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

Merge pull request #985 from broadinstitute/sa_refactor_cleansing_hack_negative_zeros_973_depends_on_841 

removed in-line conditional (hack) that changed the result from 0.0 to -0.0; see issue #841
This commit is contained in:
Geraldine Van der Auwera 2015-05-23 00:02:52 -04:00
parent 27d3bafcbd 8d25b2ba40
commit 526f7c0d07
1 changed files with 2 additions and 6 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

8
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypingEngine.java
View File

@ -250,12 +250,8 @@ public abstract class GenotypingEngine<Config extends StandardCallerArgumentColl
final GenomeLoc loc = genomeLocParser.createGenomeLoc(vc);
final List<Allele> outputAlleles = outputAlternativeAlleles.outputAlleles(vc.getReference());
final VariantContextBuilder builder = new VariantContextBuilder(callSourceString(), loc.getContig(), loc.getStart(), loc.getStop(), outputAlleles);
// Seems that when log10PError is 0.0, you must pass -0.0 to get a nice output at the other end otherwise is a "-0".
// Truth is that this should be fixed in the "variant" dependency code but perhaps it can be amended also in the VariantContextWriter.
//TODO Please remove this comment when this has been fixed (PT https://www.pivotaltracker.com/story/show/69492530)
//TODO and change the code below accordingly.
builder.log10PError(log10Confidence == 0.0 ? -0.0 : log10Confidence);
builder.log10PError(log10Confidence);
if ( ! passesCallThreshold(phredScaledConfidence) )
builder.filter(GATKVCFConstants.LOW_QUAL_FILTER_NAME);