From 042930153659d3fca1c5b754f130a72acbab37c3 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 26 Jan 2011 14:52:38 +0000
Subject: [PATCH] Added ability to output just sites (no genotypes) from UG
 with the --sites_only argument.  Note that we do still genotype in this mode
 so that the INFO annotations are identical, but we strip the genotypes out of
 the VC right before writing to output.  In other words, this is not designed
 to make UG go faster; the point here is to allow downstream tools not to have
 to parse GTs if they don't want to.  Here you go, Ryan.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5081 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/genotyper/UnifiedArgumentCollection.java     | 4 ++++
 .../sting/gatk/walkers/genotyper/UnifiedGenotyper.java        | 3 +++
 .../sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java  | 3 +++
 3 files changed, 10 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
index 4efc0b8a9..001687b74 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
@@ -45,6 +45,9 @@ public class UnifiedArgumentCollection {
     public Double PCR_error = DiploidSNPGenotypeLikelihoods.DEFAULT_PCR_ERROR_RATE;
 
     // control the output
+    @Argument(fullName = "sites_only", shortName = "sites_only", doc = "Should we output just sites without genotypes (i.e. only the first 8 columns of the VCF)?", required = false)
+    public boolean SITES_ONLY = false;
+
     @Argument(fullName = "genotype", shortName = "genotype", doc = "Should we output confident genotypes (i.e. including ref calls) or just the variants?", required = false)
     public boolean GENOTYPE_MODE = false;
 
@@ -106,6 +109,7 @@ public class UnifiedArgumentCollection {
         uac.GLmodel = GLmodel;
         uac.heterozygosity = heterozygosity;
         uac.PCR_error = PCR_error;
+        uac.SITES_ONLY = SITES_ONLY;
         uac.GENOTYPE_MODE = GENOTYPE_MODE;
         uac.ALL_BASES_MODE = ALL_BASES_MODE;
         uac.NO_SLOD = NO_SLOD;
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 c6f6d986a..bf0879a73 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -129,6 +129,9 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
         annotationEngine = new VariantAnnotatorEngine(getToolkit(), Arrays.asList(annotationClassesToUse), annotationsToUse);
         UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, verboseWriter, annotationEngine, samples);
 
+        if ( UAC.SITES_ONLY )
+            samples.clear();
+
         // initialize the header
         writer.writeHeader(new VCFHeader(getHeaderInfo(), samples)) ;
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index 9ea341d92..d4f009937 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -400,6 +400,9 @@ public class UnifiedGenotyperEngine {
             vcCall = variantContexts.iterator().next(); // we know the collection will always have exactly 1 element.
         }
 
+        if ( UAC.SITES_ONLY )
+            vcCall = VariantContext.modifyGenotypes(vcCall, null);
+
         VariantCallContext call = new VariantCallContext(vcCall, passesCallThreshold(phredScaledConfidence, atTriggerTrack));
         call.setRefBase(refContext.getBase());
         return call;