Examples with SAMFileHeader htsjdk.samtools.SAMFileHeader used on opensource projects

Example 31 with SAMFileHeader

use of htsjdk.samtools.SAMFileHeader in project gatk by broadinstitute.

the class ReadPileupUnitTest method testSplitBySampleMissingReadGroupException.

@Test(expectedExceptions = UserException.ReadMissingReadGroup.class)
public void testSplitBySampleMissingReadGroupException() throws Exception {
    final SAMFileHeader header = ArtificialReadUtils.createArtificialSamHeader(1, 1, 1000);
    final GATKRead read = ArtificialReadUtils.createArtificialRead(header, "nullRG", 0, 1, 10);
    final ReadPileup pileup = new ReadPileup(loc, Collections.singletonList(read), 1);
    final Map<String, ReadPileup> error = pileup.splitBySample(header, null);
}

Example 32 with SAMFileHeader

use of htsjdk.samtools.SAMFileHeader in project gatk by broadinstitute.

the class ReadPileupUnitTest method testInvalidConstructorParametersReadsAndOffsetsLists.

@Test(expectedExceptions = IllegalArgumentException.class)
public void testInvalidConstructorParametersReadsAndOffsetsLists() {
    final SAMFileHeader header = ArtificialReadUtils.createArtificialSamHeader(1, 1, 1000);
    final GATKRead read1 = ArtificialReadUtils.createArtificialRead(header, "read1", 0, 1, 10);
    new ReadPileup(loc, Arrays.asList(read1), Arrays.asList(1, 2, 3));
}

Example 33 with SAMFileHeader

use of htsjdk.samtools.SAMFileHeader in project gatk by broadinstitute.

the class ReadPileupUnitTest method testNullConstructorParametersLoc.

@Test(expectedExceptions = IllegalArgumentException.class)
public void testNullConstructorParametersLoc() {
    final SAMFileHeader header = ArtificialReadUtils.createArtificialSamHeader(1, 1, 1000);
    final GATKRead read1 = ArtificialReadUtils.createArtificialRead(header, "read1", 0, 1, 10);
    new ReadPileup(null, Arrays.asList(read1), Arrays.asList(1));
}

Example 34 with SAMFileHeader

use of htsjdk.samtools.SAMFileHeader in project gatk by broadinstitute.

the class BedToIntervalList method doWork.

@Override
protected Object doWork() {
    IOUtil.assertFileIsReadable(INPUT);
    IOUtil.assertFileIsReadable(SEQUENCE_DICTIONARY);
    IOUtil.assertFileIsWritable(OUTPUT);
    try {
        final SAMFileHeader header = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).getFileHeader(SEQUENCE_DICTIONARY);
        final IntervalList intervalList = new IntervalList(header);
        /**
             * NB: BED is zero-based, but a BEDCodec by default (since it is returns tribble Features) has an offset of one,
             * so it returns 1-based starts.  Ugh.  Set to zero.
             */
        final FeatureReader<BEDFeature> bedReader = AbstractFeatureReader.getFeatureReader(INPUT.getAbsolutePath(), new BEDCodec(BEDCodec.StartOffset.ZERO), false);
        final CloseableTribbleIterator<BEDFeature> iterator = bedReader.iterator();
        final ProgressLogger progressLogger = new ProgressLogger(logger, (int) 1e6);
        while (iterator.hasNext()) {
            final BEDFeature bedFeature = iterator.next();
            final String sequenceName = bedFeature.getContig();
            /**
                 * NB: BED is zero-based, so we need to add one here to make it one-based.  Please observe we set the start
                 * offset to zero when creating the BEDCodec.
                 */
            final int start = bedFeature.getStart() + 1;
            /**
                 * NB: BED is 0-based OPEN (which, for the end is equivalent to 1-based closed).
                 */
            final int end = bedFeature.getEnd();
            // NB: do not use an empty name within an interval
            String name = bedFeature.getName();
            if (name.isEmpty())
                name = null;
            final SAMSequenceRecord sequenceRecord = header.getSequenceDictionary().getSequence(sequenceName);
            // Do some validation
            if (null == sequenceRecord) {
                throw new GATKException(String.format("Sequence '%s' was not found in the sequence dictionary", sequenceName));
            } else if (start < 1) {
                throw new GATKException(String.format("Start on sequence '%s' was less than one: %d", sequenceName, start));
            } else if (sequenceRecord.getSequenceLength() < start) {
                throw new GATKException(String.format("Start on sequence '%s' was past the end: %d < %d", sequenceName, sequenceRecord.getSequenceLength(), start));
            } else if (end < 1) {
                throw new GATKException(String.format("End on sequence '%s' was less than one: %d", sequenceName, end));
            } else if (sequenceRecord.getSequenceLength() < end) {
                throw new GATKException(String.format("End on sequence '%s' was past the end: %d < %d", sequenceName, sequenceRecord.getSequenceLength(), end));
            } else if (end < start - 1) {
                throw new GATKException(String.format("On sequence '%s', end < start-1: %d <= %d", sequenceName, end, start));
            }
            final Interval interval = new Interval(sequenceName, start, end, bedFeature.getStrand() == Strand.POSITIVE, name);
            intervalList.add(interval);
            progressLogger.record(sequenceName, start);
        }
        CloserUtil.close(bedReader);
        // Sort and write the output
        intervalList.uniqued().write(OUTPUT);
    } catch (final IOException e) {
        throw new RuntimeException(e);
    }
    return null;
}

Example 35 with SAMFileHeader

use of htsjdk.samtools.SAMFileHeader in project gatk by broadinstitute.

the class AddCommentsToBam method doWork.

@Override
protected Object doWork() {
    IOUtil.assertFileIsReadable(INPUT);
    IOUtil.assertFileIsWritable(OUTPUT);
    if (INPUT.getAbsolutePath().endsWith(".sam")) {
        throw new UserException("SAM files are not supported");
    }
    final SAMFileHeader samFileHeader = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).getFileHeader(INPUT);
    for (final String comment : COMMENT) {
        if (comment.contains("\n")) {
            throw new UserException("Comments can not contain a new line");
        }
        samFileHeader.addComment(comment);
    }
    BamFileIoUtils.reheaderBamFile(samFileHeader, INPUT, OUTPUT, CREATE_MD5_FILE, CREATE_INDEX);
    return null;
}