zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Cleanup: remove code to calculate the MLE AC in the UGE.

This commit is contained in:
Christopher Hartl 2012-01-03 15:58:51 -05:00
parent 2d093828a4
commit 9093de1132
1 changed files with 0 additions and 5 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

5
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
View File

@ -401,11 +401,6 @@ public class UnifiedGenotyperEngine {
// *** note that calculating strand bias involves overwriting data structures, so we do that last // *** note that calculating strand bias involves overwriting data structures, so we do that last
final HashMap<String, Object> attributes = new HashMap<String, Object>(); final HashMap<String, Object> attributes = new HashMap<String, Object>();
List<Integer> mlecounts = new ArrayList<Integer>(AFresult.log10AlleleFrequencyPosteriors.length);
for ( int i = 0; i < AFresult.log10AlleleFrequencyLikelihoods.length ; i++) {
mlecounts.add(MathUtils.maxElementIndex(AFresult.log10AlleleFrequencyLikelihoods[i]));
}
attributes.put("MLEAC",Utils.join(",",mlecounts));
// if the site was downsampled, record that fact // if the site was downsampled, record that fact
if ( !limitedContext && rawContext.hasPileupBeenDownsampled() ) if ( !limitedContext && rawContext.hasPileupBeenDownsampled() )