From eb55061fd079d79ebfbe2f6091d31ba3dca5763b Mon Sep 17 00:00:00 2001
From: Guillermo del Angel <delangel@broadinstitute.org>
Date: Tue, 24 Jul 2012 12:16:15 -0400
Subject: [PATCH] a) Document BEAGLE codec, b) Bug fix: inbreeding coefficient
 shouldn't be computed for non-diploid organisms in current implementaiton

---
 .../walkers/annotator/InbreedingCoeff.java    |  3 ++
 .../utils/codecs/beagle/BeagleCodec.java      | 30 ++++++++++++++-----
 2 files changed, 26 insertions(+), 7 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
index fa3a7459b..715895526 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
@@ -68,6 +68,9 @@ public class InbreedingCoeff extends InfoFieldAnnotation implements StandardAnno
             if ( g.isNoCall() || !g.hasLikelihoods() )
                 continue;
 
+            if (g.getPloidy() != 2) // only work for diploid samples
+                continue;
+
             N++;
             final double[] normalizedLikelihoods = MathUtils.normalizeFromLog10( g.getLikelihoods().getAsVector() );
             refCount += normalizedLikelihoods[idxAA];
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java
index 3f72359fa..656b95e7a 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java
@@ -38,25 +38,41 @@ import java.util.*;
 import java.util.regex.Pattern;
 
 /**
- * TODO GUILLERMO DEL ANGEL
+ * Codec for Beagle imputation engine
  *
  * <p>
- * Codec Description
+ * Reads in tabular files with site markers and genotype posteriors, genotypes and phasing that Beagle produced
  * </p>
  *
  * <p>
- * See also: @see <a href="http://vcftools.sourceforge.net/specs.html">VCF specification</a><br>
+ * See also: @see <a href="http://faculty.washington.edu/browning/beagle/beagle.html">BEAGLE home page</a><br>
  * </p>
 
  * </p>
  *
- * <h2>File format example</h2>
+ * <h2>File format example for phased genotypes file</h2>
  * <pre>
- *     line 1
- *     line 2
- *     line 3
+ *     dummy header
+ *      20:60251 T T T T T T
+ *      20:60321 G G G G G G
+ *      20:60467 G G G G G G
  * </pre>
  *
+ * <h2>File format example for genotype posteriors</h2>
+ * <pre>
+ *     marker alleleA alleleB NA07056 NA07056 NA07056
+ *     20:60251 T C 0.9962 0.0038 0 0.99245 0.00755 0 0.99245 0.00755 0
+ *     20:60321 G T 0.98747 0.01253 0 0.99922 0.00078 0 0.99368 0.00632 0
+ *     20:60467 G C 0.97475 0.02525 0 0.98718 0.01282 0 0.98718 0.01282 0
+ * </pre>
+ *
+ * <h2>File format example for r2 file
+ * <pre>
+ *      20:60251        0.747
+ *      20:60321        0.763
+ *      20:60467        0.524
+ * </pre>
+ * </h2>
  * @author Mark DePristo
  * @since 2010
  */