# $Id$

APP_PROJ = agp_validate agp_renumber

srcdir = @srcdir@
include @builddir@/Makefile.meta

TESTS=bad_test big_int_pos test2 acc_test fa_test un_test obj_len_test order_test overlap_test new_test space_test runs_of_ns\
  chr_scaf_test chr_scaf_test2 chr_scaf_test_bad ver2.0 ver2.0_bad comp_test sub_test unplaced_singleton

.PHONY : noalt test $(TESTS) alt_test

noalt: $(TESTS)
	echo All tests except -alt succeeded.

test: $(TESTS) alt_test
	echo All tests succeeded.

bad_test : agp_validate
	-sh -c "./agp_validate $(srcdir)/test/bad_test.agp >bad_test.out 2>&1"
	diff ${DOPT} -u $(srcdir)/test/bad_test.out bad_test.out

big_int_pos : agp_validate
	-sh -c "./agp_validate $(srcdir)/test/big_int_pos.agp >big_int_pos.out 2>&1"
	diff ${DOPT} -u $(srcdir)/test/big_int_pos.out big_int_pos.out

alt_test : agp_validate
	-sh -c "./agp_validate -alt $(srcdir)/test/alt_bad_test.agp >alt_bad_test.out 2>&1"
	diff ${DOPT} -I 'CId2ReaderBase: bad reply serial number' -u $(srcdir)/test/alt_bad_test.out alt_bad_test.out

test2 : agp_validate
	-sh -c 'curdir=`pwd` && cd $(srcdir) && $$curdir/agp_validate test/bad_test.agp test/alt_bad_test.agp >$$curdir/test2.out 2>&1'
	diff ${DOPT} -u $(srcdir)/test/test2.out test2.out

acc_test : agp_validate
	-sh -c "./agp_validate $(srcdir)/test/bad_accessions.agp >bad_accessions.out 2>&1"
	diff ${DOPT} -u $(srcdir)/test/bad_accessions.out bad_accessions.out

fa_test : agp_validate
	-sh -c "./agp_validate $(srcdir)/test/fa_test.fa $(srcdir)/test/fa_test.agp >fa_test.out 2>&1"
	diff ${DOPT} -u $(srcdir)/test/fa_test.out fa_test.out
	-sh -c "./agp_validate $(srcdir)/test/fa_test.fa $(srcdir)/test/fa_test1.agp >fa_test1_2.out 2>&1"
	-sh -c "echo ===================================================== >> fa_test1_2.out"
	-sh -c "./agp_validate $(srcdir)/test/fa_test.fa $(srcdir)/test/fa_test2.agp>>fa_test1_2.out 2>&1"
	diff ${DOPT} -u $(srcdir)/test/fa_test1_2.out fa_test1_2.out

un_test : agp_validate
	-sh -c "./agp_validate -un $(srcdir)/test/fa_test.fa $(srcdir)/test/un_test.agp >un_test.out 2>&1"
	diff ${DOPT} -u $(srcdir)/test/un_test.out un_test.out

sub_test : agp_validate
	-sh -c "./agp_validate -sub -un $(srcdir)/test/fa_test.fa $(srcdir)/test/un_test.agp >sub_test.out 2>&1"
	diff ${DOPT} -u $(srcdir)/test/sub_test.out sub_test.out

obj_len_test : agp_validate
	-sh -c "./agp_validate -obj $(srcdir)/test/obj_len_test.fa $(srcdir)/test/obj_len_test.agp >obj_len_test.out 2>&1"
	diff ${DOPT} -u $(srcdir)/test/obj_len_test.out obj_len_test.out

order_test: agp_validate
	-sh -c "./agp_validate $(srcdir)/test/obj_id_OrderNotNumerical.agp >obj_id_OrderNotNumerical.out 2>&1"
	diff ${DOPT} -u $(srcdir)/test/obj_id_OrderNotNumerical.out obj_id_OrderNotNumerical.out

overlap_test: agp_validate
	-sh -c "./agp_validate $(srcdir)/test/overlap_test.agp >overlap_test.out 2>&1"
	diff ${DOPT} -u $(srcdir)/test/overlap_test.out overlap_test.out

new_test: agp_validate
	-sh -c "./agp_validate -un $(srcdir)/test/new_test.agp >new_test.out 2>&1"
	diff ${DOPT} -u $(srcdir)/test/new_test.out new_test.out

