Examples with DefaultedMap org.apache.commons.collections4.map.DefaultedMap used on opensource projects

Example 1 with DefaultedMap

use of org.apache.commons.collections4.map.DefaultedMap in project gatk by broadinstitute.

the class AlleleBiasedDownsamplingUtils method loadContaminationFile.

/**
     * Create sample-contamination maps from file.
     * The format is: tab-separated with no header,
     * each line is: sampleID contaminationFraction
     *
     * @param file   Filename containing two columns: SampleID and Contamination
     * @param defaultContaminationFraction default contamination fraction, used for samples that do no specify one
     * @param sampleIDs          Set of Samples of interest (no reason to include every sample in file) or null to turn off checking
     * @param logger                      for logging output
     * @return sample-contamination Map. The returned map is a {@link DefaultedMap} that defaults to the defaultContaminationFraction for unspecified samples
     * @throws UserException if there's an IO problem reading the file.
     * @throws UserException if the file is malformed
     */
public static DefaultedMap<String, Double> loadContaminationFile(final File file, final double defaultContaminationFraction, final Set<String> sampleIDs, final Logger logger) {
    final DefaultedMap<String, Double> sampleContamination = new DefaultedMap<>(defaultContaminationFraction);
    final Set<String> nonSamplesInContaminationFile = new LinkedHashSet<>(sampleContamination.keySet());
    try (final XReadLines reader = new XReadLines(file, true)) {
        for (final String line : reader) {
            if (line.isEmpty()) {
                continue;
            }
            final String[] fields = line.split("\t");
            if (fields.length != 2) {
                throw new UserException.MalformedFile("Contamination file must have exactly two, tab-delimited columns. Offending line:\n" + line);
            }
            if (fields[0].isEmpty() || fields[1].isEmpty()) {
                throw new UserException.MalformedFile("Contamination file can not have empty strings in either column. Offending line:\n" + line);
            }
            final double contamination;
            try {
                contamination = Double.parseDouble(fields[1]);
            } catch (final NumberFormatException e) {
                throw new UserException.MalformedFile("Contamination file contains unparsable double in the second field. Offending line: " + line);
            }
            final String sampleName = fields[0];
            if (sampleContamination.containsKey(sampleName)) {
                throw new UserException.MalformedFile("Contamination file contains duplicate entries for input name " + sampleName);
            }
            if (contamination < 0.0 || contamination > 1.0) {
                throw new UserException.MalformedFile("Contamination file contains unacceptable contamination value (must be 0<=x<=1): " + line);
            }
            if (sampleIDs == null || sampleIDs.contains(sampleName)) {
                sampleContamination.put(sampleName, contamination);
            } else {
                nonSamplesInContaminationFile.add(sampleName);
            }
        }
        //output to the user info lines telling which samples are in the Contamination File
        if (!sampleContamination.isEmpty()) {
            logger.info(String.format("The following samples were found in the Contamination file and will be processed at the contamination level therein: %s", sampleContamination.keySet().toString()));
            //output to the user info lines telling which samples are NOT in the Contamination File
            if (sampleIDs != null) {
                final Set<String> samplesNotInContaminationFile = Sets.difference(sampleIDs, sampleContamination.keySet());
                if (!samplesNotInContaminationFile.isEmpty()) {
                    logger.info(String.format("The following samples were NOT found in the Contamination file and will be processed at the default contamination level: %s", samplesNotInContaminationFile.toString()));
                }
            }
        }
        //output to the user Samples that do not have lines in the Contamination File
        if (!nonSamplesInContaminationFile.isEmpty()) {
            logger.info(String.format("The following entries were found in the Contamination file but were not SAMPLEIDs. They will be ignored: %s", nonSamplesInContaminationFile.toString()));
        }
        return sampleContamination;
    } catch (IOException e) {
        throw new UserException.CouldNotReadInputFile("I/O Error while reading sample-contamination file " + file.getAbsolutePath() + ": " + e.getMessage());
    }
}