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

Example 56 with UserException

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

the class RnaSeqMetricsCollector method makeOverlapDetector.

public static OverlapDetector<Interval> makeOverlapDetector(final File samFile, final SAMFileHeader header, final File ribosomalIntervalsFile) {
    OverlapDetector<Interval> ribosomalSequenceOverlapDetector = new OverlapDetector<>(0, 0);
    if (ribosomalIntervalsFile != null) {
        final IntervalList ribosomalIntervals = IntervalList.fromFile(ribosomalIntervalsFile);
        try {
            SequenceUtil.assertSequenceDictionariesEqual(header.getSequenceDictionary(), ribosomalIntervals.getHeader().getSequenceDictionary());
        } catch (SequenceUtil.SequenceListsDifferException e) {
            throw new UserException("Sequence dictionaries differ in " + samFile.getAbsolutePath() + " and " + ribosomalIntervalsFile.getAbsolutePath(), e);
        }
        final IntervalList uniquedRibosomalIntervals = ribosomalIntervals.uniqued();
        final List<Interval> intervals = uniquedRibosomalIntervals.getIntervals();
        ribosomalSequenceOverlapDetector.addAll(intervals, intervals);
    }
    return ribosomalSequenceOverlapDetector;
}

Example 57 with UserException

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

the class SamToFastq method doWork.

@Override
protected Object doWork() {
    IOUtil.assertFileIsReadable(INPUT);
    final SamReader reader = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(INPUT);
    final Map<String, SAMRecord> firstSeenMates = new HashMap<>();
    final FastqWriterFactory factory = new FastqWriterFactory();
    factory.setCreateMd5(CREATE_MD5_FILE);
    final Map<SAMReadGroupRecord, FastqWriters> writers = generateWriters(reader.getFileHeader().getReadGroups(), factory);
    final ProgressLogger progress = new ProgressLogger(logger);
    for (final SAMRecord currentRecord : reader) {
        if (currentRecord.isSecondaryOrSupplementary() && !INCLUDE_NON_PRIMARY_ALIGNMENTS)
            continue;
        // Skip non-PF reads as necessary
        if (currentRecord.getReadFailsVendorQualityCheckFlag() && !INCLUDE_NON_PF_READS)
            continue;
        final FastqWriters fq = writers.get(currentRecord.getReadGroup());
        if (currentRecord.getReadPairedFlag()) {
            final String currentReadName = currentRecord.getReadName();
            final SAMRecord firstRecord = firstSeenMates.remove(currentReadName);
            if (firstRecord == null) {
                firstSeenMates.put(currentReadName, currentRecord);
            } else {
                assertPairedMates(firstRecord, currentRecord);
                final SAMRecord read1 = currentRecord.getFirstOfPairFlag() ? currentRecord : firstRecord;
                final SAMRecord read2 = currentRecord.getFirstOfPairFlag() ? firstRecord : currentRecord;
                writeRecord(read1, 1, fq.getFirstOfPair(), READ1_TRIM, READ1_MAX_BASES_TO_WRITE);
                final FastqWriter secondOfPairWriter = fq.getSecondOfPair();
                if (secondOfPairWriter == null) {
                    throw new UserException("Input contains paired reads but no SECOND_END_FASTQ specified.");
                }
                writeRecord(read2, 2, secondOfPairWriter, READ2_TRIM, READ2_MAX_BASES_TO_WRITE);
            }
        } else {
            writeRecord(currentRecord, null, fq.getUnpaired(), READ1_TRIM, READ1_MAX_BASES_TO_WRITE);
        }
        progress.record(currentRecord);
    }
    CloserUtil.close(reader);
    // Close all the fastq writers being careful to close each one only once!
    for (final FastqWriters writerMapping : new HashSet<>(writers.values())) {
        writerMapping.closeAll();
    }
    if (!firstSeenMates.isEmpty()) {
        SAMUtils.processValidationError(new SAMValidationError(SAMValidationError.Type.MATE_NOT_FOUND, "Found " + firstSeenMates.size() + " unpaired mates", null), VALIDATION_STRINGENCY);
    }
    return null;
}

