From eca09426449a2e2fced71dda26fd77b6f34635eb Mon Sep 17 00:00:00 2001 From: chartl Date: Wed, 4 Nov 2009 17:14:55 +0000 Subject: [PATCH] Oops. Let's make sure only to write calls that the pool supports to the auxiliary vcf files. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1974 348d0f76-0448-11de-a6fe-93d51630548a --- python/expandedSummaryToVCF.py | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/python/expandedSummaryToVCF.py b/python/expandedSummaryToVCF.py index 2fa3d4821..8affcfdc4 100755 --- a/python/expandedSummaryToVCF.py +++ b/python/expandedSummaryToVCF.py @@ -145,10 +145,11 @@ for line in callFile: except KeyError: # do nothing pass - #print this out to the file - chromsplit = chrompos.split(":") - outstr=chromsplit[0]+"\t"+chromsplit[1]+"\t"+dbSNP+"\t"+ref+"\t"+variant+"\t"+str(qual)+"\t0\t"+"DP="+str(depth)+";SB="+str(slod)+"\n" - pooledOutputFiles[i].write(outstr) + if grep(poolInternalIDs[i],supportingPools): + #print this out to the file + chromsplit = chrompos.split(":") + outstr=chromsplit[0]+"\t"+chromsplit[1]+"\t"+dbSNP+"\t"+ref+"\t"+variant+"\t"+str(qual)+"\t0\t"+"DP="+str(depth)+";SB="+str(slod)+"\n" + pooledOutputFiles[i].write(outstr) #now update data total_slod = total_slod + float(slod) total_depth = total_depth + int(depth) @@ -163,7 +164,7 @@ for line in callFile: #propagate individual pool information for i in range(len(poolNames)): phase = "0/0" - if grep(poolNames[i],supportingPools): + if grep(poolInternalIDs[i],supportingPools): phase = "0/1" else: phase = "0/0"