SRC= ./src/

SIMPLESOURCES= $(SRC)ComplexSimple.c\
        $(SRC)ParseCommands.c\
        $(SRC)ReadPedFile.c\
        $(SRC)ReadLinkageFile.c\
        $(SRC)getancestry.c\
        $(SRC)calcpeelingorder.c\
        $(SRC)ReadPeelFiles.c\
        $(SRC)GetCutPeelPedIndex.c\
        $(SRC)createspaces.c\
        $(SRC)ComplexCreateSpaces.c\
        $(SRC)ComplexGetHaplabel.c\
        $(SRC)gethaplabel.c\
        $(SRC)getibdobs.c\
        $(SRC)ibdblank.c\
        $(SRC)readrecombfracs.c\
        $(SRC)ReadDistances.c\
        $(SRC)createdistances.c\
        $(SRC)chs.c\
        $(SRC)alloc_proc.c\
        $(SRC)mapmatrix.c\
        $(SRC)recomb_pp.c\
        $(SRC)hanshu.c\
        $(SRC)calcibdprobs.c\
        $(SRC)calcmarginprobs.c\
        $(SRC)getprobibdobs.c\
        $(SRC)createmarkerppots.c\
        $(SRC)CreateDiseasePrePPots.c\
        $(SRC)creatediseaseppots.c\
        $(SRC)GetWPP.c\
        $(SRC)GetTransIndex.c\
        $(SRC)GetRIndex.c\
        $(SRC)peel.c\
        $(SRC)ComplexPeel.c\
        $(SRC)condprob.c\
        $(SRC)calcweight.c\
        $(SRC)ComplexCalcWeight.c\
        $(SRC)simulate.c\
        $(SRC)ComplexSimulate.c\
        $(SRC)simblank.c\
        $(SRC)readblank.c\
        $(SRC)calcblank.c\
        $(SRC)ibdreset.c\
        $(SRC)rnd.c\
        $(SRC)DumpCommands.c\
        $(SRC)DumpHaps.c\
        $(SRC)dumpibds.c\
        $(SRC)utils.c


scanSOURCES= $(SRC)scan.c\
        $(SRC)ReadPedFile.c\
        $(SRC)ReadLinkageFile.c\
        $(SRC)ParseCommands.c\
        $(SRC)readrecombfracs.c\
        $(SRC)ReadDistances.c\
        $(SRC)CreateDistances.LR.c\
        $(SRC)CreateDistances.noLR.c\
        $(SRC)chs.c\
        $(SRC)alloc_proc.c\
        $(SRC)mapmatrix.c\
        $(SRC)recomb_pp.c\
        $(SRC)calcibdprobs.c\
        $(SRC)calcmarginprobs.c\
        $(SRC)utility.c\
        $(SRC)getancestry.c\
        $(SRC)ReadSIMPLE.c\
        $(SRC)SimJointIBDs.c\
        $(SRC)SimIBDs.c\
        $(SRC)CalcLikRatio.c\
        $(SRC)GetIBDStates.c\
        $(SRC)CalcScorePairs.c\
        $(SRC)CalcScoreAll.c\
        $(SRC)DumpCommands.c\
        $(SRC)PrintScores.c\
        $(SRC)CalcQTLlod.c\
        $(SRC)FindPairs.c\
        $(SRC)DebugIBDprob.c\
        $(SRC)EM.c\
        $(SRC)DumpPairs.c\
        $(SRC)DumpProbs.c\
        $(SRC)rnd.c

CFLAGS= -g

CC= cc

scanOBJS= $(scanSOURCES:.c=.o)

SIMPLEOBJS= $(SIMPLESOURCES:.c=.o)

SUFFIXES: .c .o $(.SUFFIXES)

.c.o:
	$(CC) $(CFLAGS) -c $< -o $*.o

.KEEP_STATE:


scan: $(scanOBJS)
	$(CC) $(CFLAGS) -o scan $(scanOBJS) -lm -g

simple:  $(SIMPLEOBJS)
	$(CC) $(CFLAGS) -o simple $(SIMPLEOBJS) -lm
