From 92cf7744a603a8d68b8cc31bc2d8b8d1c1c53fbc Mon Sep 17 00:00:00 2001
From: fromer <fromer@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 3 Dec 2010 16:31:13 +0000
Subject: [PATCH] Set minMQ = max(minMQ, minBQ) for phasing since anyway we cap
 BQ by MQ; also, lowered MIN_BASE_QUALITY_SCORE for phasing to 17 (was
 previously 20)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4781 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/phasing/ReadBackedPhasingWalker.java  | 15 ++++++++++++---
 .../phasing/ReadBackedPhasingIntegrationTest.java | 12 ++++++------
 2 files changed, 18 insertions(+), 9 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
index 50466f5e0..307809a46 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
@@ -81,10 +81,10 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
     protected String variantStatsFilePrefix = null;
     private PhasingQualityStatsWriter statsWriter = 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 = 20;
+    @Argument(fullName = "min_base_quality_score", shortName = "mbq", doc = "Minimum base quality required to consider a base for phasing [default: 17]", required = false)
+    public int MIN_BASE_QUALITY_SCORE = 17;
 
-    @Argument(fullName = "min_mapping_quality_score", shortName = "mmq", doc = "Minimum read mapping quality required to consider a read for phasing [default: 10]", required = false)
+    @Argument(fullName = "min_mapping_quality_score", shortName = "mmq", doc = "Minimum read mapping quality required to consider a read for phasing [default: 20]", required = false)
     public int MIN_MAPPING_QUALITY_SCORE = 20;
 
     private GenomeLoc mostDownstreamLocusReached = null;
@@ -122,6 +122,15 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
         rodNames = new LinkedList<String>();
         rodNames.add("variant");
 
+        /*
+         Since we cap each base quality (BQ) by its read's mapping quality (MQ) [in Read.updateBaseAndQuality()], then:
+         if minBQ > minMQ, then we require that MQ be >= minBQ as well.
+         [Otherwise, we end up capping BQ by MQ only AFTER we tried removing bases with BQ < minBQ, which is WRONG!]
+
+         To do this properly, we set: minMQ = max(minMQ, minBQ)
+         */
+        MIN_MAPPING_QUALITY_SCORE = Math.max(MIN_MAPPING_QUALITY_SCORE, MIN_BASE_QUALITY_SCORE);
+
         unphasedSiteQueue = new LinkedList<VariantAndReads>();
         partiallyPhasedSites = new DoublyLinkedList<UnfinishedVariantAndReads>();
 
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java
index 27dfa353c..b0e77820e 100644
--- a/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java
@@ -26,7 +26,7 @@ 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("3994aed2a117b93aa5010ea131033aea"));
+                Arrays.asList("ce29d2e84ab6e4f4ed3a81467f19694d"));
         executeTest("MAX 10 het sites [TEST ONE]; require PQ >= 10", spec);
     }
 
@@ -36,7 +36,7 @@ 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("61768bcdcbf9aeef62bfd44862155ec3"));
+                Arrays.asList("4f4773bb7463c0892d427c2a3db385d7"));
         executeTest("MAX 10 het sites [TEST TWO]; require PQ >= 10", spec);
     }
 
@@ -46,7 +46,7 @@ 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("98261406ac4c587eb4444ad06d40507b"));
+                Arrays.asList("92d5b82dd0fa9268a5067ae633cb1a65"));
         executeTest("MAX 2 het sites [TEST THREE]; require PQ >= 30", spec);
     }
 
@@ -56,7 +56,7 @@ 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("d8464f2d2cf07e344986e417be8fce14"));
+                Arrays.asList("33d390ff7b6009f1bc767dac985e3aac"));
         executeTest("MAX 5 het sites [TEST FOUR]; require PQ >= 100", spec);
     }
 
@@ -66,7 +66,7 @@ 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("1dee7950ab0ec27e1ee081c064159776"));
+                Arrays.asList("f1cd792644664330d19bd8be11154450"));
         executeTest("MAX 7 het sites [TEST FIVE]; require PQ >= 10; cacheWindow = 1000", spec);
     }
 
@@ -76,7 +76,7 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
                 baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10)
                         + " -L chr20:652810-681757",
                 1,
-                Arrays.asList("e4f4de185bdbfaf067004c187419ac4c"));
+                Arrays.asList("699e02c132b08fa4e572f1ead3045e3e"));
         executeTest("MAX 10 het sites [TEST SIX]; require PQ >= 10; cacheWindow = 20000; has inconsistent sites", spec);
     }