Source:
public static AssemblyResultSet assembleReads(final AssemblyRegion region, final List<VariantContext> givenAlleles, final AssemblyBasedCallerArgumentCollection argumentCollection, final SAMFileHeader header, final SampleList sampleList, final Logger logger, final CachingIndexedFastaSequenceFile referenceReader, final ReadThreadingAssembler assemblyEngine){ finalizeRegion(region, argumentCollection.errorCorrectReads, argumentCollection.dontUseSoftClippedBases, (byte)(argumentCollection.minBaseQualityScore - 1), header, sampleList); if( argumentCollection.debug) { logger.info("Assembling " + region.getSpan() + " with " + region.size() + " reads: (with overlap region = " + region.getExtendedSpan() + ")"); } final int REFERENCE_PADDING = 500; final byte[] fullReferenceWithPadding = region.getAssemblyRegionReference(referenceReader, REFERENCE_PADDING); final SimpleInterval paddedReferenceLoc = getPaddedReferenceLoc(region, REFERENCE_PADDING, referenceReader); final Haplotype referenceHaplotype = createReferenceHaplotype(region, paddedReferenceLoc, referenceReader); final ReadErrorCorrector readErrorCorrector = argumentCollection.errorCorrectReads ? new ReadErrorCorrector( argumentCollection.assemblerArgs.kmerLengthForReadErrorCorrection, HaplotypeCallerEngine.MIN_TAIL_QUALITY_WITH_ERROR_CORRECTION, argumentCollection.assemblerArgs.minObservationsForKmerToBeSolid, argumentCollection.debug, fullReferenceWithPadding) : null; try { final AssemblyResultSet assemblyResultSet = assemblyEngine.runLocalAssembly(region, referenceHaplotype, fullReferenceWithPadding, paddedReferenceLoc, givenAlleles, readErrorCorrector, header); assemblyResultSet.debugDump(logger); return assemblyResultSet; } catch (final Exception e){ if (argumentCollection.captureAssemblyFailureBAM){ try (final SAMFileWriter writer = ReadUtils.createCommonSAMWriter(new File("assemblyFailure.bam"), null, header, false, false, false)){ for (final GATKRead read : region.getReads()) { writer.addAlignment(read.convertToSAMRecord(header)); } } } throw e; } }

Target:
public static AssemblyResultSet assembleReads(final AssemblyRegion region, final List<VariantContext> givenAlleles, final AssemblyBasedCallerArgumentCollection argumentCollection, final SAMFileHeader header, final SampleList sampleList, final Logger logger, final CachingIndexedFastaSequenceFile referenceReader, final ReadThreadingAssembler assemblyEngine){ finalizeRegion(region, argumentCollection.errorCorrectReads, argumentCollection.dontUseSoftClippedBases, (byte)(argumentCollection.minBaseQualityScore - 1), header, sampleList); if( argumentCollection.debug) { logger.info("Assembling " + region.getSpan() + " with " + region.size() + " reads: (with overlap region = " + region.getExtendedSpan() + ")"); } final byte[] fullReferenceWithPadding = region.getAssemblyRegionReference(referenceReader, REFERENCE_PADDING_FOR_ASSEMBLY); final SimpleInterval paddedReferenceLoc = getPaddedReferenceLoc(region, REFERENCE_PADDING_FOR_ASSEMBLY, referenceReader); final Haplotype referenceHaplotype = createReferenceHaplotype(region, paddedReferenceLoc, referenceReader); final ReadErrorCorrector readErrorCorrector = argumentCollection.errorCorrectReads ? new ReadErrorCorrector(argumentCollection.assemblerArgs.kmerLengthForReadErrorCorrection, HaplotypeCallerEngine.MIN_TAIL_QUALITY_WITH_ERROR_CORRECTION, argumentCollection.assemblerArgs.minObservationsForKmerToBeSolid, argumentCollection.debug, fullReferenceWithPadding) : null; try { final AssemblyResultSet assemblyResultSet = assemblyEngine.runLocalAssembly(region, referenceHaplotype, fullReferenceWithPadding, paddedReferenceLoc, givenAlleles, readErrorCorrector, header); assemblyResultSet.debugDump(logger); return assemblyResultSet; } catch (final Exception e){ if (argumentCollection.captureAssemblyFailureBAM){ try (final SAMFileWriter writer = ReadUtils.createCommonSAMWriter(new File("assemblyFailure.bam"), null, header, false, false, false)){ for (final GATKRead read : region.getReads()) { writer.addAlignment(read.convertToSAMRecord(header)); } } } throw e; } }