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##/*************************************************************************************
## The MIT License
##
## BWA-MEM2 (Sequence alignment using Burrows-Wheeler Transform),
## Copyright (C) 2019 Intel Corporation, Heng Li.
##
## Permission is hereby granted, free of charge, to any person obtaining
## a copy of this software and associated documentation files (the
## "Software"), to deal in the Software without restriction, including
## without limitation the rights to use, copy, modify, merge, publish,
## distribute, sublicense, and/or sell copies of the Software, and to
## permit persons to whom the Software is furnished to do so, subject to
## the following conditions:
##
## The above copyright notice and this permission notice shall be
## included in all copies or substantial portions of the Software.
##
## THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
## EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
## MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
## NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
## BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
## ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
## CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
## SOFTWARE.
##
##Contacts: Vasimuddin Md <vasimuddin.md@intel.com>; Sanchit Misra <sanchit.misra@intel.com>;
## Heng Li <hli@jimmy.harvard.edu>
##*****************************************************************************************/
EXE= fmi_test smem2_test bwt_seed_strategy_test sa2ref_test xeonbsw
CXX= icpc
CXXFLAGS= -std=c++11 -fopenmp -mtune=native -march=native
CPPFLAGS= -DENABLE_PREFETCH
INCLUDES= -I../src
LIBS= -L.. -fopenmp -lz -lbwa ../ext/safestringlib/libsafestring.a
.PHONY:all clean depend
.SUFFIXES:.cpp .o
.cpp.o:
$(CXX) -c $(CXXFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
all:$(EXE)
fmi_test:fmi_test.o
$(CXX) -o $@ $^ $(LIBS)
smem2_test: smem2_test.o
$(CXX) -o $@ $^ $(LIBS)
sa2ref_test: sa2ref_test.o
$(CXX) -o $@ $^ $(LIBS)
bwt_seed_strategy_test:bwt_seed_strategy_test.o
$(CXX) -o $@ $^ $(LIBS)
xeonbsw:main_banded.o
$(CXX) -o $@ $^ $(LIBS)
clean:
rm -fr *.o $(EXE)
# DO NOT DELETE
bwt_seed_strategy_test.o: ../src/FMI_search.h ../src/bntseq.h ../src/read_index_ele.h
bwt_seed_strategy_test.o: ../src/bwa.h ../src/bwt.h ../src/utils.h ../src/macro.h
fmi_test.o: ../src/FMI_search.h ../src/bntseq.h ../src/read_index_ele.h
fmi_test.o: ../src/bwa.h ../src/bwt.h ../src/utils.h ../src/macro.h
main_banded.o: ../src/bandedSWA.h ../src/macro.h
sa2ref_test.o: ../src/FMI_search.h ../src/bntseq.h ../src/read_index_ele.h
sa2ref_test.o: ../src/bwa.h ../src/bwt.h ../src/utils.h ../src/macro.h
smem2_test.o: ../src/FMI_search.h ../src/bntseq.h ../src/read_index_ele.h
smem2_test.o: ../src/bwa.h ../src/bwt.h ../src/utils.h ../src/macro.h
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