INNER CODE UNIT · Python

altBase

aquaskyline/Clairvoyante · clairvoyante/callVar.py:121

                        altBase = refBase + altBase
                elif varType == 3: # DEL
                    if varLength == 0: varLength = 1
                    af = sum(XBatch[j,param.flankingBaseNum+1,:,2]) / dp
                    # infer the deletion length
                    if varLength == maxVarLength:
                        for k in range(param.flankingBaseNum+1, 2*param.flankingBaseNum+1):
                            if k < (param.flankingBaseNum + maxVarLength) or sum(XBatch[j,k,:,2]) >= (inferIndelLengthMinimumAF * sum(XBatch[j,k,:,0])):
                                inferredIndelLength += 1
                            else:
                               break
                    # deletions longer than (param.flankingBaseNum-1) are marked SV
                    coordination = int(coordination)
                    if inferredIndelLength >= param.flankingBaseNum:
                        refBase = refSeq[param.flankingBaseNum]
                        altBase = "<DEL>"
                        info.append("SVTYPE=DEL")
                    elif varLength != maxVarLength:

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