f6661ff227fb278c77b0b78f15645e7af8dd749b,src/main/java/uk/ac/ebi/pride/utilities/data/exporters/MzTabBedConverter.java,MzTabBedConverter,convertProBedToBigBed,#File#File#File#File#File#,463

Before Change



    public static File convertProBedToBigBed(File aSQL, File bedToBigBed, File bigBedConverter, File sortedProBed, File inputChromSizes) throws IOException, InterruptedException{
        File result = null;
        if (!System.getProperty("os.name").startsWith("Windows")) {
            result = new File(sortedProBed.getParentFile().getPath() + File.separator + FilenameUtils.getBaseName(sortedProBed.getName()) + ".bb");
            logger.info("command to run: \n" +
                            bedToBigBed.getPath() + ", " +

After Change


    public static File convertProBedToBigBed(File aSQL, String bedColumnsType, File sortedProBed, File inputChromSizes, File bigBedConverter) throws IOException, InterruptedException, URISyntaxException{
       logger.info("convertProBedToBigBed: " + aSQL.getAbsolutePath() +" , " + sortedProBed.getAbsolutePath() + ", " + inputChromSizes.getAbsolutePath());
        File result;
        final String OS = System.getProperty("os.name").toLowerCase();
        logger.info("OS version: " + OS);
        if (!OS.contains("win")) {
            InputStream inputStream = MzTabBedConverter.class.getClassLoader().getResourceAsStream("bedBigBed.sh");