INNER CODE UNIT · Python

refBase

aquaskyline/Clairvoyante · clairvoyante/callVar.py:139

                        refBase = refSeq[param.flankingBaseNum:param.flankingBaseNum+varLength+1]
                        altBase = refSeq[param.flankingBaseNum]
                    else:
                        refBase = refSeq[param.flankingBaseNum:param.flankingBaseNum+inferredIndelLength+1]
                        altBase = refSeq[param.flankingBaseNum]
                if inferredIndelLength > 0 and inferredIndelLength < param.flankingBaseNum: info.append("LENGUESS=%d" % inferredIndelLength)
                infoStr = ""
                if len(info) == 0: infoStr = "."
                else: infoStr = ";".join(info)
                gtStr = ""
                if varType == 0: gtStr = "0/0"
                elif varZygosity == 0: gtStr = "0/1"
                elif varZygosity == 1: gtStr = "1/1"

                print >> call_fh, "%s\t%d\t.\t%s\t%s\t%d\t%s\t%s\tGT:GQ:DP:AF\t%s:%d:%d:%.4f" % (chromosome, coordination, refBase, altBase, qual, filt, infoStr, gtStr, qual, dp, af)


def PrintVCFHeader(args, call_fh):

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