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# ===========================================================================
#
# 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: std
std:
clean:
.PHONY: default std $(TARGETS)
PYTHON_VERS = $(shell python -V 2>&1)
# there is a separate set of sources for 2.5 and 2.6
ifeq (Python 2.6,$(shell expr "$(PYTHON_VERS)" : "\(Python 2.6\)"))
PYTHON_VERS=26
elif (Python 2.5,$(shell expr "$(PYTHON_VERS)" : "\(Python 2.5\)"))
PYTHON_VERS=26
else
PYTHON_VERS=
endif
NGS_EXAMPLES = \
FragTest \
AlignTest \
AlignSliceTest \
PileupTest \
RefTest \
# ===========================================================================
#
# example runs
#
# NOTE: Expect libngs-sdk.so and libncbi-vdb.so somewhere inside $LD_LIBRARY_PATH
run_frag:
python FragTest$(PYTHON_VERS).py ERR225922 10000 2 $(REDIRECT)
run_align:
python AlignTest$(PYTHON_VERS).py ERR225922 10000 2 $(REDIRECT)
run_align_slice:
python AlignSliceTest$(PYTHON_VERS).py SRR1121656 1 1 9999 $(REDIRECT)
run_pileup:
python PileupTest$(PYTHON_VERS).py SRR1121656 1 9999 10003 $(REDIRECT)
run_ref:
python RefTest$(PYTHON_VERS).py SRR1121656 $(REDIRECT)
ALL_TESTS = run_frag run_align run_align_slice run_pileup run_ref
run_all: $(ALL_TESTS)
.PHONY: run_align run_align_slice run_frag
# ===========================================================================
#
# expected results for auto-testing
#
expected.txt update_expected:
rm -f expected.txt; $(MAKE) run_all REDIRECT=">>expected.txt"
run_and_diff: expected.txt
rm -f actual.txt; $(MAKE) run_all REDIRECT=">>actual.txt"
diff expected.txt actual.txt && rm actual.txt && echo NGS Python examples work as expected
.PHONY: update_expected run_and_diff
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