/**
* 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);
}
}
}
}
}
private static void runTest(
final GATKSAMReadGroupRecord rg, final String expected, final ReadGroupCovariate covariate) {
GATKSAMRecord read = ReadUtils.createRandomRead(10);
read.setReadGroup(rg);
ReadCovariates readCovariates = new ReadCovariates(read.getReadLength(), 1);
covariate.recordValues(read, readCovariates);
verifyCovariateArray(readCovariates.getMismatchesKeySet(), expected, covariate);
}
@Test(enabled = false)
public void testCovariateGeneration() {
final String RGID = "id";
final int length = 10;
final RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection();
GATKSAMRecord read = ReadUtils.createRandomRead(length, false);
GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord(RGID);
rg.setPlatform("illumina");
read.setReadGroup(rg);
final byte[] mQuals = read.getBaseQualities(EventType.BASE_SUBSTITUTION);
final byte[] iQuals = read.getBaseQualities(EventType.BASE_INSERTION);
final byte[] dQuals = read.getBaseQualities(EventType.BASE_DELETION);
ReadGroupCovariate rgCov = new ReadGroupCovariate();
QualityScoreCovariate qsCov = new QualityScoreCovariate();
ContextCovariate coCov = new ContextCovariate();
CycleCovariate cyCov = new CycleCovariate();
rgCov.initialize(RAC);
qsCov.initialize(RAC);
coCov.initialize(RAC);
cyCov.initialize(RAC);
Covariate[] requestedCovariates = new Covariate[4];
requestedCovariates[0] = rgCov;
requestedCovariates[1] = qsCov;
requestedCovariates[2] = coCov;
requestedCovariates[3] = cyCov;
ReadCovariates rc = RecalDataManager.computeCovariates(read, requestedCovariates);
// check that the length is correct
Assert.assertEquals(rc.getMismatchesKeySet().length, length);
Assert.assertEquals(rc.getInsertionsKeySet().length, length);
Assert.assertEquals(rc.getDeletionsKeySet().length, length);
for (int i = 0; i < length; i++) {
// check that read group is always the same
Assert.assertEquals(rgCov.formatKey(rc.getMismatchesKeySet(i)[0]), RGID);
Assert.assertEquals(rgCov.formatKey(rc.getInsertionsKeySet(i)[0]), RGID);
Assert.assertEquals(rgCov.formatKey(rc.getDeletionsKeySet(i)[0]), RGID);
// check quality score
Assert.assertEquals(qsCov.formatKey(rc.getMismatchesKeySet(i)[1]), "" + mQuals[i]);
Assert.assertEquals(qsCov.formatKey(rc.getInsertionsKeySet(i)[1]), "" + iQuals[i]);
Assert.assertEquals(qsCov.formatKey(rc.getDeletionsKeySet(i)[1]), "" + dQuals[i]);
// check context
Assert.assertEquals(
coCov.formatKey(rc.getMismatchesKeySet(i)[2]),
ContextCovariateUnitTest.expectedContext(read, i, RAC.MISMATCHES_CONTEXT_SIZE));
Assert.assertEquals(
coCov.formatKey(rc.getInsertionsKeySet(i)[2]),
ContextCovariateUnitTest.expectedContext(read, i, RAC.INDELS_CONTEXT_SIZE));
Assert.assertEquals(
coCov.formatKey(rc.getDeletionsKeySet(i)[2]),
ContextCovariateUnitTest.expectedContext(read, i, RAC.INDELS_CONTEXT_SIZE));
// check cycle
Assert.assertEquals(cyCov.formatKey(rc.getMismatchesKeySet(i)[3]), "" + (i + 1));
Assert.assertEquals(cyCov.formatKey(rc.getInsertionsKeySet(i)[3]), "" + (i + 1));
Assert.assertEquals(cyCov.formatKey(rc.getDeletionsKeySet(i)[3]), "" + (i + 1));
}
}
@BeforeMethod
public void initCache() {
ReadCovariates.clearKeysCache();
}
