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Committing a broken version of BaseRecalibration 

-- I'm committing because there's some kind of fundamental problem with the ReadCovariates cache, in that historical data isn't being cleared / computed properly, and I'd rather it fail for a while than leave it in JIRA.
-- The integration tests test the -nct with PrintReads to get 1, 2, 4 and the 4 fails.  But that's because of this incorrect calculation
-- Updating GATKPerformanceOverTime with the new @ClassType annotation
This commit is contained in:
Mark DePristo 2012-10-25 14:46:09 -04:00
parent 6dc7d872ec
commit cc8c12b954
2 changed files with 21 additions and 10 deletions
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22
protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java
View File

@ -5,7 +5,9 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
/**
* @author ebanks
@ -118,20 +120,26 @@ public class BQSRIntegrationTest extends WalkerTest {
@DataProvider(name = "PRTest")
public Object[][] createPRTestData() {
return new Object[][]{
{new PRTest("", "ab2f209ab98ad3432e208cbd524a4c4a")},
{new PRTest(" -qq -1", "5226c06237b213b9e9b25a32ed92d09a")},
{new PRTest(" -qq 6", "b592a5c62b952a012e18adb898ea9c33")},
{new PRTest(" -DIQ", "8977bea0c57b808e65e9505eb648cdf7")}
};
List<Object[]> tests = new ArrayList<Object[]>();
tests.add(new Object[]{1, new PRTest(" -qq -1", "a1d87da5dcbde35170d6ba6bc3ee2812")});
tests.add(new Object[]{1, new PRTest(" -qq 6", "a0fecae6d0e5ab9917862fa306186d10")});
tests.add(new Object[]{1, new PRTest(" -DIQ", "8977bea0c57b808e65e9505eb648cdf7")});
for ( final int nct : Arrays.asList(1, 2, 4) ) {
tests.add(new Object[]{nct, new PRTest("", "d1bbb4ce6aa93e866f106f8b11d888ed")});
}
return tests.toArray(new Object[][]{});
}
@Test(dataProvider = "PRTest")
public void testPR(PRTest params) {
public void testPR(final int nct, PRTest params) {
WalkerTestSpec spec = new WalkerTestSpec(
"-T PrintReads" +
" -R " + hg18Reference +
" -I " + privateTestDir + "HiSeq.1mb.1RG.bam" +
" -nct " + nct +
" -BQSR " + privateTestDir + "HiSeq.20mb.1RG.table" +
params.args +
" -o %s",

9
public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
View File

@ -116,9 +116,12 @@ public class BaseRecalibration {
// Compute all covariates for the read
// TODO -- the need to clear here suggests there's an error in the indexing / assumption code
// TODO -- for BI and DI. Perhaps due to the indel buffer size on the ends of the reads?
// TODO -- the output varies with -nt 1 and -nt 2 if you don't call clear here
// TODO -- needs to be fixed.
final ReadCovariates readCovariates = readCovariatesCache.get().clear();
// TODO -- the output varies depending on whether we clear or not
//final ReadCovariates readCovariates = readCovariatesCache.get().clear();
// the original code -- doesn't do any clearing
final ReadCovariates readCovariates = readCovariatesCache.get();
RecalUtils.computeCovariates(read, requestedCovariates, readCovariates);
for (final EventType errorModel : EventType.values()) { // recalibrate all three quality strings