# ===========================================================================
#
#							PUBLIC DOMAIN NOTICE
#			   National Center for Biotechnology Information
#
#  This software/database is a "United States Government Work" under the
#  terms of the United States Copyright Act.  It was written as part of
#  the author's official duties as a United States Government employee and
#  thus cannot be copyrighted.  This software/database is freely available
#  to the public for use. The National Library of Medicine and the U.S.
#  Government have not placed any restriction on its use or reproduction.
#
#  Although all reasonable efforts have been taken to ensure the accuracy
#  and reliability of the software and data, the NLM and the U.S.
#  Government do not and cannot warrant the performance or results that
#  may be obtained by using this software or data. The NLM and the U.S.
#  Government disclaim all warranties, express or implied, including
#  warranties of performance, merchantability or fitness for any particular
#  purpose.
#
#  Please cite the author in any work or product based on this material.
#
# ===========================================================================


default: runtests

TOP ?= $(abspath ../..)
MODULE = test/align

TEST_TOOLS = \
	test-load-index \
	test-samextract \
	test-estimator

include $(TOP)/build/Makefile.env

$(TEST_TOOLS): makedirs
	@ $(MAKE_CMD) $(TEST_BINDIR)/$@

clean: stdclean

INCDIRS += -I$(TOP)/libs/align -I$(TOP)/../ngs-tools/libs/general-writer/inc

#-------------------------------------------------------------------------------
# test-load-index
#
TEST_INDEX_SRC = \
	indextest

TEST_INDEX_OBJ = \
	$(addsuffix .$(OBJX),$(TEST_INDEX_SRC))

TEST_INDEX_LIB = \
	-skapp \
	-sktst \
	-sncbi-vdb 

$(TEST_BINDIR)/test-load-index: $(TEST_INDEX_OBJ)
	$(LP) --exe -o $@ $^ $(TEST_INDEX_LIB)

#-------------------------------------------------------------------------------
# test-estimator
#
TEST_ESTIMATOR_SRC = \
	pileup_estimator

TEST_ESTIMATOR_OBJ = \
	$(addsuffix .$(OBJX),$(TEST_ESTIMATOR_SRC))

TEST_ESTIMATOR_LIB = \
	-skapp \
	-sktst \
	-sncbi-ngs-c++ \
	-sncbi-ngs \
	-sncbi-vdb \
	-L$(NGS_LIBDIR) \
	-sngs-c++

$(TEST_BINDIR)/test-estimator: $(TEST_ESTIMATOR_OBJ)
	$(LP) --exe -o $@ $^ $(TEST_ESTIMATOR_LIB)

#-------------------------------------------------------------------------------
# samtogw
#
SAMTOGW_SRC = \
		samtogw

SAMTOGW_OBJ = \
		$(addsuffix .$(OBJX),$(SAMTOGW_SRC))

SAMTOGW_LIB = \
		-L/home/vartanianmh/ncbi-outdir/ngs-tools/linux/gcc/x86_64/dbg/ilib/ \
		-skapp \
		-sktst \
		-ssam-extract\
		-sncbi-vdb \
		-sgeneral-writer

$(TEST_BINDIR)/samtogw: $(SAMTOGW_OBJ)
		$(LP) --exe -o $@ $^ $(SAMTOGW_LIB)

#-------------------------------------------------------------------------------
# bamfuzz
#
BAMFUZZ_SRC = \
		bamfuzz

BAMFUZZ_OBJ = \
		$(addsuffix .$(OBJX),$(BAMFUZZ_SRC))

BAMFUZZ_LIB = \
		-skapp \
		-sktst \
		-ssam-extract\
		-sncbi-vdb

$(TEST_BINDIR)/bamfuzz: $(BAMFUZZ_OBJ)
		$(LP) --exe -o $@ $^ $(BAMFUZZ_LIB)

#-------------------------------------------------------------------------------
# irvrfy
#
IRVRFY_SRC = \
		irvrfy

IRVRFY_OBJ = \
		$(addsuffix .$(OBJX),$(IRVRFY_SRC))

IRVRFY_LIB = \
		-L/home/vartanianmh/ncbi-outdir/ngs-tools/linux/gcc/x86_64/dbg/ilib/ \
		-skapp \
		-sktst \
		-ssam-extract\
		-sncbi-wvdb \
		-sgeneral-writer

$(TEST_BINDIR)/irvrfy: $(IRVRFY_OBJ)
		$(LP) --exe -o $@ $^ $(IRVRFY_LIB)


#-------------------------------------------------------------------------------
# test-samextract
#
TEST_SAMEXTRACT_SRC = \
		test-samextract

TEST_SAMEXTRACT_OBJ = \
		$(addsuffix .$(OBJX),$(TEST_SAMEXTRACT_SRC))

TEST_SAMEXTRACT_LIB = \
		-skapp \
		-ssam-extract\
		-sktst \
		-sncbi-vdb

$(TEST_BINDIR)/test-samextract: $(TEST_SAMEXTRACT_OBJ)
		$(LP) --exe -o $@ $^ $(TEST_SAMEXTRACT_LIB)

valgrind_samextract: std
	valgrind --ncbi --show-reachable=no $(TEST_BINDIR)/test-samextract

run-test-samextract: test-samextract
		@ export LD_LIBRARY_PATH=$(LIBDIR) ; $(TEST_BINDIR)/test-samextract


# runtests
#runtests: run-test-samextract run-test-load-index
runtests: run-test-samextract

miketoys: $(TEST_BINDIR)/irvrfy $(TEST_BINDIR)/samtogw $(TEST_BINDIR)/bamfuzz

.PHONY: $(TEST_TOOLS)


