2ef51576f7fd4bfb67e0d2c771ff6b956cd83fcb,src/samTextViewer/Main.java,Main,main,#String[]#,31

Before Change


		initGenomeList.add(genome);
		gch.current().setGenome(initGenomeList);

		TrackProcessor proc= new TrackProcessor(new TrackSet(inputFileList, gch.current()), gch);

		if(proc.getGenomicCoordsHistory().current().getFastaFile() != null){
			TrackSeqRegex re= new TrackSeqRegex(proc.getGenomicCoordsHistory().current());
			proc.getTrackSet().add(re, "regex_seq_matches");;
		}
		
		proc.setNoFormat(opts.getBoolean("noFormat"));
		
		// Put here the previous command so that it is re-issued if no imput is given
		// You have to initialize this var outside the while loop that processes input files.
		String currentCmdConcatInput= ""; 

		if(!proc.isNoFormat()){
			System.out.print("\033[48;5;231m");
		}

		// Batch processing file of regions
		final String batchFile= opts.getString("batchFile");
		if(! batchFile.isEmpty()){

			if(! new File(batchFile).exists()){
				System.err.print("\033[0m");
				System.err.println("File " + batchFile + " does not exist.");
				System.exit(1);
			}

			console.clearScreen();
			console.flush();

			BufferedReader br= new BufferedReader(new FileReader(new File(batchFile)));
			String line = null;  
			while ((line = br.readLine()) != null){
				// Start processing intervals one by one
				IntervalFeature target= new IntervalFeature(line, TrackFormat.BED);
				String reg= target.getChrom() + ":" + target.getFrom() + "-" + target.getTo();
				String gotoAndExec= ("goto " + reg + " && " + exec).trim().replaceAll("&&$", "");
				InteractiveInput itr = new InteractiveInput();
				proc= itr.processInput(gotoAndExec, proc);
				if (itr.getInteractiveInputExitCode() != 0){
					System.err.println("Error processing '" + gotoAndExec + "' at line '" + line + "'");
					System.exit(1);
				}
			}
			br.close();
			System.exit(0);
		}

		// See if we need to process the exec arg before going to interactive mode. 
		// Also if we are in non-interactive mode, we process the track set now and later exit 
		console.clearScreen();
		console.flush();
		proc.iterateTracks();
		if(!exec.isEmpty() || opts.getBoolean("nonInteractive")){

			InteractiveInput itr = new InteractiveInput();
			proc= itr.processInput(exec, proc);
			if(opts.getBoolean("nonInteractive")){
				System.out.print("\033[0m");
				System.exit(0);

After Change


		initGenomeList.add(genome);
		gch.current().setGenome(initGenomeList);
		final TrackSet trackSet= new TrackSet(inputFileList, gch.current());
		final TrackProcessor proc= new TrackProcessor(trackSet, gch);
		
		if(proc.getGenomicCoordsHistory().current().getFastaFile() != null){
			TrackSeqRegex re= new TrackSeqRegex(proc.getGenomicCoordsHistory().current());
			proc.getTrackSet().add(re, "regex_seq_matches");;
		}

		proc.setNoFormat(opts.getBoolean("noFormat"));
		
		// Put here the previous command so that it is re-issued if no imput is given
		// You have to initialize this var outside the while loop that processes input files.
		String currentCmdConcatInput= ""; 

		if(!proc.isNoFormat()){
			System.out.print("\033[48;5;231m");
		}

		// Batch processing file of regions
		final String batchFile= opts.getString("batchFile");
		if(! batchFile.isEmpty()){

			if(! new File(batchFile).exists()){
				System.err.print("\033[0m");
				System.err.println("File " + batchFile + " does not exist.");
				System.exit(1);
			}

			console.clearScreen();
			console.flush();

			BufferedReader br= new BufferedReader(new FileReader(new File(batchFile)));
			String line = null;  
			while ((line = br.readLine()) != null){
				// Start processing intervals one by one
				IntervalFeature target= new IntervalFeature(line, TrackFormat.BED);
				String reg= target.getChrom() + ":" + target.getFrom() + "-" + target.getTo();
				String gotoAndExec= ("goto " + reg + " && " + exec).trim().replaceAll("&&$", "");
				InteractiveInput itr = new InteractiveInput();
				itr.processInput(gotoAndExec, proc);
				if (itr.getInteractiveInputExitCode() != 0){
					System.err.println("Error processing '" + gotoAndExec + "' at line '" + line + "'");
					System.exit(1);
				}
			}
			br.close();
			System.exit(0);
		}

		// See if we need to process the exec arg before going to interactive mode. 
		// Also if we are in non-interactive mode, we process the track set now and later exit 
		console.clearScreen();
		console.flush();
		proc.iterateTracks();
		if(!exec.isEmpty() || opts.getBoolean("nonInteractive")){

			InteractiveInput itr = new InteractiveInput();
			itr.processInput(exec, proc);
			if(opts.getBoolean("nonInteractive")){
				System.out.print("\033[0m");
				System.exit(0);