Examples of SWPairwiseAlignment

org.broadinstitute.gatk.utils.smithwaterman.SWPairwiseAlignment
Pairwise discrete smith-waterman alignment * **** IMPORTANT NOTE: **** This class assumes that all bytes come from UPPERCASED chars! * User: asivache Date: Mar 23, 2009 Time: 1:54:54 PM

Examples of org.broadinstitute.gatk.utils.smithwaterman.SWPairwiseAlignment

    }


    private void createAndAddAlternateConsensus(final byte[] read, final Set<Consensus> altConsensesToPopulate, final byte[] reference) {


        // do a pairwise alignment against the reference
         SWPairwiseAlignment swConsensus = new SWPairwiseAlignment(reference, read, swParameters);
         Consensus c = createAlternateConsensus(swConsensus.getAlignmentStart2wrt1(), swConsensus.getCigar(), reference, read);
         if ( c != null )
             altConsensesToPopulate.add(c);
    }

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Examples of org.broadinstitute.gatk.utils.smithwaterman.SWPairwiseAlignment

              int myScore = altAlignment.second;
              if ( myScore == 0 ) {exactMatchesFound++; return; }// read matches perfectly to a known alt consensus - no need to run SW, we already know the answer
         }
         // do a pairwise alignment against the reference
         SWalignmentRuns++;
         SWPairwiseAlignment swConsensus = new SWPairwiseAlignment(reference, read.getReadBases(), swParameters);
         Consensus c = createAlternateConsensus(swConsensus.getAlignmentStart2wrt1(), swConsensus.getCigar(), reference, read.getReadBases());
         if ( c != null ) {
             altConsensesToPopulate.add(c);
             SWalignmentSuccess++;
         }
    }

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Examples of org.broadinstitute.gatk.utils.smithwaterman.SWPairwiseAlignment

    private void resolveByHaplotype(final ReferenceContext refContext) {


        final byte[] source1Haplotype = generateHaplotype(sourceVCs1, refContext);
        final byte[] source2Haplotype = generateHaplotype(sourceVCs2, refContext);


        final SWPairwiseAlignment swConsensus1 = new SWPairwiseAlignment( refContext.getBases(), source1Haplotype, SW_MATCH, SW_MISMATCH, SW_GAP, SW_GAP_EXTEND );
        final SWPairwiseAlignment swConsensus2 = new SWPairwiseAlignment( refContext.getBases(), source2Haplotype, SW_MATCH, SW_MISMATCH, SW_GAP, SW_GAP_EXTEND );


        // protect against SW failures
        if( swConsensus1.getCigar().toString().contains("S") || swConsensus1.getCigar().getReferenceLength() < 20 ||
                swConsensus2.getCigar().toString().contains("S") || swConsensus2.getCigar().getReferenceLength() < 20 ) {
            // TODO -- handle errors appropriately
            logger.debug("Bad SW alignment; aborting at " + refContext.getLocus());
            return;
        }


        // order results by start position
        final TreeMap<Integer, VariantContext> source1Map = new TreeMap<Integer, VariantContext>(HaplotypeCallerGenotypingEngine.generateVCsFromAlignment(new Haplotype(source1Haplotype, false, 0, swConsensus1.getCigar()), refContext.getBases(), refContext.getWindow(), source1));
        final TreeMap<Integer, VariantContext> source2Map = new TreeMap<Integer, VariantContext>(HaplotypeCallerGenotypingEngine.generateVCsFromAlignment(new Haplotype(source2Haplotype, false, 0, swConsensus2.getCigar()), refContext.getBases(), refContext.getWindow(), source2));
        if ( source1Map.size() == 0 || source2Map.size() == 0 ) {
            // TODO -- handle errors appropriately
            logger.debug("No source alleles; aborting at " + refContext.getLocus());
            return;
        }

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Examples of org.broadinstitute.gatk.utils.smithwaterman.SWPairwiseAlignment

            hap = hapString.getBytes();
            this.expected = expected;
        }
        
        public Map<Integer,VariantContext> calcAlignment() {
            final SWPairwiseAlignment alignment = new SWPairwiseAlignment(ref, hap, new Parameters(3,-1,-4, -1));
            final Haplotype h = new Haplotype(hap, false, alignment.getAlignmentStart2wrt1(), alignment.getCigar());
            return HaplotypeCallerGenotypingEngine.generateVCsFromAlignment(h, ref, genomeLocParser.createGenomeLoc("4", 1, 1 + ref.length), "name");
        }

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Examples of org.broadinstitute.gatk.utils.smithwaterman.SWPairwiseAlignment

        final String referenceBases  = "ACTGACTGACTG";
        final String paddedReference = "NNNN" + referenceBases + "NNNN";
        for ( final List<Mutation> mutations : Utils.makePermutations(allMutations, 3, false) ) {
            final MutatedSequence hap = mutateSequence(referenceBases, mutations);
            final Haplotype haplotype = new Haplotype(hap.seq.getBytes());
            final SWPairwiseAlignment align = new SWPairwiseAlignment(paddedReference.getBytes(), hap.seq.getBytes());
            haplotype.setAlignmentStartHapwrtRef(align.getAlignmentStart2wrt1());
            haplotype.setCigar(align.getCigar());


            for ( final List<Mutation> readMutations : Utils.makePermutations(allMutations, 3, false) ) {
                final MutatedSequence readBases = mutateSequence(hap.seq, readMutations);
                final GATKSAMRecord read = makeRead(readBases.seq);
                tests.add(new Object[]{i++, read, paddedReference, haplotype, hap.numMismatches + readBases.numMismatches});

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Examples of org.broadinstitute.gatk.utils.smithwaterman.SWPairwiseAlignment


        final Cigar nonStandard;


        final String paddedRef = SW_PAD + new String(refSeq) + SW_PAD;
        final String paddedPath = SW_PAD + new String(altSeq) + SW_PAD;
        final SmithWaterman alignment = new SWPairwiseAlignment( paddedRef.getBytes(), paddedPath.getBytes(), NEW_SW_PARAMETERS);


        if ( isSWFailure(alignment) ) {
            return null;
        }




        // cut off the padding bases
        final int baseStart = SW_PAD.length();
        final int baseEnd = paddedPath.length() - SW_PAD.length() - 1; // -1 because it's inclusive
        nonStandard = AlignmentUtils.trimCigarByBases(alignment.getCigar(), baseStart, baseEnd);


        if ( nonStandard.getReferenceLength() != refSeq.length ) {
            nonStandard.add(new CigarElement(refSeq.length - nonStandard.getReferenceLength(), CigarOperator.D));
        }

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Examples of org.broadinstitute.gatk.utils.smithwaterman.SWPairwiseAlignment

        if ( haplotype == null ) throw new IllegalArgumentException("haplotype cannot be null");
        if ( haplotype.getCigar() == null ) throw new IllegalArgumentException("Haplotype cigar not set " + haplotype);
        if ( referenceStart < 1 ) throw new IllegalArgumentException("reference start much be >= 1 but got " + referenceStart);


        // compute the smith-waterman alignment of read -> haplotype
        final SWPairwiseAlignment swPairwiseAlignment = new SWPairwiseAlignment(haplotype.getBases(), originalRead.getReadBases(), CigarUtils.NEW_SW_PARAMETERS);
        if ( swPairwiseAlignment.getAlignmentStart2wrt1() == -1 )
            // sw can fail (reasons not clear) so if it happens just don't realign the read
            return originalRead;
        final Cigar swCigar = consolidateCigar(swPairwiseAlignment.getCigar());


        // since we're modifying the read we need to clone it
        final GATKSAMRecord read = (GATKSAMRecord)originalRead.clone();


        // only informative reads are given the haplotype tag to enhance visualization
        if ( isInformative )
            read.setAttribute(HAPLOTYPE_TAG, haplotype.hashCode());


        // compute here the read starts w.r.t. the reference from the SW result and the hap -> ref cigar
        final Cigar extendedHaplotypeCigar = haplotype.getConsolidatedPaddedCigar(1000);
        final int readStartOnHaplotype = calcFirstBaseMatchingReferenceInCigar(extendedHaplotypeCigar, swPairwiseAlignment.getAlignmentStart2wrt1());
        final int readStartOnReference = referenceStart + haplotype.getAlignmentStartHapwrtRef() + readStartOnHaplotype;
        read.setAlignmentStart(readStartOnReference);
        read.resetSoftStartAndEnd();


        // compute the read -> ref alignment by mapping read -> hap -> ref from the
        // SW of read -> hap mapped through the given by hap -> ref
        final Cigar haplotypeToRef = trimCigarByBases(extendedHaplotypeCigar, swPairwiseAlignment.getAlignmentStart2wrt1(), extendedHaplotypeCigar.getReadLength() - 1);
        final Cigar readToRefCigarRaw = applyCigarToCigar(swCigar, haplotypeToRef);
        final Cigar readToRefCigarClean = cleanUpCigar(readToRefCigarRaw);
        final Cigar readToRefCigar = leftAlignIndel(readToRefCigarClean, haplotype.getBases(),
                originalRead.getReadBases(), swPairwiseAlignment.getAlignmentStart2wrt1(), 0, true);


        read.setCigar(readToRefCigar);


        if ( readToRefCigar.getReadLength() != read.getReadLength() )
            throw new IllegalStateException("Cigar " + readToRefCigar + " with read length " + readToRefCigar.getReadLength()

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