Examples of org.broadinstitute.gatk.utils.sam.GATKSAMRecord

Package org.broadinstitute.gatk.utils.sam

Examples of org.broadinstitute.gatk.utils.sam.GATKSAMRecord

org.broadinstitute.gatk.utils.sam.GATKSAMRecord
@author ebanks, depristoGATKSAMRecord this class extends the samtools BAMRecord class (and SAMRecord) and caches important (and oft-accessed) data that's not already cached by the SAMRecord class IMPORTANT NOTE: Because ReadGroups are not set through the SAMRecord, if they are ever modified externally then one must also invoke the setReadGroup() method here to ensure that the cache is kept up-to-date. WARNING -- GATKSAMRecords cache several values (that are expensive to compute) that depending on the inferred insert size and alignment starts and stops of this read and its mate. Changing these values in any way will invalidate the cached value. However, we do not monitor those setter functions, so modifying a GATKSAMRecord in any way may result in stale cached values.

        public byte[] getRefBases() { return ref.getBytes(); }
        public int getRefLength() { return ref.length(); }


        public GATKSAMRecord makeRead(final int start, final int length) {
            final byte[] quals = Utils.dupBytes((byte)30, length);
            final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "read " + readCounter++, 0, start + getStart(), ref.substring(start, start + length).getBytes(), quals, length + "M");
            read.setReadGroup(rg);
            return read;
        }

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    }


    @Test
    public void testUnmappedReadsDoNotFail() {
        // create an unmapped read
        final GATKSAMRecord read = new GATKSAMRecord(ArtificialSAMUtils.createArtificialSamHeader());
        read.setReadName("foo");
        read.setReferenceName("*");
        read.setAlignmentStart(100);
        read.setCigarString("*");
        read.setReadUnmappedFlag(true);


        // try to add it to the manager
        final OverhangFixingManager manager = new OverhangFixingManager(null, null, null, 100, 1, 30, false);
        manager.addRead(read); // we just want to make sure that the following call does not fail
        Assert.assertTrue(true);

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        final byte[] quals = new byte[READ_LENGTH];


        Arrays.fill(quals,(byte)30);


        for (int k=0; k < NUM_GOOD_READS; k++) {
            final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(bases.getBytes(), quals,READ_LENGTH+"M");
            finalizedReadList.add(read);
        }


        ReadErrorCorrector readErrorCorrector = new ReadErrorCorrector(kmerLengthForReadErrorCorrection,(byte)6,10, debug,refChunkHard.getBytes());
        readErrorCorrector.addReadsToKmers(finalizedReadList);

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        Arrays.fill(quals,(byte)30);


        for (int k=0; k < NUM_GOOD_READS; k++) {
            final byte[] bases = Arrays.copyOfRange(refChunk.getBytes(),offset,offset+READ_LENGTH);
            final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(bases, quals,READ_LENGTH+"M");
            finalizedReadList.add(read);
            offset++;
            if (offset >= refChunk.length()-READ_LENGTH)
                offset = 0;
        }
        offset = 2;
        // coverage profile is now perfectly triangular with "good" bases. Inject now bad bases with errors in them.
        for (int k=0; k < NUM_BAD_READS; k++) {
            final byte[] bases = finalizedReadList.get(k).getReadBases().clone();
            bases[offset] = 'N';
            final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(bases, quals, READ_LENGTH + "M");
            finalizedReadList.add(read);
            offset += 7;
            if (offset >= READ_LENGTH)
                offset = 4; // just some randomly circulating offset for error position
        }

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                final int aIndex = subject.alleleIndex(allele);
                Assert.assertEquals(aIndex >= 0,alleleWithLikelihoodsSet.contains(allele));
                Assert.assertTrue(aIndex < alleleCount);
                if (aIndex == -1) continue;
                for (int r = 0; r < sampleReadCount; r++) {
                    final GATKSAMRecord read = sampleToReads.get(sample).get(r);
                    final int rIndex = subject.readIndex(sIndex,read);
                    final int rIndex2 = sampleLikelihoods.readIndex(read);
                    Assert.assertEquals(rIndex,rIndex2);
                    Assert.assertEquals(rIndex >= 0,readsWithLikelihoodsSet.contains(read));
                    Assert.assertTrue(rIndex < sampleReadCount);

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            final ReadAnchoring anchoring = new ReadAnchoring(r,haplotypeGraph);
            if (anchoring.isAnchoredSomewhere())
                continue;
            final int start = anchoring.leftAnchorIndex;
            final int end = anchoring.rightAnchorIndex + haplotypeGraph.getKmerSize();
            final GATKSAMRecord clipped = new ClippedGATKSAMRecord(r, start, end);
            result.put(r, clipped);
        }
        return result;
    }

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                addBaseErrors(readBases, phredScaledErrorRate);


            byte[] readQuals = new byte[readBases.length];
            Arrays.fill(readQuals, (byte)phredScaledErrorRate);


            GATKSAMRecord read = new GATKSAMRecord(header);
            read.setBaseQualities(readQuals);
            read.setReadBases(readBases);
            read.setReadName(artificialReadName+readCounter++);


            boolean isBeforeDeletion = alleleLength<refAlleleLength;
            boolean isBeforeInsertion = alleleLength>refAlleleLength;


            int eventLength = alleleLength - refAlleleLength;
            if (isReference)
                read.setCigarString(readBases.length + "M");
            else {
                if (isBeforeDeletion || isBeforeInsertion)
                    read.setCigarString((readOffset+1)+"M"+ Math.abs(eventLength) + (isBeforeDeletion?"D":"I") +
                            (readBases.length-readOffset)+"M");
                else // SNP case
                    read.setCigarString(readBases.length+"M");
            }


            read.setReadPairedFlag(false);
            read.setAlignmentStart(readStart);
            read.setMappingQuality(artificialMappingQuality);
            read.setReferenceName(loc.getContig());
            read.setReadNegativeStrandFlag(false);
            read.setReadGroup(sampleRG(sample));


            pileupElements.add(LocusIteratorByState.createPileupForReadAndOffset(read, readOffset));
        }


        return pileupElements;

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        for ( final Map.Entry<GATKSAMRecord, Map<Allele,Double>> el : likelihoodMap.getLikelihoodReadMap().entrySet() ) {
            final MostLikelyAllele a = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue());
            if ( ! a.isInformative() )
                continue; // read is non-informative


            final GATKSAMRecord read = el.getKey();
            if ( isUsableRead(read, refLoc) ) {
                final Double value = getElementForRead(read, refLoc, a);
                if ( value == null )
                    continue;

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        int nextIndex = 0;
        for (final PileupElement p : pileup) {
            final byte qual = p.isDeletion() ? REF_MODEL_DELETION_QUAL : p.getQual();
            if (!p.isDeletion() && qual <= minBaseQual)
                continue;
            final GATKSAMRecord read = p.getRead();
            reads.add(read);
            final boolean isAlt = p.getBase() != refBase || p.isDeletion() || p.isBeforeDeletionStart()
                    || p.isAfterDeletionEnd() || p.isBeforeInsertion() || p.isAfterInsertion() || p.isNextToSoftClip();
            final int bestAllele;
            final int worstAllele;

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     * @return an integer >= 0
     */
    protected final int calcNIndelInformativeReads(final ReadBackedPileup pileup, final int pileupOffsetIntoRef, final byte[] ref, final int maxIndelSize) {
        int nInformative = 0;
        for ( final PileupElement p : pileup ) {
            final GATKSAMRecord read = p.getRead();
            final int offset = p.getOffset();


            // doesn't count as evidence
            if ( p.isBeforeDeletionStart() || p.isBeforeInsertion() || p.isDeletion() )
                continue;


            // todo -- this code really should handle CIGARs directly instead of relying on the above tests
            if ( isReadInformativeAboutIndelsOfSize(read.getReadBases(), read.getBaseQualities(), offset, ref, pileupOffsetIntoRef, maxIndelSize) ) {
                nInformative++;
                if( nInformative > MAX_N_INDEL_INFORMATIVE_READS ) {
                    return MAX_N_INDEL_INFORMATIVE_READS;
                }
            }

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