Package org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading

Examples of org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler

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        } catch( FileNotFoundException e ) {
            throw new UserException.CouldNotReadInputFile(getToolkit().getArguments().referenceFile, e);
        }

        // create and setup the assembler
        assemblyEngine = new ReadThreadingAssembler(maxNumHaplotypesInPopulation, kmerSizes, dontIncreaseKmerSizesForCycles, allowNonUniqueKmersInRef, numPruningSamples);

        assemblyEngine.setErrorCorrectKmers(errorCorrectKmers);
        assemblyEngine.setPruneFactor(MIN_PRUNE_FACTOR);
        assemblyEngine.setDebug(SCAC.DEBUG);
        assemblyEngine.setDebugGraphTransformations(debugGraphTransformations);
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        final int nReadsToUse = 5;

        for ( int startI = start; startI < end; startI += stepSize) {
            final int endI = startI + windowSize;
            final GenomeLoc refLoc = genomeLocParser.createGenomeLoc(contig, startI, endI);
            tests.add(new Object[]{new ReadThreadingAssembler(), refLoc, nReadsToUse});
        }

        return tests.toArray(new Object[][]{});
    }
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        for ( int startI = start; startI < end; startI += stepSize) {
            final int endI = startI + windowSize;
            final GenomeLoc refLoc = genomeLocParser.createGenomeLoc(contig, startI, endI);
            for ( int variantStart = windowSize / 2 - 10; variantStart < windowSize / 2 + 10; variantStart += variantStepSize ) {
                tests.add(new Object[]{new ReadThreadingAssembler(), refLoc, nReadsToUse, variantStart});
            }
        }

        return tests.toArray(new Object[][]{});
    }
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            for ( int snpPos = 0; snpPos < windowSize; snpPos++) {
                if ( snpPos > excludeVariantsWithinXbp && (windowSize - snpPos) >= excludeVariantsWithinXbp ) {
                    final byte[] altBases = ref.getBytes();
                    altBases[snpPos] = altBases[snpPos] == 'A' ? (byte)'C' : (byte)'A';
                    final String alt = new String(altBases);
                    tests.add(new Object[]{"SNP at " + snpPos, new ReadThreadingAssembler(), refLoc, ref, alt});
                }
            }

        return tests.toArray(new Object[][]{});
    }
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Related Classes of org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler

  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.AssemblyResult
  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller
  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.LocalAssemblyEngineUnitTest
  • java.io.File
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