Examples with AlleleFractionData org.broadinstitute.hellbender.tools.exome.allelefraction.AlleleFractionData used on opensource projects

Example 1 with AlleleFractionData

use of org.broadinstitute.hellbender.tools.exome.allelefraction.AlleleFractionData in project gatk by broadinstitute.

the class AllelicCNV method calculateAllelicBias.

//use AlleleFractionInitializer to determine mean of global allelic-bias distribution given SNP segmentation file
private double calculateAllelicBias(final Genome genome, final File snpSegmentFile) {
    final SegmentedGenome segmentedGenomeForSNPSegmentation = new SegmentedGenome(snpSegmentFile, genome);
    final AlleleFractionData data = new AlleleFractionData(segmentedGenomeForSNPSegmentation);
    final AlleleFractionState initialState = new AlleleFractionInitializer(data).getInitializedState();
    return initialState.meanBias();
}

Example 2 with AlleleFractionData

use of org.broadinstitute.hellbender.tools.exome.allelefraction.AlleleFractionData in project gatk-protected by broadinstitute.

the class AllelicCNV method calculateAllelicBias.

//use AlleleFractionInitializer to determine mean of global allelic-bias distribution given SNP segmentation file
private double calculateAllelicBias(final Genome genome, final File snpSegmentFile) {
    final SegmentedGenome segmentedGenomeForSNPSegmentation = new SegmentedGenome(snpSegmentFile, genome);
    final AlleleFractionData data = new AlleleFractionData(segmentedGenomeForSNPSegmentation);
    final AlleleFractionState initialState = new AlleleFractionInitializer(data).getInitializedState();
    return initialState.meanBias();
}