Changed min MQ and BQ to 20 (for phasing)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4469 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java

@@ -77,10 +77,10 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
     protected String variantStatsFilePrefix = null;
 
     @Argument(fullName = "min_base_quality_score", shortName = "mbq", doc = "Minimum base quality required to consider a base for phasing [default: 10]", required = false)
-    public int MIN_BASE_QUALITY_SCORE = 10;
+    public int MIN_BASE_QUALITY_SCORE = 20;
 
     @Argument(fullName = "min_mapping_quality_score", shortName = "mmq", doc = "Minimum read mapping quality required to consider a read for phasing [default: 10]", required = false)
-    public int MIN_MAPPING_QUALITY_SCORE = 10;
+    public int MIN_MAPPING_QUALITY_SCORE = 20;
 
     private LinkedList<VariantAndReads> unphasedSiteQueue = null;
     private DoublyLinkedList<UnfinishedVariantAndReads> partiallyPhasedSites = null; // the phased VCs to be emitted, and the alignment bases at these positions

java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypePhasingEvaluator.java

@@ -229,7 +229,7 @@ public class GenotypePhasingEvaluator extends VariantEvaluator {
     }
 
     public String toString(AllelePair prev, AllelePair cur) {
-        return prev.getTopAllele().getBaseString() + "," + cur.getTopAllele().getBaseString() + "|" + prev.getBottomAllele().getBaseString() + "," + cur.getBottomAllele().getBaseString();
+        return prev.getTopAllele().getBaseString() + "+" + cur.getTopAllele().getBaseString() + "|" + prev.getBottomAllele().getBaseString() + "+" + cur.getBottomAllele().getBaseString();
     }
 
     public void finalizeEvaluation() {

java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java

@@ -25,7 +25,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10)
                         + " -L chr20:332341-382503",
                 1,
-                Arrays.asList("c59e8773efe79e1195b320d2735e1c16"));
+                Arrays.asList("87537a80ea09d694470d52f579276b37"));
         executeTest("MAX 10 het sites [TEST ONE]; require PQ >= 10", spec);
     }
 
@@ -35,7 +35,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10)
                         + " -L chr20:1232503-1332503",
                 1,
-                Arrays.asList("d9cf20f506f2d0aa196fa89c051532c6"));
+                Arrays.asList("44b711c53d435015d32039114860ff0d"));
         executeTest("MAX 10 het sites [TEST TWO]; require PQ >= 10", spec);
     }
 
@@ -45,7 +45,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 2, 30)
                         + " -L chr20:332341-382503",
                 1,
-                Arrays.asList("e3ea64260f517830633b0060b3594178"));
+                Arrays.asList("71eb6bfc7568897f023200d13a60eca0"));
         executeTest("MAX 2 het sites [TEST THREE]; require PQ >= 30", spec);
     }
 
@@ -55,7 +55,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 5, 100)
                         + " -L chr20:332341-382503",
                 1,
-                Arrays.asList("435825a2a034ca27047fbd8a1dc1e0b2"));
+                Arrays.asList("b09d2a1415045b963292f9e04675111b"));
         executeTest("MAX 5 het sites [TEST FOUR]; require PQ >= 100", spec);
     }
 
@@ -65,8 +65,19 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 1000, 7, 10)
                         + " -L chr20:332341-482503",
                 1,
-                Arrays.asList("d5897638dd317c3347b15ef05a13e53a"));
+                Arrays.asList("7639dd25101081288520b343bfe1fa61"));
         executeTest("MAX 7 het sites [TEST FIVE]; require PQ >= 10; cacheWindow = 1000", spec);
     }
 
+    @Test
+    public void test6() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10)
+                        + " -L chr20:652810-681757",
+                1,
+                Arrays.asList("5c60272590daa6cdbafac234137528ef"));
+        executeTest("MAX 10 het sites [TEST SIX]; require PQ >= 10; cacheWindow = 20000; has inconsistent sites", spec);
+    }
+
+
 }