Examples of org.broad.igv.feature.genome.GenomeManager

                BamToBed.convert(new File(ifile), new File(ofile), pairOption);
            } else if (command.equalsIgnoreCase("genGenomeList")) {
                //Generate a genomes.txt list file based on a directory
                //TODO Probably a better place for this. Users won't generally use it
                File inDir = new File(ifile);
                GenomeManager manager = GenomeManager.getInstance();
                manager.generateGenomeList(inDir, nonOptionArgs[2], nonOptionArgs[3]);
            } else {
                throw new PreprocessingException("Unknown command: " + argv[EXT_FACTOR]);
            }
        } catch (IOException e) {
            throw new PreprocessingException("Unexpected IO error: ", e);


    public static Genome loadGenome(String genomeFileOrID) throws IOException {


        String rootDir = FileUtils.getInstallDirectory();


        final GenomeManager genomeManager = GenomeManager.getInstance();
        Genome genome = genomeManager.getCurrentGenome();
        if (genome != null && genome.getId().equals(genomeFileOrID)) {
            return genome;
        }


        File genomeFile = new File(genomeFileOrID);
        if (!genomeFile.exists()) {
            genomeFile = new File(rootDir, "genomes" + File.separator + genomeFileOrID + ".genome");


        }
        if(!genomeFile.exists()) {
            genomeFile = new File(rootDir, "genomes" + File.separator + genomeFileOrID + ".chrom.sizes");
        }
        if (!genomeFile.exists()) {
            genomeFile = new File(rootDir, "genomes" + File.separator + genomeFileOrID);


        }
        if (!genomeFile.exists()) {
            throw new PreprocessingException("Genome definition file not found for: " + genomeFileOrID);
        }




        //TODO Prevents loading genome again if loading from path.
        //May or may not want this, for now we just use it for testing
        if (Globals.isTesting() && genomeFile.getAbsolutePath().endsWith(".genome")) {
            GenomeDescriptor genomeDescriptor = GenomeManager.parseGenomeArchiveFile(genomeFile);
            if (genome != null && genomeDescriptor.getId().equals(genome.getId())) {
                return genome;
            }
        }


        genome = genomeManager.loadGenome(genomeFile.getAbsolutePath(), null);
        if (genome == null) {
            throw new PreprocessingException("Error loading: " + genomeFileOrID);
        }
        return genome;
    }

Examples of org.broad.igv.feature.genome.GenomeManager

Related Classes of org.broad.igv.feature.genome.GenomeManager