# Now using MORGAN2.3 with beta-version for Sim_ibd_link
# Test files for the Pavia course, Sept 2000
# Updated for NCSU ST610F Fall, 2000

# You may need change the following macros to the correct path
# of the programs installed.

LMAUTO = lm_auto
LMLODS = lm_lods
SIBDLK = sim_ibd_link
AUTOLK = autolink
GENEDP = genedrop
PEDCHK = pedcheck
MULTIVAR = multivar

# ===== No editing necessary below. ======

SHELL = /bin/sh

# This is the Makefile for the lm_auto programs, using MORGAN 2.3-beta

autolink.out:
	$(AUTOLK) autolink_ped > autolink.out4 2>&1

sim_ibd1.out:
	$(SIBDLK) jv_ibd_ped > sim_ibd1.out4 2>&1

sim_ibd2.out:
	$(SIBDLK) jv_ibd_4c > sim_ibd2.out4 2>&1

sim_ibd3.out:
	$(SIBDLK) jv_ibd_parents > sim_ibd3.out4 2>&1

# Genedrop from MORGAN_V2.3/Genedrop

genedrop.out:
	$(GENEDP) genedrop_par > genedrop.out4  2>&1

# Pedcheck from MORGAN_V2.3/Checkers

pedchk1.out: 
	$(PEDCHK) pedchk_par >pedchk1.out4 2>&1

pedchk2.out:
	$(PEDCHK) pedchk_par2 >pedchk2.out4 2>&1

pedchk3.out:
	$(PEDCHK) /dev/null ped pedchk_sex \
              oped /dev/null  > pedchk3.out4 2>&1

pedchk4.out: 
	$(PEDCHK) /dev/null ped pedchk_dup \
              oped /dev/null  > pedchk4.out4 2>&1

pedchk.apob: 
	$(PEDCHK) apob_chk.par > apob.out 2>&1

# lmauto examples

lmauto1.out:
	$(LMAUTO) par15a oscor /dev/null > lmauto1.out4 2>&1

lmauto2.out:
	$(LMAUTO) par45a > lmauto2.out4 2>&1

# lmlods examples

lmlods1.out:
	$(LMLODS) par15b oscor /dev/null > lmlods1.out4 2>&1

lmlods2.out:
	$(LMLODS) par45b  > lmlods2.out4 2>&1

# PolyEM (multivar) example

multivar.out:
	$(MULTIVAR) polyem_90_par2 > multivar90.out 2>&1

# clean etc.

clean:
	rm -f o* *out4
	rm -f *out* apob_chked.dat