htsjdk.tribble.bed.BEDCodec Java Examples

@NotNull
public static SortedSetMultimap<String, GenomeRegion> fromBedFile(@NotNull String bedFile) throws IOException {
    final SortedSetMultimap<String, GenomeRegion> regionMap = TreeMultimap.create();

    String prevChromosome = null;
    GenomeRegion prevRegion = null;
    try (final AbstractFeatureReader<BEDFeature, LineIterator> reader = getFeatureReader(bedFile, new BEDCodec(), false)) {
        for (final BEDFeature bedFeature : reader.iterator()) {
            final String chromosome = bedFeature.getContig();
            final long start = bedFeature.getStart();
            final long end = bedFeature.getEnd();

            if (end < start) {
                LOGGER.warn("Invalid genome region found in chromosome {}: start={}, end={}", chromosome, start, end);
            } else {
                final GenomeRegion region = GenomeRegions.create(chromosome, start, end);
                if (prevRegion != null && chromosome.equals(prevChromosome) && prevRegion.end() >= start) {
                    LOGGER.warn("BED file is not sorted, please fix! Current={}, Previous={}", region, prevRegion);
                } else {
                    regionMap.put(chromosome, region);
                    prevChromosome = chromosome;
                    prevRegion = region;
                }
            }
        }
    }

    return regionMap;
}
 

@DataProvider(name = "DetectCorrectFileFormatTestData")
public Object[][] getDetectCorrectFileFormatTestData() {
    return new Object[][] {
            { new File(FEATURE_MANAGER_TEST_DIRECTORY + "minimal_vcf4_file.vcf"), VCFCodec.class },
            { new File(FEATURE_MANAGER_TEST_DIRECTORY + "minimal_vcf3_file.vcf"), VCF3Codec.class },
            { new File(FEATURE_MANAGER_TEST_DIRECTORY + "minimal_bcf_file.bcf"), BCF2Codec.class },
            { new File(FEATURE_MANAGER_TEST_DIRECTORY + "minimal_bed_file.bed"), BEDCodec.class},
            { new File(FEATURE_MANAGER_TEST_DIRECTORY + "minimal_table_file.table"), TableCodec.class}
    };
}
 

public LongISLNDReadAlignmentMap(final Collection<String> readAlignmentMapFiles) throws IOException {
    for (final String readAlignmentMapFileName : readAlignmentMapFiles) {
        log.info("Reading in read map from " + readAlignmentMapFileName);
        final AbstractFeatureReader<BEDFeature, LineIterator> featureReader = AbstractFeatureReader.getFeatureReader(readAlignmentMapFileName, new BEDCodec(), false);
        try {
            final CloseableTribbleIterator<BEDFeature> featureIterator = featureReader.iterator();
            while (featureIterator.hasNext()) {
                final BEDFeature feature = featureIterator.next();
                readAlignmentMap.put(feature.getName(), new LongISLNDReadMapRecord(feature).toReadMapRecord());
            }
        } finally {
            featureReader.close();
        }
    }
}
 

public long getNumNonNBases(final File regions) throws IOException {
    loadAllSequences();
    long count = 0;

    final FeatureCodec<BEDFeature, LineIterator> bedCodec = new BEDCodec(BEDCodec.StartOffset.ONE);
    final LineIterator lineIterator = new AsciiLineReaderIterator(new AsciiLineReader(new FileInputStream(regions)));

    while (lineIterator.hasNext()) {
        final BEDFeature bedFeature = bedCodec.decode(lineIterator);
        count += data.get(new ChrString(bedFeature.getContig())).getNumNonNBases(bedFeature.getStart(), bedFeature.getEnd());
    }
    return count;
}
 

public void loadReplicationOrigins(final String filename)
{
    if(filename.isEmpty())
        return;

    try
    {
        String currentChr = "";
        List<ReplicationOriginRegion> regionList = null;
        int regionCount = 0;

        final AbstractFeatureReader<BEDFeature, LineIterator> reader = getFeatureReader(filename, new BEDCodec(), false);

        for (final BEDFeature bedFeature : reader.iterator())
        {
            final String chromosome = refGenomeChromosome(bedFeature.getContig(), RG_VERSION);

            if (!chromosome.equals(currentChr))
            {
                currentChr = chromosome;
                regionList = mReplicationOrigins.get(chromosome);

                if (regionList == null)
                {
                    regionList = Lists.newArrayList();
                    mReplicationOrigins.put(currentChr, regionList);
                }
            }

