Examples with NestedIntegerArray org.broadinstitute.hellbender.utils.collections.NestedIntegerArray used on opensource projects

Example 1 with NestedIntegerArray

use of org.broadinstitute.hellbender.utils.collections.NestedIntegerArray in project gatk by broadinstitute.

the class RecalUtils method generateReportTables.

public static List<GATKReportTable> generateReportTables(final RecalibrationTables recalibrationTables, final StandardCovariateList covariates) {
    final List<GATKReportTable> result = new LinkedList<>();
    int rowIndex = 0;
    GATKReportTable allCovsReportTable = null;
    for (NestedIntegerArray<RecalDatum> table : recalibrationTables) {
        // initialize the array to hold the column names
        final ArrayList<Pair<String, String>> columnNames = new ArrayList<>();
        // save the required covariate name so we can reference it in the future
        columnNames.add(new MutablePair<>(covariates.getReadGroupCovariate().parseNameForReport(), "%s"));
        if (!recalibrationTables.isReadGroupTable(table)) {
            // save the required covariate name so we can reference it in the future
            columnNames.add(new MutablePair<>(covariates.getQualityScoreCovariate().parseNameForReport(), "%d"));
            if (recalibrationTables.isAdditionalCovariateTable(table)) {
                columnNames.add(covariateValue);
                columnNames.add(covariateName);
            }
        }
        // the order of these column names is important here
        columnNames.add(eventType);
        columnNames.add(empiricalQuality);
        if (recalibrationTables.isReadGroupTable(table)) {
            // only the read group table needs the estimated Q reported
            columnNames.add(estimatedQReported);
        }
        columnNames.add(nObservations);
        columnNames.add(nErrors);
        final String reportTableName = getReportTableName(recalibrationTables, table);
        final GATKReportTable.Sorting sort = GATKReportTable.Sorting.SORT_BY_COLUMN;
        final GATKReportTable reportTable;
        final boolean addToList;
        //XXX this "if" implicitly uses the knowledge about the ordering of tables.
        if (!recalibrationTables.isAdditionalCovariateTable(table)) {
            reportTable = makeNewTableWithColumns(columnNames, reportTableName, sort);
            // reset the row index since we're starting with a new table
            rowIndex = 0;
            addToList = true;
        } else if (allCovsReportTable == null && recalibrationTables.isAdditionalCovariateTable(table)) {
            reportTable = makeNewTableWithColumns(columnNames, reportTableName, sort);
            // reset the row index since we're starting with a new table
            rowIndex = 0;
            allCovsReportTable = reportTable;
            addToList = true;
        } else {
            reportTable = allCovsReportTable;
            addToList = false;
        }
        for (final NestedIntegerArray.Leaf<RecalDatum> row : table.getAllLeaves()) {
            final RecalDatum datum = row.value;
            final int[] keys = row.keys;
            int columnIndex = 0;
            int keyIndex = 0;
            reportTable.set(rowIndex, columnNames.get(columnIndex++).getLeft(), covariates.getReadGroupCovariate().formatKey(keys[keyIndex++]));
            if (!recalibrationTables.isReadGroupTable(table)) {
                reportTable.set(rowIndex, columnNames.get(columnIndex++).getLeft(), covariates.getQualityScoreCovariate().formatKey(keys[keyIndex++]));
                if (recalibrationTables.isAdditionalCovariateTable(table)) {
                    final Covariate covariate = recalibrationTables.getCovariateForTable(table);
                    reportTable.set(rowIndex, columnNames.get(columnIndex++).getLeft(), covariate.formatKey(keys[keyIndex++]));
                    reportTable.set(rowIndex, columnNames.get(columnIndex++).getLeft(), covariate.parseNameForReport());
                }
            }
            final EventType event = EventType.eventFrom(keys[keyIndex]);
            reportTable.set(rowIndex, columnNames.get(columnIndex++).getLeft(), event.toString());
            reportTable.set(rowIndex, columnNames.get(columnIndex++).getLeft(), datum.getEmpiricalQuality());
            if (recalibrationTables.isReadGroupTable(table)) {
                // we only add the estimated Q reported in the RG table
                reportTable.set(rowIndex, columnNames.get(columnIndex++).getLeft(), datum.getEstimatedQReported());
            }
            reportTable.set(rowIndex, columnNames.get(columnIndex++).getLeft(), datum.getNumObservations());
            reportTable.set(rowIndex, columnNames.get(columnIndex).getLeft(), datum.getNumMismatches());
            rowIndex++;
        }
        if (addToList) {
            //XXX using a set would be slow because the equals method on GATKReportTable is expensive.
            result.add(reportTable);
        }
    }
    return result;
}