if "chr" not in chrom:
chrom="chr"+chrom
coord=intWithComma(fields[colCoordinate])
alleleA=fields[colAlleleA]
alleleB=fields[colAlleleB]
if leftGet>=coord:
leftGet=coord-1
leftBound=coord-leftGet
rightBound=coord+rightGet
bedSeqResult=bedSeqClient.getBedSeq(chrom+"\t"+str(leftBound-1)+"\t"+str(rightBound))
seqGot=bedSeqResult.split("\t")[3].upper()
alleleGotNt=seqGot[leftGet] #if 0, then get the 0th char, if 1, then get the 1th char
if alleleGotNt not in [alleleA,alleleB]:
print >> stderr,"error: allele info not consistent with genome seq lino=%d GenomeSeq=%s alleleGot=%s alleleA=%s alleleB=%s coordSNP=%s:%d-%d coordBound=%s:%d-%d" %(lino,seqGot,alleleGotNt,alleleA,alleleB,chrom,coord,coord,chrom,leftBound,rightBound)
exit(1)
alleleASeq=seqGot[:leftGet]+alleleA+seqGot[leftGet+1:]
alleleBSeq=seqGot[:leftGet]+alleleB+seqGot[leftGet+1:]
fields+=[alleleASeq,alleleBSeq]
print >> stdout,fs.join(fields)
lino+=1
lin=lin.rstrip("\r\n")
fields=lin.split("\t")
pair1Name=fields[4]
pair1Chrom=fields[1]
pair1Start0=int(fields[2])
pair1End1=int(fields[3])
pair1Strand=fields[6]
pair2Name=fields[11]
pair2Start0=int(fields[9])
pair2End1=int(fields[10])
pair2Strand=fields[13]
minStart0=min(pair1Start0,pair2Start0)
maxEnd1=max(pair1End1,pair2End1)
#print >> stderr,pair1Start0,pair1End1,pair2Start0,pair2End1,#flankingLen+pair1End1-pair1Start0-minStart0,pair1Strand
flankingStart0=minStart0-flankingLen
flankingEnd1=maxEnd1+flankingLen
matchName=(pair1Name+"_"+pair2Name).replace(":","_")
gbWriter=GenbankFileWriter(matchName)
gbWriter.source=pair1Chrom+":"+str(minStart0+1)+"-"+str(maxEnd1)
gbWriter.organism=pair1Chrom+":"+str(minStart0+1)+"-"+str(maxEnd1)
gbWriter.sequence=bseq.getBedSeq(pair1Chrom+"\t"+str(flankingStart0)+"\t"+str(flankingEnd1)).split("\t")[3]
#print >> stderr,gbWriter.sequence
gbWriter.addFeature(flankingLen+pair1Start0-minStart0+1,flankingLen+pair1End1-minStart0,pair1Strand,"pair1")
gbWriter.addFeature(flankingLen+pair2Start0-minStart0+1,flankingLen+pair2End1-minStart0,pair2Strand,"pair2")
gbWriter.writeGenbankFile(str(lino)+"_"+matchName+".gb")
fil.close()