            ++regionCount;

            double originValue = Double.parseDouble(bedFeature.getName()) / 100;

            regionList.add(new ReplicationOriginRegion(
                    chromosome,
                    bedFeature.getStart(),
                    bedFeature.getEnd(),
                    originValue));
        }

        LNX_LOGGER.debug("loaded {} replication origins", regionCount);
    }
    catch(IOException exception)
    {
        LNX_LOGGER.error("Failed to read replication origin BED file({})", filename);
    }
}
 

@Override
protected int doWork() {
    IOUtil.assertFileIsReadable(INPUT);
    IOUtil.assertFileIsReadable(SEQUENCE_DICTIONARY);
    IOUtil.assertFileIsWritable(OUTPUT);
    try {
        // create a new header that we will assign the dictionary provided by the SAMSequenceDictionaryExtractor to.
        final SAMFileHeader header = new SAMFileHeader();
        final SAMSequenceDictionary samSequenceDictionary = SAMSequenceDictionaryExtractor.extractDictionary(SEQUENCE_DICTIONARY.toPath());
        header.setSequenceDictionary(samSequenceDictionary);
        // set the sort order to be sorted by coordinate, which is actually done below
        // by getting the .uniqued() intervals list before we write out the file
        header.setSortOrder(SAMFileHeader.SortOrder.coordinate);
        final IntervalList intervalList = new IntervalList(header);

        final FeatureReader<BEDFeature> bedReader = AbstractFeatureReader.getFeatureReader(INPUT.getAbsolutePath(), new BEDCodec(), false);
        final CloseableTribbleIterator<BEDFeature> iterator = bedReader.iterator();
        final ProgressLogger progressLogger = new ProgressLogger(LOG, (int) 1e6);

        while (iterator.hasNext()) {
            final BEDFeature bedFeature = iterator.next();
            final String sequenceName = bedFeature.getContig();
            final int start = bedFeature.getStart();
            final int end = bedFeature.getEnd();
            // NB: do not use an empty name within an interval
            final String name;
            if (bedFeature.getName().isEmpty()) {
                name = null;
            } else {
                name = bedFeature.getName();
            }

            final SAMSequenceRecord sequenceRecord = header.getSequenceDictionary().getSequence(sequenceName);

            // Do some validation
            if (null == sequenceRecord) {
                if (DROP_MISSING_CONTIGS) {
                    LOG.info(String.format("Dropping interval with missing contig: %s:%d-%d", sequenceName, bedFeature.getStart(), bedFeature.getEnd()));
                    missingIntervals++;
                    missingRegion += bedFeature.getEnd() - bedFeature.getStart();
                    continue;
                }
                throw new PicardException(String.format("Sequence '%s' was not found in the sequence dictionary", sequenceName));
            } else if (start < 1) {
                throw new PicardException(String.format("Start on sequence '%s' was less than one: %d", sequenceName, start));
            } else if (sequenceRecord.getSequenceLength() < start) {
                throw new PicardException(String.format("Start on sequence '%s' was past the end: %d < %d", sequenceName, sequenceRecord.getSequenceLength(), start));
            } else if ((end == 0 && start != 1 ) //special case for 0-length interval at the start of a contig
                    || end < 0 ) {
                throw new PicardException(String.format("End on sequence '%s' was less than one: %d", sequenceName, end));
            } else if (sequenceRecord.getSequenceLength() < end) {
                throw new PicardException(String.format("End on sequence '%s' was past the end: %d < %d", sequenceName, sequenceRecord.getSequenceLength(), end));
            } else if (end < start - 1) {
                throw new PicardException(String.format("On sequence '%s', end < start-1: %d <= %d", sequenceName, end, start));
            }

            final boolean isNegativeStrand = bedFeature.getStrand() == Strand.NEGATIVE;
            final Interval interval = new Interval(sequenceName, start, end, isNegativeStrand, name);
            intervalList.add(interval);

            progressLogger.record(sequenceName, start);
        }
        CloserUtil.close(bedReader);

        if (DROP_MISSING_CONTIGS) {
            if (missingRegion == 0) {
                LOG.info("There were no missing regions.");
            } else {
                LOG.warn(String.format("There were %d missing regions with a total of %d bases", missingIntervals, missingRegion));
            }
        }
        // Sort and write the output
        IntervalList out = intervalList;
        if (SORT) {
            out = out.sorted();
        }
        if (UNIQUE) {
            out = out.uniqued();
        }
        out.write(OUTPUT);
        LOG.info(String.format("Wrote %d intervals spanning a total of %d bases", out.getIntervals().size(),out.getBaseCount()));

    } catch (final IOException e) {
        throw new RuntimeException(e);
    }

    return 0;
}