From 1dfaacfeb5f1e7b31b10be94605f15622d2a4cbc Mon Sep 17 00:00:00 2001
From: Menachem Fromer <fromer@broadinstitute.org>
Date: Thu, 22 Mar 2012 12:40:15 -0400
Subject: [PATCH] Check for consistency of the BAM and VCF sample names, with a
 command line disable to throw if you know what you are doing

---
 .../phasing/ReadBackedPhasingWalker.java      | 23 +++++++++++++++----
 1 file changed, 19 insertions(+), 4 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
index 9470ce2f4..734ade376 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
@@ -36,8 +36,10 @@ import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.HasGenomeLocation;
+import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.variantcontext.*;
@@ -121,8 +123,11 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
     public int MIN_MAPPING_QUALITY_SCORE = 20;
 
     @Argument(fullName = "sampleToPhase", shortName = "sampleToPhase", doc = "Only include these samples when phasing", required = false)
-    protected Set
-            <String> samplesToPhase = null;
+    protected Set<String> samplesToPhase = null;
+
+    @Hidden
+    @Argument(fullName = "permitNoSampleOverlap", shortName = "permitNoSampleOverlap", doc = "Don't exit (just WARN) when the VCF and BAMs do not overlap in samples", required = false)
+    private boolean permitNoSampleOverlap = false;
 
     private GenomeLoc mostDownstreamLocusReached = null;
 
@@ -205,8 +210,18 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
         // todo -- fix samplesToPhase
         String trackName = variantCollection.variants.getName();
         Map<String, VCFHeader> rodNameToHeader = getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName));
-        Set<String> samples = new TreeSet<String>(samplesToPhase == null ? rodNameToHeader.get(trackName).getGenotypeSamples() : samplesToPhase);
-        writer.writeHeader(new VCFHeader(hInfo, samples));
+        Set<String> vcfSamples = new TreeSet<String>(samplesToPhase == null ? rodNameToHeader.get(trackName).getGenotypeSamples() : samplesToPhase);
+        writer.writeHeader(new VCFHeader(hInfo, vcfSamples));
+
+        Set<String> readSamples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader());
+        readSamples.retainAll(vcfSamples);
+        if (readSamples.isEmpty()) {
+            String noPhaseString = "No common samples in VCF and BAM headers" + (samplesToPhase == null ? "" : " (limited to sampleToPhase parameters)") + ", so nothing could possibly be phased!";
+            if (permitNoSampleOverlap)
+                logger.warn(noPhaseString);
+            else
+                throw new UserException(noPhaseString);
+        }
     }
 
     public boolean generateExtendedEvents() {