Examples with Nucleotide org.broadinstitute.hellbender.utils.Nucleotide used on opensource projects

Example 6 with Nucleotide

use of org.broadinstitute.hellbender.utils.Nucleotide in project gatk by broadinstitute.

the class BayesianHetPulldownCalculatorUnitTest method loadPileup.

/**
     * load the fake fileup from file
     *
     * @throws IOException
     */
@BeforeClass
public void loadPileup() throws IOException {
    /* load fake pileup and likelihoods from disk */
    StringMapper<String> stringStripper = s -> s.substring(s.indexOf(':') + 1).replaceAll("\\s+", "");
    StringMapper<Double> parseToDouble = s -> Double.parseDouble(stringStripper.of(s));
    StringMapper<ArrayList<Double>> parseToDoubleArray = s -> {
        String[] tokenizedLine = stringStripper.of(s).split(",");
        ArrayList<Double> errorList = new ArrayList<>();
        if (tokenizedLine.length >= 1 && !tokenizedLine[0].equals("")) {
            errorList.addAll(Arrays.asList(tokenizedLine).stream().map(Double::parseDouble).collect(Collectors.toList()));
        }
        return errorList;
    };
    Scanner reader = new Scanner(new FileInputStream(FAKE_PILEUP_FILE));
    while (reader.hasNextLine()) {
        Map<Nucleotide, List<BayesianHetPulldownCalculator.BaseQuality>> baseQualities = new HashMap<>();
        for (Nucleotide base : new Nucleotide[] { Nucleotide.A, Nucleotide.C, Nucleotide.T, Nucleotide.G }) {
            /* load base read error list */
            ArrayList<Double> readErrorList = parseToDoubleArray.of(reader.nextLine());
            /* set the mapping error probability to 1e-6 */
            ArrayList<Double> mappingErrorList = new ArrayList<>();
            mappingErrorList.addAll(IntStream.range(0, readErrorList.size()).mapToDouble(i -> 1e-6).boxed().collect(Collectors.toList()));
            /* contruct the BaseQuality list */
            List<BayesianHetPulldownCalculator.BaseQuality> baseQualityList = new ArrayList<>();
            baseQualityList.addAll(IntStream.range(0, readErrorList.size()).mapToObj(i -> new BayesianHetPulldownCalculator.BaseQuality(readErrorList.get(i), mappingErrorList.get(i))).collect(Collectors.toList()));
            baseQualities.put(base, baseQualityList);
        }
        fakePileupBaseQualities.add(baseQualities);
        fakePileupHetLogLikelihoodArray.add(parseToDouble.of(reader.nextLine()));
        fakePileupHomLogLikelihoodArray.add(parseToDouble.of(reader.nextLine()));
    }
    numPileupEntries = fakePileupBaseQualities.size();
}

Example 7 with Nucleotide

use of org.broadinstitute.hellbender.utils.Nucleotide in project gatk by broadinstitute.

the class BayesianHetPulldownCalculatorUnitTest method inputTestGetHomLogLikelihood.

@DataProvider(name = "inputTestGetHomLogLikelihood")
public Object[][] inputTestGetHomLogLikelihood() {
    Nucleotide alleleRef = Nucleotide.A;
    Nucleotide alleleAlt = Nucleotide.T;
    double homRefPrior = 0.5;
    Object[][] out = new Object[numPileupEntries][];
    for (int i = 0; i < numPileupEntries; i++) {
        out[i] = new Object[] { fakePileupBaseQualities.get(i), alleleRef, alleleAlt, homRefPrior, fakePileupHomLogLikelihoodArray.get(i) };
    }
    return out;
}

Example 8 with Nucleotide

use of org.broadinstitute.hellbender.utils.Nucleotide in project gatk-protected by broadinstitute.

the class BayesianHetPulldownCalculatorUnitTest method loadPileup.

