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package jgi;
import java.io.File;
import java.io.PrintStream;
import java.util.ArrayList;
import fileIO.ByteFile;
import fileIO.ByteFile1;
import fileIO.ByteFile2;
import fileIO.ByteStreamWriter;
import fileIO.FileFormat;
import fileIO.ReadWrite;
import shared.Parse;
import shared.Parser;
import shared.PreParser;
import shared.Shared;
import shared.Timer;
import shared.Tools;
import stream.ConcurrentGenericReadInputStream;
import stream.FastaReadInputStream;
/**
* @author Brian Bushnell
* @date March 8, 2017
*
*/
public class MergeSam {
public static void main(String[] args){
Timer t=new Timer();
MergeSam x=new MergeSam(args);
x.process(t);
//Close the print stream if it was redirected
Shared.closeStream(x.outstream);
}
public MergeSam(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=true;
ReadWrite.setZipThreads(Shared.threads());
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(a.equals("invalid")){
outInvalid=b;
}else if(a.equals("lines")){
maxLines=Long.parseLong(b);
if(maxLines<0){maxLines=Long.MAX_VALUE;}
}else if(a.equals("verbose")){
verbose=Parse.parseBoolean(b);
ByteFile1.verbose=verbose;
ByteFile2.verbose=verbose;
stream.FastaReadInputStream.verbose=verbose;
ConcurrentGenericReadInputStream.verbose=verbose;
stream.FastqReadInputStream.verbose=verbose;
ReadWrite.verbose=verbose;
}else if(a.equals("in")){
in.add(b);
}else if(a.equals("out")){
out=b;
}else if(b==null && new File(arg).exists()){
in.add(arg);
}else if(parser.parse(arg, a, b)){//Parse standard flags in the parser
//do nothing
}else{
outstream.println("Unknown parameter "+args[i]);
assert(false) : "Unknown parameter "+args[i];
// throw new RuntimeException("Unknown parameter "+args[i]);
}
}
{//Process parser fields
overwrite=parser.overwrite;
append=parser.append;
}
assert(FastaReadInputStream.settingsOK());
if(in==null){throw new RuntimeException("Error - at least one input file is required.");}
if(out!=null && out.equalsIgnoreCase("null")){out=null;}
if(!Tools.testOutputFiles(overwrite, append, false, out)){
outstream.println((out==null)+", "+out);
throw new RuntimeException("\n\noverwrite="+overwrite+"; Can't write to output files "+out+"\n");
}
ffout=FileFormat.testOutput(out, FileFormat.SAM, null, true, overwrite, append, false);
ffoutInvalid=FileFormat.testOutput(outInvalid, FileFormat.SAM, null, true, overwrite, append, false);
ffin=FileFormat.testInputList(in, FileFormat.SAM, null, true, true);
}
void process(Timer t){
ByteStreamWriter bsw=null;
if(ffout!=null){
bsw=new ByteStreamWriter(ffout);
bsw.start();
}
ByteStreamWriter bswInvalid=null;
if(ffoutInvalid!=null){
bswInvalid=new ByteStreamWriter(ffoutInvalid);
bswInvalid.start();
}
boolean headerMode=true;
for(int fnum=0; fnum<ffin.length; fnum++){
ByteFile bf=ByteFile.makeByteFile(ffin[fnum]);
byte[] line=bf.nextLine();
while(line!=null){
if(line.length>0){
if(maxLines>0 && linesProcessed>=maxLines){break;}
linesProcessed++;
bytesProcessed+=line.length;
boolean valid=true;
if(line[0]=='@'){valid=headerMode;}
else{headerMode=false;}
if(valid){
linesValid++;
if(bsw!=null){
bsw.println(line);
}
}else{
if(bswInvalid!=null){
bswInvalid.println(line);
}
}
}
line=bf.nextLine();
}
errorState|=bf.close();
}
if(bsw!=null){errorState|=bsw.poisonAndWait();}
if(bswInvalid!=null){errorState|=bswInvalid.poisonAndWait();}
t.stop();
outstream.println(Tools.timeLinesBytesProcessed(t, linesProcessed, bytesProcessed, 8));
outstream.println();
outstream.println("Valid Lines: \t"+linesValid);
outstream.println("Invalid Lines: \t"+(linesProcessed-linesValid));
if(errorState){
throw new RuntimeException(getClass().getName()+" terminated in an error state; the output may be corrupt.");
}
}
/*--------------------------------------------------------------*/
/*--------------------------------------------------------------*/
private ArrayList<String> in=new ArrayList<String>();
private String out="stdout.sam";
private String outInvalid=null;
/*--------------------------------------------------------------*/
private long linesProcessed=0;
private long linesValid=0;
private long bytesProcessed=0;
private long maxLines=Long.MAX_VALUE;
/*--------------------------------------------------------------*/
private final FileFormat[] ffin;
private final FileFormat ffout;
private final FileFormat ffoutInvalid;
/*--------------------------------------------------------------*/
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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