From b3c0abd9e8bc2c8565afcf1eb90b6d8633aa3d67 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Sat, 20 Apr 2013 14:42:33 -0400
Subject: [PATCH] Remove REF_N status from DiagnoseTargets

This is not really feasible with the current mandate of this walker. We would have to traverse by reference and that would make the runtime much higher, and we are not really interested in the status 99% of the time anyway. There are other walkers that can report this, and just this, status more cheaply.

[fixes #48442663]
---
 .../gatk/walkers/diagnostics/targets/CallableStatus.java      | 2 --
 .../gatk/walkers/diagnostics/targets/IntervalStatistics.java  | 3 ---
 .../gatk/walkers/diagnostics/targets/SampleStatistics.java    | 4 ----
 .../diagnostics/targets/DiagnoseTargetsIntegrationTest.java   | 4 ++--
 4 files changed, 2 insertions(+), 11 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/CallableStatus.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/CallableStatus.java
index 4bc318b02..959c002ad 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/CallableStatus.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/CallableStatus.java
@@ -54,8 +54,6 @@ package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
  */
 public enum CallableStatus {
 
-    REF_N("the reference base was an N, which is not considered callable the GATK"),
-
     PASS("the base satisfied the min. depth for calling but had less than maxDepth to avoid having EXCESSIVE_COVERAGE"),
 
     COVERAGE_GAPS("absolutely no coverage was observed at a locus, regardless of the filtering parameters"),
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/IntervalStatistics.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/IntervalStatistics.java
index 0a6b73dae..4fd9a20ef 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/IntervalStatistics.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/IntervalStatistics.java
@@ -154,9 +154,6 @@ class IntervalStatistics {
                 output.add(status);
         }
 
-        if (hasNref)
-            output.add(CallableStatus.REF_N);
-
         // get median DP of each sample
         final double minMedianDepth = thresholds.getLowMedianDepthThreshold() * samples.size();
         final int nSamples = samples.size();
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatistics.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatistics.java
index 9efdbefe1..051369b94 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatistics.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatistics.java
@@ -139,10 +139,6 @@ class SampleStatistics {
         if ((totals.get(CallableStatus.POOR_QUALITY) / intervalSize) >= thresholds.getQualityStatusThreshold())
             output.add(CallableStatus.POOR_QUALITY);
 
-        if (totals.get(CallableStatus.REF_N) > 0)
-            output.add(CallableStatus.REF_N);
-
-
         if (output.isEmpty()) {
             output.add(CallableStatus.PASS);
         }
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargetsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargetsIntegrationTest.java
index a9330f2dd..a435a33ad 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargetsIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargetsIntegrationTest.java
@@ -66,11 +66,11 @@ public class DiagnoseTargetsIntegrationTest extends WalkerTest {
 
     @Test(enabled = true)
     public void testSingleSample() {
-        DTTest("testSingleSample ", "-I " + singleSample + " -max 75", "bd614643284a849724bf8ee6bc4df8bf");
+        DTTest("testSingleSample ", "-I " + singleSample + " -max 75", "3d558ec8828c269774ee45e5df086a5f");
     }
 
     @Test(enabled = true)
     public void testMultiSample() {
-        DTTest("testMultiSample ", "-I " + multiSample, "145f5d4641abfdeadbc59ee74ce1560f");
+        DTTest("testMultiSample ", "-I " + multiSample, "d40cf1f1daf68f2740cd411e2cf361fc");
     }
 }