Package au.org.intersect.samifier.runner

Examples of au.org.intersect.samifier.runner.SamifierRunner.run()

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                File translationTableFile = new File(line.getOptionValue("t"));
                SamifierRunner samifier = new SamifierRunner(
                        searchResultsPaths, genomeFile, mapFile, chromosomeDir,
                        outfile, bedfilePath, confidenScore,
                        translationTableFile);
                samifier.run();
            } else {
                SamifierRunner samifier = new SamifierRunner(
                        searchResultsPaths, genomeFile, mapFile, chromosomeDir,
                        outfile, bedfilePath, confidenScore);
                samifier.run();
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                samifier.run();
            } else {
                SamifierRunner samifier = new SamifierRunner(
                        searchResultsPaths, genomeFile, mapFile, chromosomeDir,
                        outfile, bedfilePath, confidenScore);
                samifier.run();
            }

        } catch (ParseException pe) {
            System.err.println(pe);
            System.err.println("Version = " + VERSION);
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