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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
#DEBUGGING = -d
TARGETS = \
NGS-JavaTest.jar
std: $(TARGETS)
clean:
rm -f $(TARGETS) examples/*.class
.PHONY: default std $(TARGETS)
NGS_EXAMPLES = \
AlignSliceTest \
AlignTest \
DumpReferenceFASTA \
FragTest \
PileupTest \
ReadGroupTest \
RefTest \
NGS_EXAMPLES_PATH = \
$(addprefix examples/,$(addsuffix .java,$(NGS_EXAMPLES)))
NGS_CLASS_PATH = ..
NGS-JavaTest.jar: $(NGS_EXAMPLES_PATH)
javac $(DEBUGGING) $^ -d .
( jar cf $@ `find examples -name "*.class"`; chmod -x,o-w $@ ) || ( rm -f $@ && false )
# ===========================================================================
#
# example runs
JAVAFLAGS = -classpath $(CLASSPATH):$(NGS_CLASS_PATH):.
# Expect libngs-sdk.so and libncbi-vdb.so somewhere inside $LD_LIBRARY_PATH;
# if the libraries are not found, error out.
# Comment out to rely on "smart load" instead (may download libraries from NCBI):
JAVAFLAGS += -Djava.library.path=$(LD_LIBRARY_PATH) -Dvdb.System.loadLibrary=1
# uncomment to see detailed log"
JAVAFLAGS += -Dvdb.log=FINEST
run_frag: NGS-JavaTest.jar
java $(JAVAFLAGS) examples.FragTest ERR225922 10000 2 $(REDIRECT)
run_align: NGS-JavaTest.jar
java $(JAVAFLAGS) examples.AlignTest ERR225922 10000 2 $(REDIRECT)
run_dump: NGS-JavaTest.jar
java $(JAVAFLAGS) examples.DumpReferenceFASTA SRR520124 1 $(REDIRECT)
run_align_slice: NGS-JavaTest.jar
java $(JAVAFLAGS) examples.AlignSliceTest SRR1121656 1 1 9999 $(REDIRECT)
run_pileup: NGS-JavaTest.jar
java $(JAVAFLAGS) examples.PileupTest SRR1121656 1 9999 10003 $(REDIRECT)
run_ref: NGS-JavaTest.jar
java $(JAVAFLAGS) examples.RefTest SRR1121656 $(REDIRECT)
run_read_group: NGS-JavaTest.jar
java $(JAVAFLAGS) examples.ReadGroupTest SRR1121656 $(REDIRECT)
ALL_TESTS = run_frag run_align run_align_slice \
run_pileup run_ref run_read_group run_dump
run_all: $(ALL_TESTS)
.PHONY: $(ALL_TESTS)
# ===========================================================================
#
# 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 Java examples work as expected
.PHONY: update_expected run_and_diff
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