From cc8c12b9548cc24d13dbcc9f798e3f3dab4ded98 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Thu, 25 Oct 2012 14:46:09 -0400
Subject: [PATCH] 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
---
 .../walkers/bqsr/BQSRIntegrationTest.java     | 22 +++++++++++++------
 .../recalibration/BaseRecalibration.java      |  9 +++++---
 2 files changed, 21 insertions(+), 10 deletions(-)

diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java
index 90d67d393..a50219f48 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java
@@ -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",
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
index 7ad9302a8..2f9387acb 100644
--- a/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
+++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
@@ -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