Examples with GATKException org.broadinstitute.hellbender.exceptions.GATKException used on opensource projects

Example 66 with GATKException

use of org.broadinstitute.hellbender.exceptions.GATKException in project gatk by broadinstitute.

the class HDF5PCACoveragePoN method readMatrixAndCheckDimensions.

/**
     * Reads a matrix from the underlying PoN file and check its dimensions.
     * @param fullPath the target data-set full path within the HDF5 file.
     * @param expectedRowCount a predicate that returns true iff its argument is an expected number of rows.
     * @param expectedColumnCount a predicate that returns true iff its argument is an expected number of columns.
     * @return GATKException if the result matrix dimensions do not match the expectations or
     *  any other cause as described in {@link #readMatrix(String)}.
     */
private RealMatrix readMatrixAndCheckDimensions(final String fullPath, final IntPredicate expectedRowCount, final IntPredicate expectedColumnCount) {
    final RealMatrix result = readMatrix(fullPath);
    if (expectedRowCount.test(result.getRowDimension()) && expectedColumnCount.test(result.getColumnDimension())) {
        return result;
    }
    final RealMatrix transpose = result.transpose();
    if (!expectedRowCount.test(transpose.getRowDimension())) {
        throw new GATKException(String.format("wrong number of rows in '%s' matrix from file '%s': %d", fullPath, file.getFile(), result.getRowDimension()));
    }
    if (!expectedColumnCount.test(transpose.getColumnDimension())) {
        throw new GATKException(String.format("wrong number of columns in '%s' from file '%s': %d", fullPath, file.getFile(), result.getColumnDimension()));
    }
    return transpose;
}

Example 67 with GATKException

use of org.broadinstitute.hellbender.exceptions.GATKException in project gatk by broadinstitute.

the class GATKReportTable method concat.

/**
     * Concatenates the rows from the table to this one
     *
     * @param table another GATK table
     */
public void concat(final GATKReportTable table) {
    if (!isSameFormat(table))
        throw new GATKException("Error trying to concatenate tables with different formats");
    // add the data
    underlyingData.addAll(table.underlyingData);
    // update the row index map
    final int currentNumRows = getNumRows();
    for (Map.Entry<Object, Integer> entry : table.rowIdToIndex.entrySet()) rowIdToIndex.put(entry.getKey(), entry.getValue() + currentNumRows);
}

Example 68 with GATKException

use of org.broadinstitute.hellbender.exceptions.GATKException in project gatk by broadinstitute.

the class PedReader method parse.

public final List<Sample> parse(Reader reader, EnumSet<MissingPedField> missingFields, SampleDB sampleDB) {
    // Determine field position ordinals
    final int familyPos = missingFields.contains(MissingPedField.NO_FAMILY_ID) ? -1 : 0;
    final int samplePos = familyPos + 1;
    final int paternalPos = missingFields.contains(MissingPedField.NO_PARENTS) ? -1 : samplePos + 1;
    final int maternalPos = missingFields.contains(MissingPedField.NO_PARENTS) ? -1 : paternalPos + 1;
    final int sexPos = missingFields.contains(MissingPedField.NO_SEX) ? -1 : Math.max(maternalPos, samplePos) + 1;
    final int phenotypePos = missingFields.contains(MissingPedField.NO_PHENOTYPE) ? -1 : Math.max(sexPos, Math.max(maternalPos, samplePos)) + 1;
    final int nExpectedFields = IntStream.of(samplePos, paternalPos, maternalPos, sexPos, phenotypePos).max().getAsInt() + 1;
    List<String> lines;
    try (final XReadLines sourceReader = new XReadLines(reader, false, commentMarker)) {
        lines = sourceReader.readLines();
    } catch (IOException e) {
        throw new UserException.CouldNotReadInputFile("Error reading pedigree input");
    }
    final List<String[]> lineParts = splitLines(reader, lines, nExpectedFields);
    boolean isQT = isQT(lineParts, phenotypePos);
    int lineNo = 1;
    final List<Sample> samples = new ArrayList<>(lineParts.size());
    for (final String[] parts : lineParts) {
        String individualID = parts[samplePos];
        String familyID = familyPos == -1 ? null : maybeMissing(parts[familyPos]);
        String paternalID = paternalPos == -1 ? null : maybeMissing(parts[paternalPos]);
        String maternalID = maternalPos == -1 ? null : maybeMissing(parts[maternalPos]);
        Sex sex = determineSex(parts, sexPos);
        Affection affection = Affection.UNKNOWN;
        String quantitativePhenotype = null;
        if (phenotypePos != -1) {
            if (isQT) {
                if (parts[phenotypePos].equals(MISSING_VALUE1)) {
                    affection = Affection.UNKNOWN;
                } else {
                    affection = Affection.OTHER;
                    quantitativePhenotype = parts[phenotypePos];
                }
            } else {
                switch(parts[phenotypePos]) {
                    case MISSING_VALUE1:
                        affection = Affection.UNKNOWN;
                        break;
                    case MISSING_VALUE2:
                        affection = Affection.UNKNOWN;
                        break;
                    case PHENOTYPE_UNAFFECTED:
                        affection = Affection.UNAFFECTED;
                        break;
                    case PHENOTYPE_AFFECTED:
                        affection = Affection.AFFECTED;
                        break;
                    default:
                        throw new GATKException("Unexpected phenotype type " + parts[phenotypePos] + " at line " + lineNo);
                }
            }
        }
        final Sample s = new Sample(individualID, familyID, paternalID, maternalID, sex, affection);
        samples.add(s);
        sampleDB.addSample(s);
        lineNo++;
    }
    for (final Sample sample : new ArrayList<>(samples)) {
        final Sample dad = maybeAddImplicitSample(sampleDB, sample.getPaternalID(), sample.getFamilyID(), Sex.MALE);
        if (dad != null) {
            samples.add(dad);
        }
        final Sample mom = maybeAddImplicitSample(sampleDB, sample.getMaternalID(), sample.getFamilyID(), Sex.FEMALE);
        if (mom != null) {
            samples.add(mom);
        }
    }
    return samples;
}

Example 69 with GATKException

use of org.broadinstitute.hellbender.exceptions.GATKException in project gatk by broadinstitute.

the class RecalUtils method generateCsv.

/**
     * Prints out a collection of reports into a file in Csv format in a way
     * that can be used by R scripts (such as the plot generator script).
     * <p/>
     * The set of covariates is take as the minimum common set from all reports.
     *
     * @param out the output file. It will be overridden.
     * @param reports map where keys are the unique 'mode' (ORIGINAL, RECALIBRATED, ...)
     *                of each report and the corresponding value the report itself.
     * @throws FileNotFoundException if <code>out</code> could not be created anew.
     */
public static void generateCsv(final File out, final Map<String, RecalibrationReport> reports) throws FileNotFoundException {
    if (reports.isEmpty()) {
        throw new GATKException("no reports");
    }
    final RecalibrationReport firstReport = reports.values().iterator().next();
    final StandardCovariateList covariates = firstReport.getCovariates();
    writeCsv(out, reports, covariates);
}

Example 70 with GATKException

use of org.broadinstitute.hellbender.exceptions.GATKException in project gatk by broadinstitute.

the class MultiHitAlignedReadIterator method nextMaybeEmpty.

private HitsForInsert nextMaybeEmpty() {
    Utils.validate(peekIterator.hasNext(), "iterator has no next");
    final String readName = peekIterator.peek().getReadName();
    final HitsForInsert hits = new HitsForInsert();
    Boolean isPaired = null;
    // Accumulate the alignments matching readName.
    do {
        final SAMRecord rec = peekIterator.next();
        replaceHardWithSoftClips(rec);
        // if the aligned input needs to be sorted.
        if (peekIterator.hasNext() && queryNameComparator.fileOrderCompare(rec, peekIterator.peek()) > 0) {
            throw new IllegalStateException("Underlying iterator is not queryname sorted: " + rec + " > " + peekIterator.peek());
        }
        if (isPaired == null) {
            isPaired = rec.getReadPairedFlag();
        } else if (isPaired != rec.getReadPairedFlag()) {
            throw new GATKException("Got a mix of paired and unpaired alignments for read " + readName);
        }
        // been determined, and then re-added into the process later
        if (!rec.getReadPairedFlag() || rec.getFirstOfPairFlag()) {
            if (rec.getSupplementaryAlignmentFlag()) {
                hits.addSupplementalFirstOfPairOrFragment(rec);
            } else {
                hits.addFirstOfPairOrFragment(rec);
            }
        } else if (rec.getSecondOfPairFlag()) {
            if (rec.getSupplementaryAlignmentFlag()) {
                hits.addSupplementalSecondOfPair(rec);
            } else {
                hits.addSecondOfPair(rec);
            }
        } else
            throw new GATKException("Read is marked as pair but neither first or second: " + readName);
    } while (peekIterator.hasNext() && peekIterator.peek().getReadName().equals(readName));
    // If there is no more than one alignment for each end, no need to do any coordination.
    if (hits.numHits() <= 1) {
        // No HI tags needed if only a single hit
        if (hits.getFirstOfPair(0) != null) {
            hits.getFirstOfPair(0).setAttribute(SAMTag.HI.name(), null);
            hits.getFirstOfPair(0).setNotPrimaryAlignmentFlag(false);
        }
        if (hits.getSecondOfPair(0) != null) {
            hits.getSecondOfPair(0).setAttribute(SAMTag.HI.name(), null);
            hits.getSecondOfPair(0).setNotPrimaryAlignmentFlag(false);
        }
    } else {
        primaryAlignmentSelectionStrategy.pickPrimaryAlignment(hits);
    }
    // Used to check that alignments for first and second were correlated, but this is no longer required.
    return hits;
}