/**
* Compiles the list of keys for the Covariates table and uses the shared parsing utility to
* produce the actual table
*
* @param reportTable the GATKReport table containing data for this table
* @param recalibrationTables the recalibration tables \
*/
private void parseAllCovariatesTable(
final GATKReportTable reportTable, final RecalibrationTables recalibrationTables) {
for (int i = 0; i < reportTable.getNumRows(); i++) {
final Object rg = reportTable.get(i, RecalUtils.READGROUP_COLUMN_NAME);
tempCOVarray[0] = requestedCovariates[0].keyFromValue(rg);
final Object qual = reportTable.get(i, RecalUtils.QUALITY_SCORE_COLUMN_NAME);
tempCOVarray[1] = requestedCovariates[1].keyFromValue(qual);
final String covName = (String) reportTable.get(i, RecalUtils.COVARIATE_NAME_COLUMN_NAME);
final int covIndex = optionalCovariateIndexes.get(covName);
final Object covValue = reportTable.get(i, RecalUtils.COVARIATE_VALUE_COLUMN_NAME);
tempCOVarray[2] =
requestedCovariates[
RecalibrationTables.TableType.OPTIONAL_COVARIATE_TABLES_START.ordinal() + covIndex]
.keyFromValue(covValue);
final EventType event =
EventType.eventFrom((String) reportTable.get(i, RecalUtils.EVENT_TYPE_COLUMN_NAME));
tempCOVarray[3] = event.ordinal();
recalibrationTables
.getTable(
RecalibrationTables.TableType.OPTIONAL_COVARIATE_TABLES_START.ordinal() + covIndex)
.put(getRecalDatum(reportTable, i, false), tempCOVarray);
}
}
/**
* Update the recalibration statistics using the information in recalInfo
*
* @param recalInfo data structure holding information about the recalibration values for a single
* read
*/
@Requires("recalInfo != null")
public void updateDataForRead(final ReadRecalibrationInfo recalInfo) {
final GATKSAMRecord read = recalInfo.getRead();
final ReadCovariates readCovariates = recalInfo.getCovariatesValues();
final RecalibrationTables tables = getUpdatableRecalibrationTables();
final NestedIntegerArray<RecalDatum> qualityScoreTable = tables.getQualityScoreTable();
for (int offset = 0; offset < read.getReadBases().length; offset++) {
if (!recalInfo.skip(offset)) {
for (final EventType eventType : EventType.values()) {
final int[] keys = readCovariates.getKeySet(offset, eventType);
final int eventIndex = eventType.ordinal();
final byte qual = recalInfo.getQual(eventType, offset);
final double isError = recalInfo.getErrorFraction(eventType, offset);
RecalUtils.incrementDatumOrPutIfNecessary(
qualityScoreTable, qual, isError, keys[0], keys[1], eventIndex);
for (int i = 2; i < covariates.length; i++) {
if (keys[i] < 0) continue;
RecalUtils.incrementDatumOrPutIfNecessary(
tables.getTable(i), qual, isError, keys[0], keys[1], keys[i], eventIndex);
}
}
}
}
}
/**
* Compiles the list of keys for the ReadGroup table and uses the shared parsing utility to
* produce the actual table
*
* @param reportTable the GATKReport table containing data for this table
* @param rgTable the map representing this table
*/
private void parseReadGroupTable(
final GATKReportTable reportTable, final NestedIntegerArray<RecalDatum> rgTable) {
for (int i = 0; i < reportTable.getNumRows(); i++) {
final Object rg = reportTable.get(i, RecalUtils.READGROUP_COLUMN_NAME);
tempRGarray[0] = requestedCovariates[0].keyFromValue(rg);
final EventType event =
EventType.eventFrom((String) reportTable.get(i, RecalUtils.EVENT_TYPE_COLUMN_NAME));
tempRGarray[1] = event.ordinal();
rgTable.put(getRecalDatum(reportTable, i, true), tempRGarray);
}
}
/**
* Compiles the list of keys for the QualityScore table and uses the shared parsing utility to
* produce the actual table
*
* @param reportTable the GATKReport table containing data for this table
* @param qualTable the map representing this table
*/
private void parseQualityScoreTable(
final GATKReportTable reportTable, final NestedIntegerArray<RecalDatum> qualTable) {
for (int i = 0; i < reportTable.getNumRows(); i++) {
final Object rg = reportTable.get(i, RecalUtils.READGROUP_COLUMN_NAME);
tempQUALarray[0] = requestedCovariates[0].keyFromValue(rg);
final Object qual = reportTable.get(i, RecalUtils.QUALITY_SCORE_COLUMN_NAME);
tempQUALarray[1] = requestedCovariates[1].keyFromValue(qual);
final EventType event =
EventType.eventFrom((String) reportTable.get(i, RecalUtils.EVENT_TYPE_COLUMN_NAME));
tempQUALarray[2] = event.ordinal();
qualTable.put(getRecalDatum(reportTable, i, false), tempQUALarray);
}
}