Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java

@@ -172,7 +172,7 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> implements T
         vcfWriter.writeHeader(vcfHeader);
     }
 
-    public static final void addVQSRStandardHeaderLines(final Set<VCFHeaderLine> hInfo) {
+    public static void addVQSRStandardHeaderLines(final Set<VCFHeaderLine> hInfo) {
         hInfo.add(VCFStandardHeaderLines.getInfoLine(VCFConstants.END_KEY));
         hInfo.add(new VCFInfoHeaderLine(VariantRecalibrator.VQS_LOD_KEY, 1, VCFHeaderLineType.Float, "Log odds ratio of being a true variant versus being false under the trained gaussian mixture model"));
         hInfo.add(new VCFInfoHeaderLine(VariantRecalibrator.CULPRIT_KEY, 1, VCFHeaderLineType.String, "The annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out"));
@@ -236,7 +236,9 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> implements T
                     filterString = tranches.get(0).name+"+";
                 }
 
-                if( !filterString.equals(VCFConstants.PASSES_FILTERS_v4) ) {
+                if( filterString.equals(VCFConstants.PASSES_FILTERS_v4) ) {
+                    builder.passFilters();
+                } else {
                     builder.filters(filterString);
                 }
 

public/java/src/org/broadinstitute/sting/utils/Haplotype.java

@@ -44,6 +44,8 @@ public class Haplotype {
     private boolean isRef = false;
     private Cigar cigar;
     private int alignmentStartHapwrtRef;
+    public int leftBreakPoint = 0;
+    public int rightBreakPoint = 0;
  
     /**
      * Create a simple consensus sequence with provided bases and a uniform quality over all bases of qual

public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java

@@ -268,7 +268,12 @@ class JEXLMap implements Map<VariantContextUtils.JexlVCMatchExp, Boolean> {
             // treat errors as no match
             jexl.put(exp, value == null ? false : value);
         } catch (Exception e) {
-            throw new UserException.CommandLineException(String.format("Invalid JEXL expression detected for %s with message %s", exp.name, e.getMessage()));
+            // if exception happens because variable is undefined (i.e. field in expression is not present), evaluate to FALSE
+            // todo - might be safer if we explicitly checked for an exception type, but Apache's API doesn't seem to have that ability
+            if (e.getMessage().contains("undefined variable"))
+                jexl.put(exp,false);
+            else
+                throw new UserException.CommandLineException(String.format("Invalid JEXL expression detected for %s with message %s", exp.name, e.getMessage()));
         }
     }
 

public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java

@@ -18,6 +18,11 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
             this.recalMD5 = recalMD5;
             this.cutVCFMD5 = cutVCFMD5;
         }
+
+        @Override
+        public String toString() {
+            return "VRTest{inVCF='" + inVCF +"'}";
+        }
     }
 
     VRTest lowPass = new VRTest("phase1.projectConsensus.chr20.raw.snps.vcf",
@@ -69,14 +74,21 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
         executeTest("testApplyRecalibration-"+params.inVCF, spec);
     }
 
-    VRTest indel = new VRTest("combined.phase1.chr20.raw.indels.sites.vcf",
+    VRTest indelUnfiltered = new VRTest(
+            "combined.phase1.chr20.raw.indels.unfiltered.sites.vcf", // all FILTERs as .
             "b7589cd098dc153ec64c02dcff2838e4",  // tranches
             "a04a9001f62eff43d363f4d63769f3ee",  // recal file
-            "888eb042dd33b807bcbb8630896fda94"); // cut VCF
+            "64f576881e21323dd4078262604717a2"); // cut VCF
+
+    VRTest indelFiltered = new VRTest(
+            "combined.phase1.chr20.raw.indels.filtered.sites.vcf", // all FILTERs as PASS
+            "b7589cd098dc153ec64c02dcff2838e4",  // tranches
+            "a04a9001f62eff43d363f4d63769f3ee",  // recal file
+            "af22c55d91394c56a222fd40d6d54781"); // cut VCF
 
     @DataProvider(name = "VRIndelTest")
-    public Object[][] createData2() {
+    public Object[][] createTestVariantRecalibratorIndel() {
-        return new Object[][]{ {indel} };
+        return new Object[][]{ {indelUnfiltered}, {indelFiltered} };
     }
 
     @Test(dataProvider = "VRIndelTest")

public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java

@@ -70,6 +70,19 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         executeTest("testComplexSelection--" + testfile, spec);
     }
 
+    @Test
+    public void testNonExistingFieldSelection() {
+        String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf";
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString(" -env -ef -select 'foo!=0||DP>0' --variant " + testfile),
+                1,
+                Arrays.asList("44e77cea624cfff2b8acc3a4b30485cb")    // should yield empty vcf because the foo!=0 will yield complete expression false
+        );
+        spec.disableShadowBCF();
+        executeTest("testNonExistingSelection--" + testfile, spec);
+    }
+
     @Test
     public void testSampleExclusion() {
         String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf";