if isinstance(thisMarker,ChrXMarker):
thisMarker.getVariantDistribution(pedNBGender,pedMemberType)
else:
thisMarker.getVariantDistribution()
#count complete and incomplete case and control trio types and populate corresponding vectors
thisMarker.populateTrioTypeCountVectors(pedMemberType,pedPhenoDict,pedNBGender)
#concatenate output string and print to output file
outputColumns = [thisMarker.markerID,str(thisMarker.maf),str(thisMarker.nVariantType),str(thisMarker.nCompleteInformativeCaseTrio_MaleNB),str(thisMarker.nCompleteInformativeCaseTrio_FemaleNB),str(thisMarker.nCompleteInformativeControlTrio_MaleNB),str(thisMarker.nCompleteInformativeControlTrio_FemaleNB),str(thisMarker.nCompleteNonInformativeCaseTrio),str(thisMarker.nCompleteNonInformativeControlTrio),str(thisMarker.nIncompleteInformativeCaseTrio_MaleNB),str(thisMarker.nIncompleteInformativeCaseTrio_FemaleNB),str(thisMarker.nIncompleteInformativeControlTrio_MaleNB),str(thisMarker.nIncompleteInformativeControlTrio_FemaleNB),str(thisMarker.nIncompleteNonInformativeCaseTrio),str(thisMarker.nIncompleteNonInformativeControlTrio),str(thisMarker.nMIE)]
# run appropriate tests based on options selected by the user, add appropriate output columns
#**************TDT***************************************************************************
if TEST == "" or TEST == "tdt":
#ADDITIVE std. TDT-------------------------------------------------------------------
if not MODELS or "a" in MODELS:
thisMarker.stdTDT("a")
outputColumns.extend([str(thisMarker.chiSq_StdTDT),str(thisMarker.pValue_StdTDT)])
#ADDITIVE mi-TDT--------------------------------------
if VERSION == "scan" or VERSION == "":
thisMarker.extendedTDT("a")
outputColumns.extend([str(thisMarker.minChiSq_rTDT),str(thisMarker.minPValue_rTDT),str(thisMarker.maxChiSq_rTDT),str(thisMarker.maxPValue_rTDT)])
#DOMINANT std. TDT----------------------------------------------------------------------------------
if "d" in MODELS:
thisMarker.stdTDT("d")
outputColumns.extend([str(thisMarker.chiSq_StdTDT),str(thisMarker.pValue_StdTDT)])
#DOMINANT mi-TDT----------------------------------------------------------------------------
if VERSION == "scan" or VERSION == "":
thisMarker.extendedTDT("d")
outputColumns.extend([str(thisMarker.minChiSq_rTDT),str(thisMarker.minPValue_rTDT),str(thisMarker.maxChiSq_rTDT),str(thisMarker.maxPValue_rTDT)])
