Examples with ReadThreadingAssembler org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler used on opensource projects

Example 1 with ReadThreadingAssembler

use of org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler in project gatk by broadinstitute.

the class AssemblyBasedCallerUtils method createReadThreadingAssembler.

public static ReadThreadingAssembler createReadThreadingAssembler(final AssemblyBasedCallerArgumentCollection args) {
    final ReadThreadingAssemblerArgumentCollection rtaac = args.assemblerArgs;
    final ReadThreadingAssembler assemblyEngine = new ReadThreadingAssembler(rtaac.maxNumHaplotypesInPopulation, rtaac.kmerSizes, rtaac.dontIncreaseKmerSizesForCycles, rtaac.allowNonUniqueKmersInRef, rtaac.numPruningSamples);
    assemblyEngine.setErrorCorrectKmers(rtaac.errorCorrectKmers);
    assemblyEngine.setPruneFactor(rtaac.minPruneFactor);
    assemblyEngine.setDebug(args.debug);
    assemblyEngine.setDebugGraphTransformations(rtaac.debugGraphTransformations);
    assemblyEngine.setRecoverDanglingBranches(!rtaac.doNotRecoverDanglingBranches);
    assemblyEngine.setMinDanglingBranchLength(rtaac.minDanglingBranchLength);
    assemblyEngine.setMinBaseQualityToUseInAssembly(args.minBaseQualityScore);
    if (rtaac.graphOutput != null) {
        assemblyEngine.setGraphWriter(new File(rtaac.graphOutput));
    }
    return assemblyEngine;
}

Example 2 with ReadThreadingAssembler

use of org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading.ReadThreadingAssembler in project gatk-protected by broadinstitute.

the class AssemblyBasedCallerUtils method createReadThreadingAssembler.

public static ReadThreadingAssembler createReadThreadingAssembler(final AssemblyBasedCallerArgumentCollection args) {
    final ReadThreadingAssemblerArgumentCollection rtaac = args.assemblerArgs;
    final ReadThreadingAssembler assemblyEngine = new ReadThreadingAssembler(rtaac.maxNumHaplotypesInPopulation, rtaac.kmerSizes, rtaac.dontIncreaseKmerSizesForCycles, rtaac.allowNonUniqueKmersInRef, rtaac.numPruningSamples);
    assemblyEngine.setErrorCorrectKmers(rtaac.errorCorrectKmers);
    assemblyEngine.setPruneFactor(rtaac.minPruneFactor);
    assemblyEngine.setDebug(args.debug);
    assemblyEngine.setDebugGraphTransformations(rtaac.debugGraphTransformations);
    assemblyEngine.setRecoverDanglingBranches(!rtaac.doNotRecoverDanglingBranches);
    assemblyEngine.setMinDanglingBranchLength(rtaac.minDanglingBranchLength);
    assemblyEngine.setMinBaseQualityToUseInAssembly(args.minBaseQualityScore);
    if (rtaac.graphOutput != null) {
        assemblyEngine.setGraphWriter(new File(rtaac.graphOutput));
    }
    return assemblyEngine;
}