From dbb8b86ed189c76b06d9ca549364963f43385bac Mon Sep 17 00:00:00 2001 From: depristo Date: Wed, 2 Dec 2009 22:53:17 +0000 Subject: [PATCH] Minor updates to correctly handle emitting FN calls git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2231 348d0f76-0448-11de-a6fe-93d51630548a --- python/snpSelector.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/python/snpSelector.py b/python/snpSelector.py index 1fd7999cd..5bdc4dbab 100755 --- a/python/snpSelector.py +++ b/python/snpSelector.py @@ -571,10 +571,13 @@ def evaluateTruth(header, callVCF, truth, truthVCF): writeRecalibratedCalls(callVCF, header, calls) + def isFN(v): + return isVariantInSample(v, OPTIONS.useSample) and not v.hasField("FN") + if truth <> None and OPTIONS.FNoutputVCF: f = open(OPTIONS.FNoutputVCF, 'w') #print 'HEADER', header - for line in formatVCF(header, filter( lambda x: not x.hasField("FN"), truth.itervalues())): + for line in formatVCF(header, filter( isFN, truth.itervalues())): print >> f, line f.close()