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package template;
import java.io.File;
import java.util.ArrayList;
import fileIO.FileFormat;
import fileIO.ReadWrite;
import shared.Parser;
import shared.PreParser;
import shared.Shared;
import shared.Timer;
import shared.Tools;
import stream.ConcurrentReadInputStream;
import stream.ConcurrentReadOutputStream;
import stream.Read;
import structures.ListNum;
/**
* Accepts multiple input files.
* Reads them each sequentially, and outputs everything to a single output file.
* Generically, it can be used to concatenate files while recompressing them
* and avoiding the use of stdio.
* @author Brian Bushnell
* @date May 10, 2024
*
*/
public class A_SampleMultipleInput {
public static void main(String[] args){
//Start a timer immediately upon code entrance.
Timer t=new Timer();
//Create an instance of this class
A_SampleMultipleInput x=new A_SampleMultipleInput(args);
//Run the object
x.process(t);
//Close the print stream if it was redirected
Shared.closeStream(x.outstream);
}
public A_SampleMultipleInput(String[] args){
{//Preparse block for help, config files, and outstream
PreParser pp=new PreParser(args, getClass(), false);
args=pp.args;
outstream=pp.outstream;
}
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(b!=null && b.equalsIgnoreCase("null")){b=null;}
if(a.equals("parse_flag_goes_here")){
//Set a variable here
}else if(a.equals("in")){
in.clear();
String[] b2=(b==null) ? null : (new File(b).exists() ? new String[] {b} : b.split(","));
for(String b3 : b2){in.add(b3);}
}else if(b==null && new File(arg).exists()){
in.add(arg);
}else if(parser.parse(arg, a, b)){
//do nothing
}else{
assert(false) : "Unknown parameter "+args[i];
outstream.println("Unknown parameter "+args[i]);
}
}
{//Process parser fields
Parser.processQuality();
maxReads=parser.maxReads;
out1=parser.out1;
}
ffout1=FileFormat.testOutput(out1, FileFormat.FASTQ, null, true, true, false, false);
}
void process(Timer t){
final ConcurrentReadOutputStream ros;
if(out1!=null){
final int buff=4;
for(String s : in) {
assert(!out1.equalsIgnoreCase(s)) : "Input file and output file have same name.";
}
ros=ConcurrentReadOutputStream.getStream(ffout1, null, buff, null, false);
ros.start();
}else{ros=null;}
for(String s : in) {
processInner(s, ros);
}
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));
}
void processInner(String fname, ConcurrentReadOutputStream ros) {
FileFormat ffin=FileFormat.testInput(fname, FileFormat.FASTQ, null, true, true);
final ConcurrentReadInputStream cris;
{
cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin, null);
cris.start();
}
boolean paired=cris.paired();
{
ListNum<Read> ln=cris.nextList();
ArrayList<Read> reads=(ln!=null ? ln.list : null);
if(reads!=null && !reads.isEmpty()){
Read r=reads.get(0);
assert((ffin==null || ffin.samOrBam()) || (r.mate!=null)==cris.paired());
}
//ln!=null prevents a compiler potential null access warning
while(ln!=null && reads!=null && reads.size()>0){
if(verbose){outstream.println("Fetched "+reads.size()+" reads.");}
for(int idx=0; idx<reads.size(); idx++){
final Read r1=reads.get(idx);
readsProcessed+=r1.pairCount();
basesProcessed+=r1.pairLength();
// ********* Process reads here *********
}
if(ros!=null){ros.add(reads, ln.id);}
cris.returnList(ln);
if(verbose){outstream.println("Returned a list.");}
ln=cris.nextList();
reads=(ln!=null ? ln.list : null);
}
if(ln!=null){
cris.returnList(ln.id, ln.list==null || ln.list.isEmpty());
}
}
ReadWrite.closeStream(cris);
}
/*--------------------------------------------------------------*/
/*--------------------------------------------------------------*/
private ArrayList<String> in=new ArrayList<String>();
private String out1=null;
private final FileFormat ffout1;
/*--------------------------------------------------------------*/
private long maxReads=-1;
private long readsProcessed=0, basesProcessed=0;
/*--------------------------------------------------------------*/
private java.io.PrintStream outstream=System.err;
public static boolean verbose=false;
}
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