/**
     * load the fake fileup from file
     *
     * @throws IOException
     */
@BeforeClass
public void loadPileup() throws IOException {
    /* load fake pileup and likelihoods from disk */
    StringMapper<String> stringStripper = s -> s.substring(s.indexOf(':') + 1).replaceAll("\\s+", "");
    StringMapper<Double> parseToDouble = s -> Double.parseDouble(stringStripper.of(s));
    StringMapper<ArrayList<Double>> parseToDoubleArray = s -> {
        String[] tokenizedLine = stringStripper.of(s).split(",");
        ArrayList<Double> errorList = new ArrayList<>();
        if (tokenizedLine.length >= 1 && !tokenizedLine[0].equals("")) {
            errorList.addAll(Arrays.asList(tokenizedLine).stream().map(Double::parseDouble).collect(Collectors.toList()));
        }
        return errorList;
    };
    Scanner reader = new Scanner(new FileInputStream(FAKE_PILEUP_FILE));
    while (reader.hasNextLine()) {
        Map<Nucleotide, List<BayesianHetPulldownCalculator.BaseQuality>> baseQualities = new HashMap<>();
        for (Nucleotide base : new Nucleotide[] { Nucleotide.A, Nucleotide.C, Nucleotide.T, Nucleotide.G }) {
            /* load base read error list */
            ArrayList<Double> readErrorList = parseToDoubleArray.of(reader.nextLine());
            /* set the mapping error probability to 1e-6 */
            ArrayList<Double> mappingErrorList = new ArrayList<>();
            mappingErrorList.addAll(IntStream.range(0, readErrorList.size()).mapToDouble(i -> 1e-6).boxed().collect(Collectors.toList()));
            /* contruct the BaseQuality list */
            List<BayesianHetPulldownCalculator.BaseQuality> baseQualityList = new ArrayList<>();
            baseQualityList.addAll(IntStream.range(0, readErrorList.size()).mapToObj(i -> new BayesianHetPulldownCalculator.BaseQuality(readErrorList.get(i), mappingErrorList.get(i))).collect(Collectors.toList()));
            baseQualities.put(base, baseQualityList);
        }
        fakePileupBaseQualities.add(baseQualities);
        fakePileupHetLogLikelihoodArray.add(parseToDouble.of(reader.nextLine()));
        fakePileupHomLogLikelihoodArray.add(parseToDouble.of(reader.nextLine()));
    }
    numPileupEntries = fakePileupBaseQualities.size();
}

Example 9 with Nucleotide

use of org.broadinstitute.hellbender.utils.Nucleotide in project gatk-protected by broadinstitute.

the class BayesianHetPulldownCalculatorUnitTest method inputTestGetHetLogLikelihood.

@DataProvider(name = "inputTestGetHetLogLikelihood")
public Object[][] inputTestGetHetLogLikelihood() {
    Nucleotide alleleRef = Nucleotide.A;
    Nucleotide alleleAlt = Nucleotide.T;
    Object[][] out = new Object[numPileupEntries][];
    for (int i = 0; i < numPileupEntries; i++) {
        out[i] = new Object[] { fakePileupBaseQualities.get(i), alleleRef, alleleAlt, fakePileupHetLogLikelihoodArray.get(i) };
    }
    return out;
}

Example 10 with Nucleotide

use of org.broadinstitute.hellbender.utils.Nucleotide in project gatk-protected by broadinstitute.

the class AllelicCountReader method createAllelicCountWithVerbosity.

static AllelicCount createAllelicCountWithVerbosity(final DataLine dataLine, final AllelicCountTableColumn.AllelicCountTableVerbosity verbosity) {
    /* mandatory (basic) fields */
    final int position = dataLine.getInt(AllelicCountTableColumn.POSITION);
    final SimpleInterval interval = new SimpleInterval(dataLine.get(AllelicCountTableColumn.CONTIG), position, position);
    final int refReadCount = dataLine.getInt(AllelicCountTableColumn.REF_COUNT);
    final int altReadCount = dataLine.getInt(AllelicCountTableColumn.ALT_COUNT);
    if (verbosity == AllelicCountTableColumn.AllelicCountTableVerbosity.BASIC) {
        return new AllelicCount(interval, refReadCount, altReadCount);
    } else {
        final Nucleotide refNucleotide = Nucleotide.valueOf(dataLine.get(AllelicCountTableColumn.REF_NUCLEOTIDE.name()).getBytes()[0]);
        final Nucleotide altNucleotide = Nucleotide.valueOf(dataLine.get(AllelicCountTableColumn.ALT_NUCLEOTIDE.name()).getBytes()[0]);
        final int readDepth = dataLine.getInt(AllelicCountTableColumn.READ_DEPTH.name());
        if (verbosity == AllelicCountTableColumn.AllelicCountTableVerbosity.INTERMEDIATE) {
            return new AllelicCount(interval, refReadCount, altReadCount, refNucleotide, altNucleotide, readDepth);
        } else {
            /* verbosity == AllelicCountTableVerbosity.FULL */
            final double hetLogOdds = dataLine.getDouble(AllelicCountTableColumn.HET_LOG_ODDS.name());
            return new AllelicCount(interval, refReadCount, altReadCount, refNucleotide, altNucleotide, readDepth, hetLogOdds);
        }
    }
}