@Test(enabled = true)
public void testForceReadgroup() {
final RecalibrationArgumentCollection forcedRAC = new RecalibrationArgumentCollection();
forcedRAC.FORCE_READGROUP = "FOO";
final ReadGroupCovariate forcedCovariate = new ReadGroupCovariate();
forcedCovariate.initialize(forcedRAC);
final GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord("NOT_FOO");
runTest(rg, "FOO", forcedCovariate);
}
private static void verifyCovariateArray(
final int[][] values, final String expected, final ReadGroupCovariate covariate) {
for (int[] value : values) {
String actual = covariate.formatKey(value[0]);
Assert.assertEquals(actual, expected);
}
}
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);
}
@BeforeClass
public void init() {
RAC = new RecalibrationArgumentCollection();
covariate = new ReadGroupCovariate();
covariate.initialize(RAC);
}
