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I hate these disabled unit tests

This commit is contained in:
Eric Banks 2012-06-14 14:03:58 -04:00
parent 065fe9a7b9
commit 676a57de7b
1 changed files with 5 additions and 7 deletions
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12
public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/CycleCovariateUnitTest.java
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@ -7,8 +7,6 @@ import org.testng.Assert;
import org.testng.annotations.BeforeClass; import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test; import org.testng.annotations.Test;
import java.util.BitSet;
/** /**
* @author Mauricio Carneiro * @author Mauricio Carneiro
* @since 3/1/12 * @since 3/1/12
@ -33,22 +31,22 @@ public class CycleCovariateUnitTest {
read.getReadGroup().setPlatform("illumina"); read.getReadGroup().setPlatform("illumina");
CovariateValues values = covariate.getValues(read); CovariateValues values = covariate.getValues(read);
verifyCovariateArray(values.getMismatches(), (short) 1, (short) 1); verifyCovariateArray(values.getMismatches(), 1, (short) 1);
read.setReadNegativeStrandFlag(true); read.setReadNegativeStrandFlag(true);
values = covariate.getValues(read); values = covariate.getValues(read);
verifyCovariateArray(values.getMismatches(), readLength, (short) -1); verifyCovariateArray(values.getMismatches(), readLength, -1);
read.setSecondOfPairFlag(true); read.setSecondOfPairFlag(true);
values = covariate.getValues(read); values = covariate.getValues(read);
verifyCovariateArray(values.getMismatches(), (short) -readLength, (short) 1); verifyCovariateArray(values.getMismatches(), -readLength, 1);
read.setReadNegativeStrandFlag(false); read.setReadNegativeStrandFlag(false);
values = covariate.getValues(read); values = covariate.getValues(read);
verifyCovariateArray(values.getMismatches(), (short) -1, (short) -1); verifyCovariateArray(values.getMismatches(), -1, -1);
} }
private void verifyCovariateArray(Long[] values, short init, short increment) { private void verifyCovariateArray(long[] values, int init, int increment) {
for (short i = 0; i < values.length; i++) { for (short i = 0; i < values.length; i++) {
short actual = Short.decode(covariate.formatKey(values[i])); short actual = Short.decode(covariate.formatKey(values[i]));
int expected = init + (increment * i); int expected = init + (increment * i);