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Makefile
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CHR1 = ../data/chr1.fa
HUMAN = ../data/hs1.fa
ELEGANS = ../data/elegans.fa
SEQ1 = data/inputs/1.fa
SEQ2 = data/inputs/2.fa
SEQ3 = data/inputs/3.fa
SEQA = data/inputs/a.fa
SMOL = data/inputs/smol.fa
ABBA = data/inputs/abba.fa
SUFR = ./target/release/sufr
CREATE_RELEASE = /usr/bin/time -l $(SUFR) --log info create
CREATE_DEBUG = cargo run -- --log debug create
perf:
perf record --call-graph dwarf $(SUFR) create -t 16 --log info $(CHR1)
r1:
$(SEARCH) C 1.sufr
testfiles: s1 s1s s1n s2 s2d s2n s2s s2ns s3 abba
cp [1-3]*.sufr data/expected/
cp abba.sufr data/inputs/
smol:
$(CREATE_DEBUG) $(SMOL) --dna -m 4
smol-mask:
$(CREATE_DEBUG) $(SMOL) --dna --seed-mask 1001 -o smol.mask.sufr
masked:
$(CREATE_DEBUG) $(SEQA) --dna --seed-mask 1001 -o a-m1011.sufr
s1:
$(CREATE_DEBUG) $(SEQ1) -n 1 --dna -o 1.sufr
s1m:
$(CREATE_DEBUG) $(SEQ1) -n 1 --dna --seed-mask 1001 -o 1m.sufr
s1s:
$(CREATE_DEBUG) $(SEQ1) -n 2 --dna -o 1s.sufr --ignore-softmask
s1n:
$(CREATE_DEBUG) $(SEQ1) -n 2 --dna --allow-ambiguity -o 1n.sufr
s2:
$(CREATE_DEBUG) $(SEQ2) -n 3 --dna
s2d:
$(CREATE_DEBUG) $(SEQ2) -n 2 --dna --sequence-delimiter 'N' -o 2d.sufr
s2n:
$(CREATE_DEBUG) $(SEQ2) -n 3 --dna --allow-ambiguity -o 2n.sufr
s2s:
$(CREATE_DEBUG) $(SEQ2) -n 3 --dna --ignore-softmask -o 2s.sufr
s2ns:
$(CREATE_DEBUG) $(SEQ2) -n 3 --dna --allow-ambiguity --ignore-softmask -o 2ns.sufr
s3:
$(CREATE_DEBUG) $(SEQ3) --dna
abba:
$(CREATE_DEBUG) $(ABBA)
elegans:
$(CREATE_RELEASE) --dna -m 12 $(ELEGANS)
ecoli:
$(CREATE_RELEASE) --dna -m 16 ../data/ecoli.fa
chr1:
$(CREATE_RELEASE) --dna -n 800 $(CHR1)
chr1-mask:
$(CREATE_RELEASE) --dna -n 800 -s 111010010100110111 -o chr1-mask.sufr $(CHR1)
hu:
$(CREATE_RELEASE) --dna -n 800 $(HUMAN)
hu-mask:
$(CREATE_RELEASE) --dna -n 800 -s 111010010100110111 -o hs1-mask.sufr $(HUMAN)
valcache:
valgrind --tool=cachegrind ./target/release/sufr create ../data/chr1.fa --ignore-start-n -o chr1.sa --log info
valcall:
valgrind --tool=callrind ./target/release/sufr create ../data/chr1.fa --ignore-start-n -o chr1.sa --log info