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EXTRA_DIST = defs ss.chr17test ss.her2 \
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             map.test.ok \
             fa.iittest iittest.iit.ok iit_get.out.ok

CLEANFILES = align.test.out \
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             gmap_setup gmapindex chr17test/chr17test.* Makefile.chr17test \
             map.test.out \
             iittest.iit iit_get.out iit_dump.out

@MAINTAINER_FALSE@TESTS = align.test coords1.test setup1.test iit.test 
@MAINTAINER_TRUE@TESTS = align.test coords1.test setup1.test iit.test \
@MAINTAINER_TRUE@        bioinfo.splicing.test

TESTS_ENVIRONMENT = top_builddir=$(top_builddir)
testsubdir = testSubDir
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clean-libtool:
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tags TAGS:

ctags CTAGS:

cscope cscopelist:


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distclean-local:
	rm -rf $(testsubdir)

okay:
	../src/gmap -A -g ss.chr17test ss.her2 > align.test.ok
#	./fa_coords -o coords.chr17test ss.chr17test
#	./gmap_setup -D . -d chr17test ss.chr17test && make -f Makefile.chr17test coords && make -f Makefile.chr17test gmapdb
	./gmap_build -D . -d chr17test ss.chr17test
	../src/gmap -D . -d chr17test ss.her2 > map.test.ok
	mv -f coords.chr17test coords1.test.ok
	mv -f chr17test.genomecomp setup.genomecomp.ok
	mv -f chr17test.ref123positions setup.ref123positions.ok
	../src/iit_store -o iittest fa.iittest
	../src/iit_get iittest 20000 > iit_get.out.ok
	mv iittest.iit iittest.iit.ok

# Tell versions [3.59,3.63) of GNU make to not export all variables.
# Otherwise a system limit (for SysV at least) may be exceeded.
.NOEXPORT: