Source:
public void ProcessFile(Map.Entry<String,String> filePaths) { DatabaseAccessor db = null; try { db = initDB(); Genome g = db.getGenomeRelease(getGenomeVersion()); if (g == null) { throw new UnsupportedOperationException("Could not find genome version: " + getGenomeVersion()); } else { String genomeFolderPath = g.folderPath; String genomeFilePrefix = g.getFilePrefix(); if (genomeFilePrefix == null) { Debug.log("Error when processing. Could not get genomeFilePrefix: " + genomeFilePrefix); throw new UnsupportedOperationException("Error when processing. Could not get genomeFilePrefix: " + genomeFilePrefix); } if (genomeFolderPath == null) { Debug.log("Error when processing. Could not get genomeFolderPath: " + genomeFolderPath); throw new UnsupportedOperationException("Error when processing. Could not get genomeFolderPath: " + genomeFolderPath); } String referenceGenome = genomeFolderPath + genomeFilePrefix; try { RawToProfileConverter rawToProfileConverter = new RawToProfileConverter(); rawToProfileConverter.procedureRaw(getParams(), getInfile(), getOutfile(), shouldKeepSam(), getGenomeVersion(), referenceGenome, filePaths); }catch (ProcessException e){ Debug.log("Error when processing. Could not execute raw to profile process. " + e.getMessage()); throw new UnsupportedOperationException("Error when processing. Could not execute " + "raw to profile process"); } } } catch (SQLException | IOException e) { Debug.log("Error when processing. Could not execute raw to profile process due to temporary " + "problems with database "+e.getMessage()); throw new UnsupportedOperationException("Error when processing. Could not execute raw to " + "profile process due to temporary problems with database."); } finally{ if (db != null) { db.close(); } } }

Target:
public void ProcessFile(Map.Entry<String,String> filePaths) { DatabaseAccessor db = null; try { db = initDB(); Genome g = db.getGenomeRelease(getGenomeVersion()); if (g == null) { throw new UnsupportedOperationException("Could not find genome version: " + getGenomeVersion()); } else { String genomeFolderPath = g.getFolderPath(); String genomeFilePrefix = g.getFilePrefix(); if (genomeFilePrefix == null) { Debug.log("Error when processing. Could not get genomeFilePrefix: " + genomeFilePrefix); throw new UnsupportedOperationException("Error when processing. Could not get genomeFilePrefix: " + genomeFilePrefix); } if (genomeFolderPath == null) { Debug.log("Error when processing. Could not get genomeFolderPath: " + genomeFolderPath); throw new UnsupportedOperationException("Error when processing. Could not get genomeFolderPath: " + genomeFolderPath); } String referenceGenome = genomeFolderPath + genomeFilePrefix; try { RawToProfileConverter rawToProfileConverter = new RawToProfileConverter(); rawToProfileConverter.procedureRaw(getParams(), getInfile(), getOutfile(), shouldKeepSam(), getGenomeVersion(), referenceGenome, filePaths); }catch (ProcessException e){ Debug.log("Error when processing. Could not execute raw to profile process. " + e.getMessage()); throw new UnsupportedOperationException("Error when processing. Could not execute " + "raw to profile process"); } } } catch (SQLException | IOException e) { Debug.log("Error when processing. Could not execute raw to profile process due to temporary " + "problems with database "+e.getMessage()); throw new UnsupportedOperationException("Error when processing. Could not execute raw to " + "profile process due to temporary problems with database."); } finally{ if (db != null) { db.close(); } } }