Example 58 with UserException

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

the class SamToFastq method makeReadGroupFile.

private File makeReadGroupFile(final SAMReadGroupRecord readGroup, final String preExtSuffix) {
    String fileName = null;
    if (RG_TAG.equalsIgnoreCase("PU")) {
        fileName = readGroup.getPlatformUnit();
    } else if (RG_TAG.equalsIgnoreCase("ID")) {
        fileName = readGroup.getReadGroupId();
    }
    if (fileName == null) {
        throw new UserException("The selected RG_TAG: " + RG_TAG + " is not present in the bam header.");
    }
    fileName = IOUtil.makeFileNameSafe(fileName);
    if (preExtSuffix != null)
        fileName += preExtSuffix;
    fileName += ".fastq";
    final File result = (OUTPUT_DIR != null) ? new File(OUTPUT_DIR, fileName) : new File(fileName);
    IOUtil.assertFileIsWritable(result);
    return result;
}

Example 59 with UserException

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

the class CalculateReadGroupChecksum method doWork.

@Override
protected Object doWork() {
    final File output = (OUTPUT == null) ? new File(INPUT.getParentFile(), getOutputFileName(INPUT)) : OUTPUT;
    IOUtil.assertFileIsWritable(output);
    final String hashText = SAMUtils.calculateReadGroupRecordChecksum(INPUT, REFERENCE_SEQUENCE);
    try (final FileWriter outputWriter = new FileWriter(output)) {
        outputWriter.write(hashText);
    } catch (final IOException ioe) {
        throw new UserException("Could not write the computed hash (" + hashText + ") to the output file: " + ioe.getMessage(), ioe);
    }
    return null;
}

Example 60 with UserException

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

the class FastqToSam method getBaseName.

/** Returns read baseName and asserts correct pair read name format:
     * <ul>
     * <li> Paired reads must either have the exact same read names or they must contain at least one "/"
     * <li> and the First pair read name must end with "/1" and second pair read name ends with "/2"
     * <li> The baseName (read name part before the /) must be the same for both read names
     * <li> If the read names are exactly the same but end in "/2" or "/1" then an exception will be thrown
     * </ul>
     */
String getBaseName(final String readName1, final String readName2, final FastqReader freader1, final FastqReader freader2) {
    String[] toks = getReadNameTokens(readName1, 1, freader1);
    final String baseName1 = toks[0];
    final String num1 = toks[1];
    toks = getReadNameTokens(readName2, 2, freader2);
    final String baseName2 = toks[0];
    final String num2 = toks[1];
    if (!baseName1.equals(baseName2)) {
        throw new UserException(String.format("In paired mode, read name 1 (%s) does not match read name 2 (%s)", baseName1, baseName2));
    }
    final boolean num1Blank = StringUtil.isBlank(num1);
    final boolean num2Blank = StringUtil.isBlank(num2);
    if (num1Blank || num2Blank) {
        if (//num1 != blank and num2   == blank
        !num1Blank)
            //num1 != blank and num2   == blank
            throw new UserException(error(freader1, "Pair 1 number is missing (" + readName1 + "). Both pair numbers must be present or neither."));
        else //num1 == blank and num =2 != blank
        if (!num2Blank)
            throw new UserException(error(freader2, "Pair 2 number is missing (" + readName2 + "). Both pair numbers must be present or neither."));
    } else {
        if (!num1.equals("1"))
            throw new UserException(error(freader1, "Pair 1 number must be 1 (" + readName1 + ")"));
        if (!num2.equals("2"))
            throw new UserException(error(freader2, "Pair 2 number must be 2 (" + readName2 + ")"));
    }
    return baseName1;
}