include ../../../inc/common.mk

L += ${MYSQLLIBS} -lm
MYLIBDIR = ../../../lib/${MACHTYPE}
MYLIBS =  ${MYLIBDIR}/jkhgap.a ${MYLIBDIR}/jkweb.a 

O = twoBitMask.o

twoBitMask: $O ${MYLIBS}
	${CC} ${COPT} -o ${BINDIR}/twoBitMask $O ${MYLIBS} $L
	${STRIP} ${BINDIR}/twoBitMask${EXE}

# reuse twoFitToFa input files. for tests
TEST_IN = ../../../utils/twoBitToFa/tests/input

test:
	${MKDIR} tests/output
	twoBitMask ${TEST_IN}/testN.2bit -type=bed /dev/null tests/output/testN_noMask.2bit
	cmp ${TEST_IN}/testN.2bit tests/output/testN_noMask.2bit
	twoBitMask -add ${TEST_IN}/testMask.2bit -type=bed /dev/null tests/output/testMask_sameMask.2bit
	cmp ${TEST_IN}/testMask.2bit tests/output/testMask_sameMask.2bit
	twoBitMask ${TEST_IN}/testMask.2bit -type=bed /dev/null tests/output/testMask_noMask.2bit
	cmp tests/expected/testMask_noMask.2bit tests/output/testMask_noMask.2bit
	twoBitMask ${TEST_IN}/testMask.2bit tests/input/testMask1.bed tests/output/testMask1.2bit
	cmp tests/expected/testMask1.2bit tests/output/testMask1.2bit
	twoBitMask ${TEST_IN}/testMask.2bit tests/input/testMask2.out tests/output/testMask2.2bit
	cmp ${TEST_IN}/testMask.2bit tests/output/testMask2.2bit
	rm -r tests/output

clean:
	rm -f $O

