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 GATKSAMRecord clipRead(ClippingRepresentation algorithm) {
        if (ops == null)
            return getRead();


        GATKSAMRecord clippedRead = read;
        for (ClippingOp op : getOps()) {
            final int readLength = clippedRead.getReadLength();
            //check if the clipped read can still be clipped in the range requested
            if (op.start < readLength) {
                ClippingOp fixedOperation = op;
                if (op.stop >= readLength)
                    fixedOperation = new ClippingOp(op.start, readLength - 1);


                clippedRead = fixedOperation.apply(algorithm, clippedRead);
            }
        }
        wasClipped = true;
        ops.clear();
        if ( clippedRead.isEmpty() )
            return GATKSAMRecord.emptyRead(clippedRead);
        return clippedRead;
    }

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               "left >= read.getAlignmentStart()", // coordinate has to be within the mapped read
               "right <= read.getAlignmentEnd()"}) // coordinate has to be within the mapped read
    private GATKSAMRecord hardClipBothEndsByReferenceCoordinates(int left, int right) {
        if (read.isEmpty() || left == right)
            return GATKSAMRecord.emptyRead(read);
        GATKSAMRecord leftTailRead = hardClipByReferenceCoordinates(right, -1);


        // after clipping one tail, it is possible that the consequent hard clipping of adjacent deletions
        // make the left cut index no longer part of the read. In that case, clip the read entirely.
        if (left > leftTailRead.getAlignmentEnd())
            return GATKSAMRecord.emptyRead(read);


        ReadClipper clipper = new ReadClipper(leftTailRead);
        return clipper.hardClipByReferenceCoordinatesLeftTail(left);
    }

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    }


    public static List<GATKSAMRecord> hardClipToRegion( final List<GATKSAMRecord> reads, final int refStart, final int refStop ) {
        final List<GATKSAMRecord> returnList = new ArrayList<GATKSAMRecord>( reads.size() );
        for( final GATKSAMRecord read : reads ) {
            final GATKSAMRecord clippedRead = hardClipToRegion( read, refStart, refStop );
            if( !clippedRead.isEmpty() ) {
                returnList.add( clippedRead );
            }
        }
        return returnList;
    }

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                else
                    break;
            }
        }


        GATKSAMRecord clippedRead = read;
        if (right >= 0 && right + 1 < clippedRead.getReadLength())                                                      // only clip if there are softclipped bases (right >= 0) and the first high quality soft clip is not the last base (right+1 < readlength)
                clippedRead = hardClipByReadCoordinates(clippedRead, right+1, clippedRead.getReadLength()-1);           // first we hard clip the low quality soft clips on the right tail
        if (left >= 0 && left - 1 > 0)                                                                                  // only clip if there are softclipped bases (left >= 0) and the first high quality soft clip is not the last base (left-1 > 0)
                clippedRead = hardClipByReadCoordinates(clippedRead, 0, left-1);                                        // then we hard clip the low quality soft clips on the left tail


        return clippedRead;
    }

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        if ( start > 0 && stop < read.getReadLength() - 1)
            throw new ReviewedGATKException(String.format("Trying to clip the middle of the read: start %d, stop %d, cigar: %s", start, stop, read.getCigarString()));


        this.addOp(new ClippingOp(start, stop));
        GATKSAMRecord clippedRead = clipRead(ClippingRepresentation.HARDCLIP_BASES);
        this.ops = null;
        return clippedRead;
    }

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        if ( duplicates.size() == 0 )
            return null;


