From 861221d0465cbce0ef2f09816e42838906ba5bee Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 4 Dec 2009 02:15:43 +0000
Subject: [PATCH] - Moved various header line printing into a single method -
 Fixed output for coverage above min depth

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2254 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../coverage/DepthOfCoverageWalker.java       | 61 ++++++++-----------
 .../DepthOfCoverageIntegrationTest.java       |  6 +-
 2 files changed, 29 insertions(+), 38 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
index 835b3ab25..7be290f8a 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
@@ -98,27 +98,7 @@ public class DepthOfCoverageWalker extends LocusWalker<DepthOfCoverageWalker.DoC
 
         // build and print the per-locus header
         out.println("\nPER_LOCUS_COVERAGE_SECTION");
-        StringBuilder header = new StringBuilder("location\ttotal_coverage\tcoverage_without_deletions");
-        if ( excludeMAPQBelowThis > 0 ) {
-            header.append("\tcoverage_atleast_MQ");
-            header.append(excludeMAPQBelowThis);
-        }
-        if ( printBaseCounts ) {
-            header.append("\tA_count\tC_count\tG_count\tT_count");
-        }
-        if ( byReadGroup ) {
-            for ( String rg : readGroupNames ) {
-                header.append("\tcoverage_for_");
-                header.append(rg);
-            }
-        }
-        if ( bySample ) {
-            for ( String sample : sampleNames ) {
-                header.append("\tcoverage_for_");
-                header.append(sample);
-            }
-        }
-        out.println(header.toString());
+        printHeaderLine(false);
     }
 
     public DoCInfo map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
@@ -217,17 +197,36 @@ public class DepthOfCoverageWalker extends LocusWalker<DepthOfCoverageWalker.DoC
 
         // build and print the per-interval header
         out.println("\n\nPER_INTERVAL_COVERAGE_SECTION");
+        printHeaderLine(true);
 
-        StringBuilder header = new StringBuilder("location\ttotal_coverage\taverage_coverage\tcoverage_without_deletions\taverage_coverage_without_deletions");
+        // print all of the individual per-interval coverage data
+        for ( Pair<GenomeLoc, DoCInfo> result : results )
+            printDoCInfo(result.first, result.second, true);
+
+        // if we need to print the histogram, do so now
+        if ( printHistogram )
+            printHisto();
+    }
+
+    private void printHeaderLine(boolean printAverageCoverage) {
+
+        StringBuilder header = new StringBuilder("location\ttotal_coverage");
+        if ( printAverageCoverage )
+            header.append("\taverage_coverage");
+        header.append("\tcoverage_without_deletions");
+        if ( printAverageCoverage )
+            header.append("\taverage_coverage_without_deletions");
         if ( excludeMAPQBelowThis > 0 ) {
             header.append("\tcoverage_atleast_MQ");
             header.append(excludeMAPQBelowThis);
-            header.append("\taverage_coverage_atleast_MQ");
-            header.append(excludeMAPQBelowThis);
+            if ( printAverageCoverage ) {
+                header.append("\taverage_coverage_atleast_MQ");
+                header.append(excludeMAPQBelowThis);
+            }
         }
-        if ( minDepthForPercentage >= 0 ) {
+        if ( printAverageCoverage && minDepthForPercentage >= 0 ) {
             header.append("\tpercent_loci_covered_atleast_depth");
-            header.append(minDepthForPercentage);            
+            header.append(minDepthForPercentage);
         }
         if ( printBaseCounts ) {
             header.append("\tA_count\tC_count\tG_count\tT_count");
@@ -245,14 +244,6 @@ public class DepthOfCoverageWalker extends LocusWalker<DepthOfCoverageWalker.DoC
             }
         }
         out.println(header.toString());
-
-        // print all of the individual per-interval coverage data
-        for ( Pair<GenomeLoc, DoCInfo> result : results )
-            printDoCInfo(result.first, result.second, true);
-
-        // if we need to print the histogram, do so now
-        if ( printHistogram )
-            printHisto();
     }
 
     private void incCov(int depth) {
@@ -348,7 +339,7 @@ public class DepthOfCoverageWalker extends LocusWalker<DepthOfCoverageWalker.DoC
             }
         }
 
-        if ( minDepthForPercentage >= 0 ) {
+        if ( printAverageCoverage && minDepthForPercentage >= 0 ) {
             sb.append("\t");
             sb.append(String.format("%.2f", ((double)info.minDepthCoveredLoci) / totalBases));            
         }
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageIntegrationTest.java
index ed7ef390c..13ff007cd 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageIntegrationTest.java
@@ -15,13 +15,13 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest {
     static {
         expectations.put("-minMAPQ 1", "8b73fad5cce4620907d5da2a985219d5");
         expectations.put("-minMAPQ 100", "1a959892d8ad0523dac2fb097eacb3c2");
-        expectations.put("-minDepth 8", "6e8c6b6d78962d110c87ad905fa5b664");
-        expectations.put("-minDepth 10", "14399e1237866540af3f1aee149030d0");
+        expectations.put("-minDepth 8", "6d549e5a5c4c55420d68e0221a955a0e");
+        expectations.put("-minDepth 10", "a367c894e6a48ebb107d2fe004cdfee7");
         expectations.put("-bySample", "93358437153b4d65bdff747e33de1d63");
         expectations.put("-byRG", "777e8427eb4bdad300b23800cb7b0592");
         expectations.put("-histogram", "96f15e1d9d598d48191e20ee84715d46");
         expectations.put("-bases", "baafcb2b90098cad1c5950da9e9932a6");
-        expectations.put("-minMAPQ 1 -bySample -byRG -minDepth 8 -histogram -bases", "eb27297504e003ce7bb42300dfd436fe");
+        expectations.put("-minMAPQ 1 -bySample -byRG -minDepth 8 -histogram -bases", "bf2094b33e0e10fc11a7216bc1097a8b");
     }
 
     @Test