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package stream;
import java.util.ArrayList;
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 structures.ListNum;
import var2.SamFilter;
import var2.ScafMap;
public class SamStreamerWrapper {
/**
* Code entrance from the command line.
* @param args Command line arguments
*/
public static void main(String[] args){
//Start a timer immediately upon code entrance.
Timer t=new Timer();
//Create an instance of this class
SamStreamerWrapper x=new SamStreamerWrapper(args);
//Run the object
x.process(t);
//Close the print stream if it was redirected
Shared.closeStream(x.outstream);
}
SamStreamerWrapper(String[] args){
{//Preparse block for help, config files, and outstream
PreParser pp=new PreParser(args, getClass(), false);
args=pp.args;
outstream=pp.outstream;
}
Shared.capBuffers(4);
ReadWrite.USE_PIGZ=ReadWrite.USE_UNPIGZ=true;
ReadWrite.setZipThreads(Shared.threads());
ReadStreamByteWriter.USE_ATTACHED_SAMLINE=true;
filter=new SamFilter();
boolean doFilter=true;
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("verbose")){
verbose=Parse.parseBoolean(b);
}else if(a.equals("ordered")){
ordered=Parse.parseBoolean(b);
}else if(a.equals("forceparse")){
forceParse=Parse.parseBoolean(b);
}else if(a.equals("ref")){
ref=b;
}else if(a.equals("reads") || a.equals("maxreads")){
maxReads=Long.parseLong(b);
}else if(a.equals("samversion") || a.equals("samv") || a.equals("sam")){
Parser.parseSam(arg, a, b);
fixCigar=true;
}
//Filter
else if(a.equals("filter")){
doFilter=Parse.parseBoolean(b);
}else if(filter.parse(arg, a, b)){
//do nothing
}
else if(parser.parse(arg, a, b)){
//do nothing
}else{
outstream.println("Unknown parameter "+args[i]);
assert(false) : "Unknown parameter "+args[i];
// throw new RuntimeException("Unknown parameter "+args[i]);
}
}
if(!doFilter){filter=null;}
{//Process parser fields
Parser.processQuality();
maxReads=parser.maxReads;
in1=parser.in1;
out1=parser.out1;
}
ffout1=FileFormat.testOutput(out1, FileFormat.FASTQ, null, true, true, false, true);
ffin1=FileFormat.testInput(in1, FileFormat.SAM, null, true, true);
if(!forceParse && !fixCigar && (ffout1==null || !ffout1.samOrBam())){
SamLine.PARSE_2=false;
SamLine.PARSE_5=false;
SamLine.PARSE_6=false;
SamLine.PARSE_7=false;
SamLine.PARSE_8=false;
SamLine.PARSE_OPTIONAL=false;
}
}
void process(Timer t){
if(ref!=null){
ScafMap.loadReference(ref, true);
SamLine.RNAME_AS_BYTES=false;
}
boolean useSharedHeader=(ffout1!=null && ffout1.samOrBam());
final SamReadStreamer ss=new SamReadStreamer(ffin1, ordered ? 1 : SamStreamer.DEFAULT_THREADS, useSharedHeader, maxReads);
ss.start();
final ConcurrentReadOutputStream ros;
if(out1!=null){
final int buff=4;
ros=ConcurrentReadOutputStream.getStream(ffout1, null, buff, null, useSharedHeader);
ros.start();
}else{ros=null;}
long readsProcessed=0, readsOut=0;
long basesProcessed=0, basesOut=0;
for(ListNum<Read> ln=ss.nextReads(); ln!=null && ln.size()>0; ln=ss.nextReads()){
ArrayList<Read> list=ln.list;
if(verbose){outstream.println("Got list of size "+ln.size());}
ArrayList<Read> out=new ArrayList<Read>(list.size());
for(Read r : list){
final int len=r.length();
readsProcessed++;
basesProcessed+=len;
final SamLine sl=r.samline;
boolean keep=filter==null || filter.passesFilter(sl);
if(keep){
if(sl.cigar!=null){
if(fixCigar){
if(SamLine.VERSION==1.3f){
sl.cigar=SamLine.toCigar13(sl.cigar);
}else{
r.toLongMatchString(false);
int start=sl.pos-1;
int stop=start+Read.calcMatchLength(r.match)-1;
sl.cigar=SamLine.toCigar14(r.match, start, stop, Integer.MAX_VALUE, r.bases);
}
}
// if(SamLine.MAKE_MD_TAG){
// //No code for this currently except from ChromArray
// if(sl.optional==null){sl.optional=new ArrayList<String>(1);}
// for(int i=0; i<sl.optional.size(); i++){
// if(sl.optional.get(i).startsWith("MD:")){sl.optional.remove(i);}
// }
// String md=makeMdTag(r.chrom, r.start, r.match, r.bases, scafloc, scaflen);
// if(md!=null){sl.optional.add(md);}
// }
}
out.add(r);
readsOut++;
basesOut+=len;
}
}
if(ros!=null){ros.add(out, ln.id);}
}
errorState|=ss.errorState;
errorState|=ReadWrite.closeStream(ros);
if(verbose){outstream.println("Finished.");}
t.stop();
outstream.println("Time: \t"+t);
outstream.println("Reads Processed: "+readsProcessed+" \t"+Tools.format("%.2fk reads/sec", (readsProcessed/(double)(t.elapsed))*1000000));
outstream.println("Bases Processed: "+basesProcessed+" \t"+Tools.format("%.2f Mbp/sec", (basesProcessed/(double)(t.elapsed))*1000));
outstream.println("Reads Out: "+readsOut);
outstream.println("Bases Out: "+basesOut);
/* Throw an exception if errors were detected */
if(errorState){
throw new RuntimeException(getClass().getSimpleName()+" terminated in an error state; the output may be corrupt.");
}
}
/*--------------------------------------------------------------*/
/*--------------------------------------------------------------*/
/*---------------- Fields ----------------*/
/*--------------------------------------------------------------*/
SamFilter filter;
private String in1=null;
private String out1=null;
private String ref=null;
private final FileFormat ffin1;
private final FileFormat ffout1;
/*--------------------------------------------------------------*/
public boolean errorState=false;
public boolean ordered=true;
private long maxReads=-1;
private boolean forceParse;
private boolean fixCigar;
/*--------------------------------------------------------------*/
private java.io.PrintStream outstream=System.err;
public static boolean verbose=false;
}
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