Package au.org.intersect.samifier.runner

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

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                File translationTableFile = new File(line.getOptionValue("t"));
                ResultAnalyserRunner analyser = new ResultAnalyserRunner(
                        searchResultsPaths, genomeFile, mapFile, outfile,
                        chromosomeDir, translationTableFile);
                if (sqlQuery == null && repId == null) {
                    analyser.run();
                } else if (sqlQuery != null
                        && (repId != null || repListFile != null)) {
                    System.err.println("Only use either reportId or sqlQuery.");
                } else if (sqlQuery != null) {
                    mainWithQuery(analyser, sqlQuery);
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            } else {
                ResultAnalyserRunner analyser = new ResultAnalyserRunner(
                        searchResultsPaths, genomeFile, mapFile, outfile,
                        chromosomeDir);
                if (sqlQuery == null && repId == null) {
                    analyser.run();
                } else if (sqlQuery != null
                        && (repId != null || repListFile != null)) {
                    System.err.println("Only use either reportId or sqlQuery.");
                } else if (sqlQuery != null) {
                    mainWithQuery(analyser, sqlQuery);
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