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Makefile
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Makefile
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prefix=$(shell pwd)
BAMTOOLS_INCLUDE_DIR=$(prefix)/bamtools/install/include/bamtools
BAMTOOLS_LIB_DIR=$(prefix)/bamtools/install/lib/bamtools
all:
g++ -std=c++14 -o Blacklist blacklist.cpp -I$(BAMTOOLS_INCLUDE_DIR) -L$(BAMTOOLS_LIB_DIR) -lbamtools -lz -Wl,-rpath,$(BAMTOOLS_LIB_DIR)
debug:
g++ -std=c++14 -g -o Blacklist blacklist.cpp -I$(BAMTOOLS_INCLUDE_DIR) -L$(BAMTOOLS_LIB_DIR) -lbamtools -lz -Wl,-rpath,$(BAMTOOLS_LIB_DIR)
blacklist:
./Blacklist chr1 > final.chr1.out
./Blacklist chr2 > final.chr2.out
./Blacklist chr3 > final.chr3.out
./Blacklist chr4 > final.chr4.out
./Blacklist chr5 > final.chr5.out
./Blacklist chr6 > final.chr6.out
./Blacklist chr7 > final.chr7.out
./Blacklist chr8 > final.chr8.out
./Blacklist chr9 > final.chr9.out
./Blacklist chr10 > final.chr10.out
./Blacklist chr11 > final.chr11.out
./Blacklist chr12 > final.chr12.out
./Blacklist chr13 > final.chr13.out
./Blacklist chr14 > final.chr14.out
./Blacklist chr15 > final.chr15.out
./Blacklist chr16 > final.chr16.out
./Blacklist chr17 > final.chr17.out
./Blacklist chr18 > final.chr18.out
./Blacklist chr19 > final.chr19.out
./Blacklist chr20 > final.chr20.out
./Blacklist chr21 > final.chr21.out
./Blacklist chr22 > final.chr22.out
./Blacklist chrX > final.chrX.out
./Blacklist chrY > final.chrY.out