INNER CODE UNIT · Python
sortBase
aquaskyline/Clairvoyante · clairvoyante/callVar.py:81
sortBase = base[j].argsort()[::-1]
base1 = num2base[sortBase[0]]
base2 = num2base[sortBase[1]]
# Initialize other variables
refBase = ""; altBase = ""; inferredIndelLength = 0; dp = 0; af = 0.; info = [];
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