Examples with OverlapDetector htsjdk.samtools.util.OverlapDetector used on opensource projects

Example 1 with OverlapDetector

use of htsjdk.samtools.util.OverlapDetector in project gatk by broadinstitute.

the class RefFlatReader method load.

OverlapDetector<Gene> load() {
    final OverlapDetector<Gene> overlapDetector = new OverlapDetector<>(0, 0);
    final int expectedColumns = RefFlatColumns.values().length;
    final TabbedTextFileWithHeaderParser parser = new TabbedTextFileWithHeaderParser(refFlatFile, RefFlatColumnLabels);
    final Map<String, List<TabbedTextFileWithHeaderParser.Row>> refFlatLinesByGene = new LinkedHashMap<>();
    for (final TabbedTextFileWithHeaderParser.Row row : parser) {
        // getCurrentLineNumber returns the number of the next line
        final int lineNumber = parser.getCurrentLineNumber();
        if (row.getFields().length != expectedColumns) {
            throw new GeneAnnotationException("Wrong number of fields in refFlat file " + refFlatFile + " at line " + lineNumber);
        }
        final String geneName = row.getField(RefFlatColumns.GENE_NAME.name());
        final String transcriptName = row.getField(RefFlatColumns.TRANSCRIPT_NAME.name());
        final String transcriptDescription = geneName + ":" + transcriptName;
        final String chromosome = row.getField(RefFlatColumns.CHROMOSOME.name());
        if (!isSequenceRecognized(chromosome)) {
            LOG.debug("Skipping " + transcriptDescription + " due to unrecognized sequence " + chromosome);
        } else {
            List<TabbedTextFileWithHeaderParser.Row> transcriptLines = refFlatLinesByGene.get(geneName);
            if (transcriptLines == null) {
                transcriptLines = new ArrayList<>();
                refFlatLinesByGene.put(geneName, transcriptLines);
            }
            transcriptLines.add(row);
        }
    }
    int longestInterval = 0;
    int numIntervalsOver1MB = 0;
    for (final List<TabbedTextFileWithHeaderParser.Row> transcriptLines : refFlatLinesByGene.values()) {
        try {
            final Gene gene = makeGeneFromRefFlatLines(transcriptLines);
            overlapDetector.addLhs(gene, gene);
            if (gene.length() > longestInterval)
                longestInterval = gene.length();
            if (gene.length() > 1000000)
                ++numIntervalsOver1MB;
        } catch (Exception e) {
            LOG.debug(e.getMessage() + " -- skipping");
        }
    }
    LOG.debug("Longest gene: " + longestInterval + "; number of genes > 1MB: " + numIntervalsOver1MB);
    return overlapDetector;
}

Example 2 with OverlapDetector

use of htsjdk.samtools.util.OverlapDetector in project gatk-protected by broadinstitute.

the class HaplotypeCallerSpark method createReadShards.

/**
     * Create an RDD of {@link Shard} from an RDD of {@link GATKRead}
     * @param shardBoundariesBroadcast  broadcast of an {@link OverlapDetector} loaded with the intervals that should be used for creating ReadShards
     * @param reads Rdd of {@link GATKRead}
     * @return a Rdd of reads grouped into potentially overlapping shards
     */
private static JavaRDD<Shard<GATKRead>> createReadShards(final Broadcast<OverlapDetector<ShardBoundary>> shardBoundariesBroadcast, final JavaRDD<GATKRead> reads) {
    final JavaPairRDD<ShardBoundary, GATKRead> paired = reads.flatMapToPair(read -> {
        final Collection<ShardBoundary> overlappingShards = shardBoundariesBroadcast.value().getOverlaps(read);
        return overlappingShards.stream().map(key -> new Tuple2<>(key, read)).iterator();
    });
    final JavaPairRDD<ShardBoundary, Iterable<GATKRead>> shardsWithReads = paired.groupByKey();
    return shardsWithReads.map(shard -> new SparkReadShard(shard._1(), shard._2()));
}

Example 3 with OverlapDetector

use of htsjdk.samtools.util.OverlapDetector in project gatk by broadinstitute.

the class HaplotypeCallerSpark method createReadShards.

/**
     * Create an RDD of {@link Shard} from an RDD of {@link GATKRead}
     * @param shardBoundariesBroadcast  broadcast of an {@link OverlapDetector} loaded with the intervals that should be used for creating ReadShards
     * @param reads Rdd of {@link GATKRead}
     * @return a Rdd of reads grouped into potentially overlapping shards
     */
private static JavaRDD<Shard<GATKRead>> createReadShards(final Broadcast<OverlapDetector<ShardBoundary>> shardBoundariesBroadcast, final JavaRDD<GATKRead> reads) {
    final JavaPairRDD<ShardBoundary, GATKRead> paired = reads.flatMapToPair(read -> {
        final Collection<ShardBoundary> overlappingShards = shardBoundariesBroadcast.value().getOverlaps(read);
        return overlappingShards.stream().map(key -> new Tuple2<>(key, read)).iterator();
    });
    final JavaPairRDD<ShardBoundary, Iterable<GATKRead>> shardsWithReads = paired.groupByKey();
    return shardsWithReads.map(shard -> new SparkReadShard(shard._1(), shard._2()));
}

Example 4 with OverlapDetector

use of htsjdk.samtools.util.OverlapDetector 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;
}