From 2b923f1568329ce3af4d1953746e74e327ea0c44 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Sat, 20 Apr 2013 13:05:14 -0400
Subject: [PATCH] fix for DiagnoseTargets multiple filter output

Problem
-------
Diagnose targets is outputting both LOW_MEDIAN_COVERAGE and NO_READS when no reads are covering the interval

Solution
--------
Only allow low median coverage check if there are reads

[fixes #48442675]
---
 .../targets/IntervalStatistics.java           | 20 ++++++++++++++-----
 .../diagnostics/targets/SampleStatistics.java |  2 +-
 .../DiagnoseTargetsIntegrationTest.java       |  4 ++--
 3 files changed, 18 insertions(+), 8 deletions(-)

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 0aea54fa0..0a6b73dae 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
@@ -148,24 +148,34 @@ class IntervalStatistics {
                 votes.put(status, votes.get(status) + 1);
 
         // output tall values above the threshold
+        final double minVotesNeeded = thresholds.getVotePercentageThreshold() * samples.size();
         for (CallableStatus status : votes.keySet()) {
-            if (votes.get(status) > (samples.size() * thresholds.getVotePercentageThreshold()) && !(status.equals(CallableStatus.PASS)))
+            if (!status.equals((CallableStatus.PASS)) && votes.get(status) > minVotesNeeded)
                 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();
         int nLowMedianDepth = 0;
+        int samplesSeen = 0;
         for (SampleStatistics sample : samples.values()) {
-            if (sample.getQuantileDepth(0.5) < thresholds.getMinimumMedianDepth())
+            samplesSeen++;
+            final double medianDepth = sample.getQuantileDepth(0.5);
+            if (medianDepth > 0 && medianDepth < thresholds.getMinimumMedianDepth()) {
                 nLowMedianDepth++;
+            }
+            if (nLowMedianDepth > minMedianDepth) {
+                output.add(CallableStatus.LOW_MEDIAN_DEPTH);
+                break;
+            }
+            if (nSamples - samplesSeen + nLowMedianDepth < minMedianDepth)
+                break;
         }
 
-        if (nLowMedianDepth > (samples.size() * thresholds.getLowMedianDepthThreshold()))
-            output.add(CallableStatus.LOW_MEDIAN_DEPTH);
 
         return output;
     }
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 ad9f287d2..9efdbefe1 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
@@ -101,7 +101,7 @@ class SampleStatistics {
      * @return the callable statuses of the entire sample
      */
     public Set<CallableStatus> getCallableStatuses(ThresHolder thresholds) {
-        // We check if reads are present ot prevent div / 0 exceptions
+        // We check if reads are present to prevent div / 0 exceptions
         if (nReads == 0) {
             return Collections.singleton(CallableStatus.NO_READS);
         }
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 2875e10d7..a9330f2dd 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", "9b51561bcf248da70a4d711380b04f7b");
+        DTTest("testSingleSample ", "-I " + singleSample + " -max 75", "bd614643284a849724bf8ee6bc4df8bf");
     }
 
     @Test(enabled = true)
     public void testMultiSample() {
-        DTTest("testMultiSample ", "-I " + multiSample, "925f88f0c41c6a9ac479be34e052dc5d");
+        DTTest("testMultiSample ", "-I " + multiSample, "145f5d4641abfdeadbc59ee74ce1560f");
     }
 }