        // make the combined read by copying the first read and setting the
        // bases and quals to new arrays
        GATKSAMRecord comb = tmpCopyRead(duplicates.get(0));
        //GATKSAMRecord comb = tmpCopyRead(duplicates.get(0));
        comb.setDuplicateReadFlag(false);
        int readLen = comb.getReadBases().length;
        byte[] bases = new byte[readLen];
        byte[] quals = new byte[readLen];


        for ( int i = 0; i < readLen; i++ ) {
            //System.out.printf("I is %d%n", i);
            //for ( GATKSAMRecord read : duplicates ) {
            //    System.out.printf("dup base %c %d%n", (char)read.getReadBases()[i], read.getBaseQualities()[i]);
            //}
            Pair<Byte, Byte> baseAndQual = combineBaseProbs(genomeLocParser,duplicates, i, maxQScore);
            bases[i] = baseAndQual.getFirst();
            quals[i] = baseAndQual.getSecond();            
        }




        comb.setBaseQualities(quals);
        comb.setReadBases(bases);


        return comb;
    }

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    }


    @Requires("hasNext()")
    @Ensures("result != null")
    public SAMRecord next()     {
        final GATKSAMRecord read = (GATKSAMRecord)it.next();
        return transformer.apply(read);
    }

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            alleleToHaplotypeMap.put(Allele.create(haplotype.getBases()), haplotype);


        final Map<GATKSAMRecord, Map<Allele, Double>> newLikelihoodReadMap = new LinkedHashMap<>(likelihoodReadMap.size());
        for( final Map.Entry<GATKSAMRecord, Map<Allele, Double>> entry : likelihoodReadMap.entrySet() ) {
            final MostLikelyAllele bestAllele = PerReadAlleleLikelihoodMap.getMostLikelyAllele(entry.getValue());
            final GATKSAMRecord alignedToRef = AlignmentUtils.createReadAlignedToRef(entry.getKey(), alleleToHaplotypeMap.get(bestAllele.getMostLikelyAllele()), paddedReferenceLoc.getStart(), bestAllele.isInformative());
            newLikelihoodReadMap.put(alignedToRef, entry.getValue());
        }


        likelihoodReadMap.clear();
        likelihoodReadMap.putAll(newLikelihoodReadMap);

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    }


    @Test(enabled = !DEBUG, expectedExceptions = IllegalArgumentException.class)
    public void testOutOfOrder() {
        final List<GATKSAMRecord> pair = ArtificialSAMUtils.createPair(header, "readpair", 100, 1, 50, true, true);
        final GATKSAMRecord left = pair.get(0);
        final GATKSAMRecord right = pair.get(1);
        final List<GATKSAMRecord> reads = Arrays.asList(right, left); // OUT OF ORDER!
        final List<Integer> offsets = Arrays.asList(0, 50);
        final ReadBackedPileup pileup = new ReadBackedPileupImpl(null, reads, offsets);
        FragmentUtils.create(pileup); // should throw exception
    }

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        final String allOverlappingBases = "ACGTACGTGGAACCTTAG";
        for ( int overlapSize = 1; overlapSize < allOverlappingBases.length(); overlapSize++ ) {
            final String overlappingBases = allOverlappingBases.substring(0, overlapSize);
            final byte[] overlappingBaseQuals = new byte[overlapSize];
            for ( int i = 0; i < overlapSize; i++ ) overlappingBaseQuals[i] = (byte)(i + 30);
            final GATKSAMRecord read1  = makeOverlappingRead(leftFlank, 20, overlappingBases, overlappingBaseQuals, "", 30, 1);
            final GATKSAMRecord read2  = makeOverlappingRead("", 20, overlappingBases, overlappingBaseQuals, rightFlank, 30, leftFlank.length() + 1);
            final GATKSAMRecord merged = makeOverlappingRead(leftFlank, 20, overlappingBases, overlappingBaseQuals, rightFlank, 30, 1);
            tests.add(new Object[]{"equalQuals", read1, read2, merged});


            // test that the merged read base quality is the
            tests.add(new Object[]{"lowQualLeft", modifyBaseQualities(read1, leftFlank.length(), overlapSize), read2, merged});
            tests.add(new Object[]{"lowQualRight", read1, modifyBaseQualities(read2, 0, overlapSize), merged});

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