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

Example 1 with CreateAllelicPanelOfNormals

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

the class AllelicPanelOfNormals method read.

/**
     * Reads an allelic panel of normals from an HDF5 or tab-separated file (file type is automatically detected).
     * Tab-separated files should have global hyperparameter values alpha and beta specified by comment lines
     * denoted by {@code GLOBAL_ALPHA_COMMENT_STRING} and {@code GLOBAL_BETA_COMMENT_STRING}:
     * <p>
     *     #GLOBAL_ALPHA=...<br>
     *     #GLOBAL_BETA=...
     * </p>
     * followed by lines specifying hyperparameter values at each site,
     * with column headers as in {@link AllelicPanelOfNormalsTableColumn}:
     * <p>
     *     CONTIG \t POSITION \t ALPHA \t BETA
     * </p>
     *
     * Note that we opt for a static read method as opposed to a constructor that takes a file parameter because
     * the former allows us to return the static {@code EMPTY_PON} if the allelic panel of normals is not present in
     * an HDF5 file.
     * @param inputFile    HDF5 file containing a coverage panel of normals created by {@link CreatePanelOfNormals}
     *                     and an allelic panel of normals created and set by {@link CreateAllelicPanelOfNormals}
     *                     ({@code EMPTY_PON} is returned if the latter was never set), or a
     *                     tab-separated file that contains global hyperparameters in comment lines and lines specifying hyperparameter values at each site
     */
public static AllelicPanelOfNormals read(final File inputFile) {
    IOUtils.canReadFile(inputFile);
    if (isHDF5File(inputFile)) {
        //construct from HDF5 file
        try (final HDF5File hdf5File = new HDF5File(inputFile)) {
            final AllelicPanelOfNormals allelicPoN = HDF5AllelicPoNUtils.read(hdf5File);
            logger.info(String.format("Loaded allelic panel of normals from HDF5 file: %s.", inputFile));
            return allelicPoN;
        }
    } else {
        //construct from TSV file
        try (final AllelicPanelOfNormalsReader reader = new AllelicPanelOfNormalsReader(inputFile)) {
            //parse comment lines for global hyperparameter values
            final AllelicPanelOfNormals.HyperparameterValues globalHyperparameterValues = parseGlobalHyperparameterValues(inputFile);
            //parse data lines for local hyperparameter values
            final Map<SimpleInterval, HyperparameterValues> siteToHyperparameterValuesMap = new HashMap<>();
            reader.stream().forEach(s -> siteToHyperparameterValuesMap.put(s.getKey(), s.getValue()));
            final AllelicPanelOfNormals allelicPoN = new AllelicPanelOfNormals(globalHyperparameterValues, siteToHyperparameterValuesMap);
            logger.info(String.format("Loaded allelic panel of normals from TSV file: %s.", inputFile));
            return allelicPoN;
        } catch (final IOException | UncheckedIOException ex) {
            throw new UserException.CouldNotReadInputFile(inputFile, ex);
        }
    }
}

Example 2 with CreateAllelicPanelOfNormals

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

the class AllelicPanelOfNormals method read.

/**
     * Reads an allelic panel of normals from an HDF5 or tab-separated file (file type is automatically detected).
     * Tab-separated files should have global hyperparameter values alpha and beta specified by comment lines
     * denoted by {@code GLOBAL_ALPHA_COMMENT_STRING} and {@code GLOBAL_BETA_COMMENT_STRING}:
     * <p>
     *     #GLOBAL_ALPHA=...<br>
     *     #GLOBAL_BETA=...
     * </p>
     * followed by lines specifying hyperparameter values at each site,
     * with column headers as in {@link AllelicPanelOfNormalsTableColumn}:
     * <p>
     *     CONTIG \t POSITION \t ALPHA \t BETA
     * </p>
     *
     * Note that we opt for a static read method as opposed to a constructor that takes a file parameter because
     * the former allows us to return the static {@code EMPTY_PON} if the allelic panel of normals is not present in
     * an HDF5 file.
     * @param inputFile    HDF5 file containing a coverage panel of normals created by {@link CreatePanelOfNormals}
     *                     and an allelic panel of normals created and set by {@link CreateAllelicPanelOfNormals}
     *                     ({@code EMPTY_PON} is returned if the latter was never set), or a
     *                     tab-separated file that contains global hyperparameters in comment lines and lines specifying hyperparameter values at each site
     */
public static AllelicPanelOfNormals read(final File inputFile) {
    IOUtils.canReadFile(inputFile);
    if (isHDF5File(inputFile)) {
        //construct from HDF5 file
        try (final HDF5File hdf5File = new HDF5File(inputFile)) {
            final AllelicPanelOfNormals allelicPoN = HDF5AllelicPoNUtils.read(hdf5File);
            logger.info(String.format("Loaded allelic panel of normals from HDF5 file: %s.", inputFile));
            return allelicPoN;
        }
    } else {
        //construct from TSV file
        try (final AllelicPanelOfNormalsReader reader = new AllelicPanelOfNormalsReader(inputFile)) {
            //parse comment lines for global hyperparameter values
            final AllelicPanelOfNormals.HyperparameterValues globalHyperparameterValues = parseGlobalHyperparameterValues(inputFile);
            //parse data lines for local hyperparameter values
            final Map<SimpleInterval, HyperparameterValues> siteToHyperparameterValuesMap = new HashMap<>();
            reader.stream().forEach(s -> siteToHyperparameterValuesMap.put(s.getKey(), s.getValue()));
            final AllelicPanelOfNormals allelicPoN = new AllelicPanelOfNormals(globalHyperparameterValues, siteToHyperparameterValuesMap);
            logger.info(String.format("Loaded allelic panel of normals from TSV file: %s.", inputFile));
            return allelicPoN;
        } catch (final IOException | UncheckedIOException ex) {
            throw new UserException.CouldNotReadInputFile(inputFile, ex);
        }
    }
}