INNER CODE UNIT · Python

dp

aquaskyline/Clairvoyante · clairvoyante/callVar.py:86

            dp = sum(XBatch[j,param.flankingBaseNum,:,0]) + sum(XBatch[j,param.flankingBaseNum+1,:,1]) + \
                 sum(XBatch[j,param.flankingBaseNum+1,:,2]) + sum(XBatch[j,param.flankingBaseNum,:,3])
            if dp != 0:
                # For SNP
                if varType == 1 or varType == 0: # SNP or REF
                    coordination = int(coordination)
                    refBase = refSeq[param.flankingBaseNum]
                    if varType == 1: # SNP
                        altBase = base1 if base1 != refBase else base2
                        #altBase = "%s,%s" % (base1, base2)
                    elif varType == 0: # REF
                        altBase = refBase
                    af = XBatch[j,param.flankingBaseNum,base2num[altBase],3] / dp
                elif varType == 2: # INS
                    # infer the insertion length
                    if varLength == 0: varLength = 1
                    af = sum(XBatch[j,param.flankingBaseNum+1,:,1]) / dp
                    if varLength != maxVarLength:

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