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

Example 26 with GATKException

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

the class SVUtils method getRefRDD.

/**
     * Create an RDD from the reference sequences.
     * The reference sequences are transformed into a single, large collection of byte arrays. The collection is then
     * parallelized into an RDD.
     * Each contig that exceeds a size given by REF_RECORD_LEN is broken into a series of REF_RECORD_LEN chunks with a
     * K-1 base overlap between successive chunks. (I.e., for K=63, the last 62 bases in chunk n match the first 62
     * bases in chunk n+1) so that we don't miss any kmers due to the chunking -- we can just kmerize each record
     * independently.
     */
public static JavaRDD<byte[]> getRefRDD(final JavaSparkContext ctx, final int kSize, final ReferenceMultiSource ref, final PipelineOptions options, final SAMSequenceDictionary readsDict, final int ref_record_len, final int ref_records_per_partition) {
    final SAMSequenceDictionary dict = ref.getReferenceSequenceDictionary(readsDict);
    if (dict == null)
        throw new GATKException("No reference dictionary available");
    final int effectiveRecLen = ref_record_len - kSize + 1;
    final List<byte[]> sequenceChunks = new ArrayList<>();
    for (final SAMSequenceRecord rec : dict.getSequences()) {
        final String seqName = rec.getSequenceName();
        final int seqLen = rec.getSequenceLength();
        final SimpleInterval interval = new SimpleInterval(seqName, 1, seqLen);
        try {
            final byte[] bases = ref.getReferenceBases(options, interval).getBases();
            for (int start = 0; start < seqLen; start += effectiveRecLen) {
                sequenceChunks.add(Arrays.copyOfRange(bases, start, Math.min(start + ref_record_len, seqLen)));
            }
        } catch (final IOException ioe) {
            throw new GATKException("Can't get reference sequence bases for " + interval, ioe);
        }
    }
    return ctx.parallelize(sequenceChunks, sequenceChunks.size() / ref_records_per_partition + 1);
}

Example 27 with GATKException

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

the class SVUtils method writeIntervalsFile.

/** Write intervals to a file. */
public static void writeIntervalsFile(final String intervalsFile, final Collection<SVInterval> intervals, final List<String> contigNames) {
    try (final OutputStreamWriter writer = new OutputStreamWriter(new BufferedOutputStream(BucketUtils.createFile(intervalsFile)))) {
        for (final SVInterval interval : intervals) {
            final String seqName = contigNames.get(interval.getContig());
            writer.write(seqName + "\t" + (interval.getStart() + 1) + "\t" + interval.getEnd() + "\n");
        }
    } catch (final IOException ioe) {
        throw new GATKException("Can't write intervals file " + intervalsFile, ioe);
    }
}

Example 28 with GATKException

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

the class BreakpointComplications method initForInsDel.