space_test: agp_validate
	-sh -c "./agp_validate $(srcdir)/test/space_test.agp>space_test.out 2>&1"
	diff ${DOPT} -u $(srcdir)/test/space_test.out space_test.out
	-sh -c "./agp_validate $(srcdir)/test/space_in_object_id.agp>space_in_object_id.out 2>&1"
	diff ${DOPT} -u $(srcdir)/test/space_in_object_id.out space_in_object_id.out

runs_of_ns: agp_validate
	sh -c "./agp_validate -out runs_of_ns.agp $(srcdir)/test/MedtrA17_3.5.head.comp_fa $(srcdir)/test/MedtrA17_3.5.head.agp>runs_of_ns.out 2>&1"
	diff ${DOPT} -u $(srcdir)/test/runs_of_ns.out runs_of_ns.out
	diff ${DOPT} -u $(srcdir)/test/runs_of_ns.agp runs_of_ns.agp

chr_scaf_test: agp_validate
	sh -c "./agp_validate -chr $(srcdir)/test/chr_from_scaffold_WGS.agp>chr_scaf_test.out 2>&1"
	sh -c "./agp_validate -scaf $(srcdir)/test/scaffold_from_contig_WGS.agp>>chr_scaf_test.out 2>&1"
	diff ${DOPT} -u $(srcdir)/test/chr_scaf_test.out chr_scaf_test.out

chr_scaf_test2: agp_validate
	-sh -c "./agp_validate -scaf $(srcdir)/test/scaffold_from_contig_WGS.agp -chr $(srcdir)/test/chr_from_scaffold_WGS.agp>chr_scaf_test2.out 2>&1"
	-sh -c "./agp_validate -scaf $(srcdir)/test/scaffold_from_contig_WGS.agp -chr $(srcdir)/test/chr_from_scaffold_WGS_bad.agp>>chr_scaf_test2.out 2>&1"
	diff ${DOPT} -u $(srcdir)/test/chr_scaf_test2.out chr_scaf_test2.out

chr_scaf_test_bad: agp_validate
	-sh -c "./agp_validate -scaf $(srcdir)/test/chr_from_scaffold_WGS.agp>chr_scaf_test_bad.out 2>&1"
	-sh -c "./agp_validate -chr $(srcdir)/test/scaffold_from_contig_WGS.agp>>chr_scaf_test_bad.out 2>&1"
	diff ${DOPT} -u $(srcdir)/test/chr_scaf_test_bad.out chr_scaf_test_bad.out

unplaced_singleton: agp_validate
	sh -c "./agp_validate $(srcdir)/test/unplaced_singleton.fa $(srcdir)/test/unplaced_singleton.agp>unplaced_singleton.out 2>&1"
	sh -c "./agp_validate $(srcdir)/test/unplaced_singleton.fa $(srcdir)/test/unplaced_singleton_bad.agp>>unplaced_singleton.out 2>&1"
	diff ${DOPT} -u $(srcdir)/test/unplaced_singleton.out unplaced_singleton.out

ver2.0: agp_validate
	-sh -c "./agp_validate -scaf $(srcdir)/test/scaffold_from_contig_WGS.agp2.0 -chr $(srcdir)/test/chr_from_scaffold_WGS.agp2.0>ver2.0.out 2>&1"
	-sh -c "./agp_validate $(srcdir)/test/chr_from_contig_BAC.agp2.0 $(srcdir)/test/chr_from_contig_WGS.agp2.0 >>ver2.0.out 2>&1"
	diff ${DOPT} -u $(srcdir)/test/ver2.0.out ver2.0.out

# W_AGPVersionCommentInvalid, W_AGPVersionCommentUnnecessary
ver2.0_bad: agp_validate
	-sh -c "./agp_validate -v 2 -scaf $(srcdir)/test/scaffold_from_contig_WGS.agp2.0 -chr $(srcdir)/test/chr_from_scaffold_WGS.agp2.0>ver2.0_bad.out 2>&1"
	-sh -c "./agp_validate $(srcdir)/test/chr_from_contig_BAC.agp2.0_bad_ver $(srcdir)/test/chr_from_contig_WGS.agp2.0 >>ver2.0_bad.out 2>&1"
	diff ${DOPT} -u $(srcdir)/test/ver2.0_bad.out ver2.0_bad.out

comp_test: agp_validate
	sh -c "./agp_validate -comp -ignoreagponly -loadlog /dev/null test/comp_test.fsa test/comp_test.fa  test/comp_test.agp>comp_test.out 2>&1"
	diff ${DOPT} -u $(srcdir)/test/comp_test.out comp_test.out