Method main

src/rnabloom/RNABloom.java:5830–7533

@param args the command line arguments

(String[] args)

     * @param args the command line arguments
     */
    public static void main(String[] args) throws IOException {        
        Timer timer = new Timer();
                    
        // Based on: http://commons.apache.org/proper/commons-cli/usage.html
        CommandLineParser parser = new DefaultParser();

        Options options = new Options();

                
        Option optLeftReads = Option.builder("l")
                                    .longOpt("left")
                                    .desc("left reads file(s)")
                                    .hasArgs()
                                    .argName("FILE FILE ...")
                                    .build();
        options.addOption(optLeftReads);
        
        Option optRightReads = Option.builder("r")
                                    .longOpt("right")
                                    .desc("right reads file(s)")
                                    .hasArgs()
                                    .argName("FILE FILE ...")
                                    .build();
        options.addOption(optRightReads);
        
        Option optPooledAssembly = Option.builder("pool")
                                    .desc("list of read files for pooled assembly")
                                    .hasArg()
                                    .argName("FILE")
                                    .build();
        options.addOption(optPooledAssembly);
        
        String defaultMinTranscriptLengthLR = "200";
        String defaultMinOverlapLR = "150";
        String defaultKmerSizeLR = "25";
        String defaultMinCoverageLR = "2";
        String defaultMaxIndelSizeLR = "50";
        String defaultMaxTipLengthLR = "50";
        String defaultMaxErrorCorrItrLR = "2";
        String defaultPercentIdentityLR = "0.7";
        String defaultMinPolyALengthLR = "12";
        String defaultLongReadPreset = "-k " + defaultKmerSizeLR + " -c " + defaultMinCoverageLR + 
                " -indel " + defaultMaxIndelSizeLR + " -e " + defaultMaxErrorCorrItrLR +
                " -p " + defaultPercentIdentityLR + " -length " + defaultMinTranscriptLengthLR +
                " -overlap " + defaultMinOverlapLR + " -tip " + defaultMaxTipLengthLR +
                " -polya " + defaultMinPolyALengthLR;
        Option optLongReads = Option.builder("long")
                                    .desc("long reads file(s)\n(Requires `minimap2` and `racon` in your environment. Presets `" + 
                                            defaultLongReadPreset + "` unless each option is defined otherwise.)")
                                    .hasArgs()
                                    .argName("FILE FILE ...")
                                    .build();
        options.addOption(optLongReads);

        Option optSeForwardReads = Option.builder("sef")
                                    .desc("single-end forward read file(s)")
                                    .hasArgs()
                                    .argName("FILE FILE ...")