private void initForInsDel(final ChimericAlignment chimericAlignment, final SimpleInterval leftReferenceInterval, final SimpleInterval rightReferenceInterval, final byte[] contigSeq) {
    final AlignedAssembly.AlignmentInterval firstContigRegion = chimericAlignment.regionWithLowerCoordOnContig;
    final AlignedAssembly.AlignmentInterval secondContigRegion = chimericAlignment.regionWithHigherCoordOnContig;
    final int r1e = leftReferenceInterval.getEnd(), r2b = rightReferenceInterval.getStart(), c1e = firstContigRegion.endInAssembledContig, c2b = secondContigRegion.startInAssembledContig;
    final int // distance-1 between the two regions on reference, denoted as d1 in the comments below
    distBetweenAlignRegionsOnRef = r2b - r1e - 1, // distance-1 between the two regions on contig, denoted as d2 in the comments below
    distBetweenAlignRegionsOnCtg = c2b - c1e - 1;
    if (distBetweenAlignRegionsOnRef > 0) {
        // Deletion:
        resolveComplicationForSimpleDel(contigSeq, firstContigRegion, secondContigRegion, distBetweenAlignRegionsOnCtg);
    } else if (distBetweenAlignRegionsOnRef == 0 && distBetweenAlignRegionsOnCtg > 0) {
        // Insertion: simple insertion, inserted sequence is the sequence [c1e+1, c2b-1] on the contig
        insertedSequenceForwardStrandRep = getInsertedSequence(firstContigRegion, secondContigRegion, contigSeq);
    } else if (distBetweenAlignRegionsOnRef == 0 && distBetweenAlignRegionsOnCtg < 0) {
        // Tandem repeat contraction: reference has two copies but one copy was deleted on the contig; duplicated sequence on reference are [r1e-|d2|+1, r1e] and [r2b, r2b+|d2|-1]
        resolveComplicationForSimpleTandupContraction(leftReferenceInterval, contigSeq, firstContigRegion, secondContigRegion, r1e, c1e, c2b);
    } else if (distBetweenAlignRegionsOnRef < 0 && distBetweenAlignRegionsOnCtg >= 0) {
        // Tandem repeat expansion:   reference bases [r1e-|d1|+1, r1e] to contig bases [c1e-|d1|+1, c1e] and [c2b, c2b+|d1|-1] with optional inserted sequence [c1e+1, c2b-1] in between the two intervals on contig
        resolveComplicationForSimpleTandupExpansion(leftReferenceInterval, contigSeq, firstContigRegion, secondContigRegion, r1e, r2b, distBetweenAlignRegionsOnCtg);
    } else if (distBetweenAlignRegionsOnRef < 0 && distBetweenAlignRegionsOnCtg < 0) {
        // most complicated case, see below
        // Deletion:  duplication with repeat number N1 on reference, N2 on contig, such that N1 <= 2*N2 (and N2<N1);
        // Insertion: duplication with repeat number N1 on reference, N2 on contig, such that N2 <= 2*N1 (and N1<N2);
        // in both cases, the equal sign on the right can be taken only when there's pseudo-homology between starting bases of the duplicated sequence and starting bases of the right flanking region
        // the reference system with a shorter overlap (i.e. with less-negative distance between regions) has a higher repeat number
        resolveComplicationForComplexTandup(contigSeq, firstContigRegion, secondContigRegion, r1e, distBetweenAlignRegionsOnRef, distBetweenAlignRegionsOnCtg);
    } else if (distBetweenAlignRegionsOnRef == 0 && distBetweenAlignRegionsOnCtg == 0) {
        // SNP & indel
        throw new GATKException("Detected badly parsed chimeric alignment for identifying SV breakpoints; no rearrangement found: " + chimericAlignment.onErrStringRep());
    }
    if (insertedSequenceForwardStrandRep.isEmpty()) {
        if (dupSeqRepeatNumOnCtg != dupSeqRepeatNumOnRef && null == dupSeqRepeatUnitRefSpan)
            throw new GATKException("An identified breakpoint pair seem to suggest insertion but the inserted sequence is empty: " + chimericAlignment.onErrStringRep());
    }
}

Example 29 with GATKException

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

the class ReadMetadata method writeMetadata.

public static void writeMetadata(final ReadMetadata readMetadata, final String filename) {
    try (final Writer writer = new BufferedWriter(new OutputStreamWriter(BucketUtils.createFile(filename)))) {
        writer.write("#reads:\t" + readMetadata.getNReads() + "\n");
        writer.write("#partitions:\t" + readMetadata.getNPartitions() + "\n");
        writer.write("max reads/partition:\t" + readMetadata.getMaxReadsInPartition() + "\n");
        writer.write("coverage:\t" + readMetadata.getCoverage() + "\n");
        for (final Map.Entry<String, ReadMetadata.ReadGroupFragmentStatistics> entry : readMetadata.getAllGroupStatistics().entrySet()) {
            final ReadMetadata.ReadGroupFragmentStatistics stats = entry.getValue();
            String name = entry.getKey();
            if (name == null)
                name = NO_GROUP;
            writer.write("group " + name + ":\t" + stats.getMedianFragmentSize() + "-" + stats.getMedianNegativeDeviation() + "+" + stats.getMedianPositiveDeviation() + "\n");
        }
    } catch (final IOException ioe) {
        throw new GATKException("Can't write metadata file.", ioe);
    }
}

Example 30 with GATKException

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

the class ReadEndsForMarkDuplicatesCodec method encode.

@Override
public void encode(final ReadEndsForMarkDuplicates read) {
    try {
        this.out.writeShort(read.score);
        this.out.writeShort(read.libraryId);
        this.out.writeByte(read.orientation);
        this.out.writeInt(read.read1ReferenceIndex);
        this.out.writeInt(read.read1Coordinate);
        this.out.writeLong(read.read1IndexInFile);
        this.out.writeInt(read.read2ReferenceIndex);
        if (read.orientation > ReadEnds.R) {
            this.out.writeInt(read.read2Coordinate);
            this.out.writeLong(read.read2IndexInFile);
        }
        this.out.writeShort(read.readGroup);
        this.out.writeShort(read.tile);
        this.out.writeShort(read.x);
        this.out.writeShort(read.y);
        this.out.writeByte(read.orientationForOpticalDuplicates);
    } catch (final IOException ioe) {
        throw new GATKException("Exception writing ReadEnds to file.", ioe);
    }
}