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package driver;
import java.io.File;
import java.io.PrintStream;
import java.util.ArrayList;
import fileIO.FileFormat;
import fileIO.ReadWrite;
import fileIO.TextStreamWriter;
import jgi.DecontaminateByNormalization;
import shared.Parse;
import shared.Parser;
import shared.PreParser;
import shared.Shared;
import shared.Timer;
import shared.Tools;
/**
* @author Brian Bushnell
* @date June 1, 2016
*
*/
public class SummarizeCrossblock {
public static void main(String[] args){
Timer t=new Timer();
SummarizeCrossblock x=new SummarizeCrossblock(args);
x.process(t);
//Close the print stream if it was redirected
Shared.closeStream(x.outstream);
}
public SummarizeCrossblock(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=false;
ReadWrite.USE_UNPIGZ=false;
ReadWrite.USE_UNBGZIP=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]);
}
}
String in=null;
{//Process parser fields
Parser.processQuality();
overwrite=parser.overwrite;
append=parser.append;
in=parser.in1;
out1=parser.out1;
}
if(in==null){throw new RuntimeException("Error - at least one input file is required.");}
if(in.contains(",")){
for(String s : in.split(",")){
inList.add(s);
}
}else{
inList.add(in);
DecontaminateByNormalization.parseStringsFromFiles(inList);
}
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);
}
void process(Timer t){
final TextStreamWriter tsw;
tsw=ffout1!=null ? new TextStreamWriter(ffout1) : null;
if(tsw!=null){tsw.start();}
if(tsw!=null){tsw.print("#fname\tcopies\tcontigs\tcontigsDiscarded\tbases\tbasesDiscarded\n");}
int i=1;
for(String fname : inList){
ParseCrossblockResults pcr=null;
try{
pcr=new ParseCrossblockResults(new String[] {"in="+fname});
Timer t2=new Timer();
pcr.process(t2);
if(tsw!=null){tsw.print(fname+"\t"+i+"\t"+pcr.contigs()+"\t"+pcr.contigsDiscarded()+"\t"+pcr.bases()+"\t"+pcr.basesDiscarded()+"\n");}
}catch(Throwable e){
System.err.println(e);
if(tsw!=null){tsw.print(fname+"\tERROR\n");}
}
i++;
}
if(tsw!=null){errorState|=tsw.poisonAndWait();}
}
/*--------------------------------------------------------------*/
/*--------------------------------------------------------------*/
private ArrayList<String> inList=new ArrayList<String>();
private String out1=null;
/*--------------------------------------------------------------*/
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;}
/*--------------------------------------------------------------*/
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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