscarded++;
}else{
basesKept+=rl.length;
contigsKept++;
}
}
/*--------------------------------------------------------------*/
private static class ResultsLine{
public ResultsLine(String s){
String[] split=s.split("\t");
length=Integer.parseInt(split[3]);
removed=Integer.parseInt(split[2])==1;
}
final int length;
final boolean removed;
}
/*--------------------------------------------------------------*/
/*--------------------------------------------------------------*/
private String in1=null;
private String out1=null;
/*--------------------------------------------------------------*/
private long maxReads=-1;
private long basesKept=0;
private long basesDiscarded=0;
private long contigsKept=0;
private long contigsDiscarded=0;
public long basesKept(){return basesKept;}
public long basesDiscarded(){return basesDiscarded;}
public long contigsKept(){return contigsKept;}
public long contigsDiscarded(){return contigsDiscarded;}
public long contigs(){return contigsKept+contigsDiscarded;}
public long bases(){return basesKept+basesDiscarded;}
/*--------------------------------------------------------------*/
private final FileFormat ffin1;
private final FileFormat ffout1;
/*--------------------------------------------------------------*/
private PrintStream outstream=System.err;
public static boolean verbose=false;
public boolean errorState=false;
private boolean overwrite=true;
private boolean append=false;
}
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