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a) Document BEAGLE codec, b) Bug fix: inbreeding coefficient shouldn't be computed for non-diploid organisms in current implementaiton

This commit is contained in:
Guillermo del Angel 2012-07-24 12:16:15 -04:00
parent c011837147
commit eb55061fd0
2 changed files with 26 additions and 7 deletions
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3
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
View File

@ -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];

30
public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java
View File

@ -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
*/