From b234019cf56e17d75b6f75296ffc5237cc090a16 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 15 Dec 2009 14:50:56 +0000
Subject: [PATCH] Readded locus printing suppression to DoC walker (and removed
 unused import from UG)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2358 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../coverage/DepthOfCoverageWalker.java        | 18 ++++++++++++------
 .../walkers/genotyper/UnifiedGenotyper.java    |  1 -
 2 files changed, 12 insertions(+), 7 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 0141539c3..b3a74168b 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
@@ -43,13 +43,16 @@ import java.util.*;
 @By(DataSource.REFERENCE)
 public class DepthOfCoverageWalker extends LocusWalker<DepthOfCoverageWalker.DoCInfo, DepthOfCoverageWalker.DoCInfo> {
 
-    @Argument(fullName="printBaseCounts", shortName = "bases", doc="Print individual base counts (A,C,G,T only)", required=false)
+    @Argument(fullName="suppressLocusPrinting", shortName= "noLocus", doc="Suppress printing", required=false)
+    public boolean suppressLocusPrinting = false;
+
+    @Argument(fullName="printBaseCounts", shortName ="bases", doc="Print individual base counts (A,C,G,T only)", required=false)
     protected boolean printBaseCounts = false;
 
-    @Argument(fullName="minMAPQ", shortName = "minMAPQ", doc="If provided, we will also list read counts with MAPQ >= this value at a locus in coverage",required=false)
+    @Argument(fullName="minMAPQ", shortName ="minMAPQ", doc="If provided, we will also list read counts with MAPQ >= this value at a locus in coverage",required=false)
     protected int excludeMAPQBelowThis = -1;
 
-    @Argument(fullName="minDepth", shortName = "minDepth", doc="If provided, we will also list the percentage of loci with depth >= this value per interval",required=false)
+    @Argument(fullName="minDepth", shortName ="minDepth", doc="If provided, we will also list the percentage of loci with depth >= this value per interval",required=false)
     protected int minDepthForPercentage = -1;
 
     @Argument(fullName="byReadGroup", shortName="byRG", doc="List read depths for each read group")
@@ -99,8 +102,10 @@ public class DepthOfCoverageWalker extends LocusWalker<DepthOfCoverageWalker.DoC
         }
 
         // build and print the per-locus header
-        out.println("\nPER_LOCUS_COVERAGE_SECTION");
-        printHeaderLine(false);
+        if ( !suppressLocusPrinting ) {
+            out.println("\nPER_LOCUS_COVERAGE_SECTION");
+            printHeaderLine(false);
+        }
     }
 
     public DoCInfo map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
@@ -153,7 +158,8 @@ public class DepthOfCoverageWalker extends LocusWalker<DepthOfCoverageWalker.DoC
         if ( printHistogram )
             incCov(info.totalCoverage);
 
-        printDoCInfo(context.getLocation(), info, false);
+        if ( !suppressLocusPrinting )
+            printDoCInfo(context.getLocation(), info, false);
 
         return info;
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index aca57e18b..da3bae24b 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -39,7 +39,6 @@ import org.broadinstitute.sting.utils.genotype.*;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeRecord;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.alignment.Alignment;
 
 import net.sf.samtools.SAMReadGroupRecord;