Method getPooledReadPaths

src/rnabloom/RNABloom.java:5066–5176

(String pooledReadPathsListFile,
            HashMap<String, ArrayList<String>> pooledLeftReadPaths,
            HashMap<String, ArrayList<String>> pooledRightReadPaths,
            HashMap<String, ArrayList<String>> pooledUnpairedForwardReadPaths,
            HashMap<String, ArrayList<String>> pooledUnpairedReverseReadPaths)

    private final static String FIELD_SEPARATOR = "\\s+"; // any white space character
    
    private static boolean getPooledReadPaths(String pooledReadPathsListFile,
            HashMap<String, ArrayList<String>> pooledLeftReadPaths,
            HashMap<String, ArrayList<String>> pooledRightReadPaths,
            HashMap<String, ArrayList<String>> pooledUnpairedForwardReadPaths,
            HashMap<String, ArrayList<String>> pooledUnpairedReverseReadPaths) throws FileNotFoundException, IOException {
        
        BufferedReader br = getTextFileReader(pooledReadPathsListFile);
        
        int nameColumnIndex = 0;
        int leftColumnIndex = 1;
        int rightColumnIndex = 2;
        int sefColumnIndex = -1;
        int serColumnIndex = -1;
        int numColumns = 3;
        
        String line;
        int lineNumber = 0;
        while ((line = br.readLine()) != null) {
            ++lineNumber;
            
            line = line.trim();
            if (!line.isEmpty()) { 
                if (line.charAt(0) == '#') {
                    String[] header = line.substring(1).split(FIELD_SEPARATOR);
                    nameColumnIndex = -1;
                    leftColumnIndex = -1;
                    rightColumnIndex = -1;
                    sefColumnIndex = -1;
                    serColumnIndex = -1;
                    numColumns = header.length;
                    for (int i=0; i<header.length; ++i) {
                        switch(header[i]) {
                            case "name":
                                nameColumnIndex = i;
                                break;
                            case "left":
                                leftColumnIndex = i;
                                break;
                            case "right":
                                rightColumnIndex = i;
                                break;
                            case "sef":
                                sefColumnIndex = i;
                                break;
                            case "ser":
                                serColumnIndex = i;
                                break;
                            default:
                                exitOnError("`-pool` input file has unrecognized column identifier \"" + header[i] + "\" on line " + lineNumber + ":\n\t" + line);
                                return false;
                        }
                    }
                }
                else {
                    String[] entry = line.split(FIELD_SEPARATOR);
                    int numFields = entry.length;
                    if (numFields != numColumns) {
                        exitOnError("`-pool` input file has unexpected number of columns on line " + lineNumber + ":\n\t" + line);