Examples with IntegerCopyNumberTransitionMatrixCollection org.broadinstitute.hellbender.tools.exome.germlinehmm.IntegerCopyNumberTransitionMatrixCollection used on opensource projects

Example 1 with IntegerCopyNumberTransitionMatrixCollection

use of org.broadinstitute.hellbender.tools.exome.germlinehmm.IntegerCopyNumberTransitionMatrixCollection in project gatk by broadinstitute.

the class GermlineCNVCaller method createIntegerCopyNumberTransitionProbabilityCacheCollection.

private IntegerCopyNumberTransitionProbabilityCacheCollection createIntegerCopyNumberTransitionProbabilityCacheCollection() {
    IntegerCopyNumberTransitionProbabilityCacheCollection transitionProbabilityCacheCollection;
    try (final Reader copyNumberTransitionPriorTableReader = getReaderFromURI(copyNumberTransitionPriorTableURI)) {
        final String parentURI = new File(copyNumberTransitionPriorTableURI).getParent();
        final IntegerCopyNumberTransitionMatrixCollection transitionMatrixCollection = IntegerCopyNumberTransitionMatrixCollection.read(copyNumberTransitionPriorTableReader, parentURI);
        transitionProbabilityCacheCollection = new IntegerCopyNumberTransitionProbabilityCacheCollection(transitionMatrixCollection, true);
    } catch (final IOException ex) {
        throw new RuntimeException("Could not close the copy number transition prior table reader", ex);
    }
    return transitionProbabilityCacheCollection;
}

Example 2 with IntegerCopyNumberTransitionMatrixCollection

use of org.broadinstitute.hellbender.tools.exome.germlinehmm.IntegerCopyNumberTransitionMatrixCollection in project gatk-protected by broadinstitute.

the class GermlineCNVCaller method createIntegerCopyNumberTransitionProbabilityCacheCollection.

private IntegerCopyNumberTransitionProbabilityCacheCollection createIntegerCopyNumberTransitionProbabilityCacheCollection() {
    IntegerCopyNumberTransitionProbabilityCacheCollection transitionProbabilityCacheCollection;
    try (final Reader copyNumberTransitionPriorTableReader = getReaderFromURI(copyNumberTransitionPriorTableURI)) {
        final String parentURI = new File(copyNumberTransitionPriorTableURI).getParent();
        final IntegerCopyNumberTransitionMatrixCollection transitionMatrixCollection = IntegerCopyNumberTransitionMatrixCollection.read(copyNumberTransitionPriorTableReader, parentURI);
        transitionProbabilityCacheCollection = new IntegerCopyNumberTransitionProbabilityCacheCollection(transitionMatrixCollection, true);
    } catch (final IOException ex) {
        throw new RuntimeException("Could not close the copy number transition prior table reader", ex);
    }
    return transitionProbabilityCacheCollection;
}