simd-sketch 0.2.0

A SIMD-accelerated library to compute a b-bit bottom-h sketch
Documentation 
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build:
    cargo build -r --example dist

bench: build

input := "input2"
stats := "py/stats2"
output := "output2"

simd_bot s: build
    ./target/release/examples/dist {{input}} -s {{s}}                   --stats {{stats}} > {{output}}/simd_bottom_s{{s}}.dist
simd_bucket s b: build
    ./target/release/examples/dist {{input}} -s {{s}} -b {{b}} --bucket --stats {{stats}} > {{output}}/simd_bucket_s{{s}}_b{{b}}.dist

simd_bot_all: (simd_bot "128") (simd_bot "1024") (simd_bot "8192") (simd_bot "32768") (simd_bot "65536")
simd_bucket_all_b s: (simd_bucket s "1") (simd_bucket s "8") (simd_bucket s "16") (simd_bucket s "32")
simd_bucket_all: (simd_bucket_all_b "128") (simd_bucket_all_b "1024") (simd_bucket_all_b "8192") (simd_bucket_all_b "32768")

simd_bucket_16: (simd_bucket "128" "16") (simd_bucket "1024" "16") (simd_bucket "8192" "16") (simd_bucket "32768" "16")

bindash_bot s:
    time -f %U ./bindash sketch {{input}}/*fna --minhashtype=0 --kmerlen=31 --sketchsize={{s}} --outfname={{output}}/tmp 2>&1 | tee >(cat 1>&2) | tail -1 > {{output}}/tmp_sketch_time
    time -f %U ./bindash dist {{output}}/tmp --outfname={{output}}/bindash_bottom_s{{s}}.dist 2>&1 | tee >(cat 1>&2) | tail -1 > {{output}}/tmp_dist_time
    echo BinDash bottom 1000 31 {{s}} 64 `cat {{output}}/tmp_sketch_time` `cat {{output}}/tmp_dist_time` >> {{stats}}
bindash_bucket s b:
    time -f %U ./bindash sketch {{input}}/*fna --minhashtype=2 --kmerlen=31 --sketchsize={{s}} --bbits={{b}} --outfname={{output}}/tmp 2>&1 | tee >(cat 1>&2) | tail -1 > {{output}}/tmp_sketch_time
    time -f %U ./bindash dist {{output}}/tmp --outfname={{output}}/bindash_bucket_s{{s}}_b{{b}}.dist 2>&1 | tee >(cat 1>&2) | tail -1 > {{output}}/tmp_dist_time
    echo BinDash bin 1000 31 {{s}} {{b}} `cat {{output}}/tmp_sketch_time` `cat {{output}}/tmp_dist_time` >> {{stats}}


bindash_bot_all: (bindash_bot "128") (bindash_bot "1024") (bindash_bot "8192") (bindash_bot "32768")
bindash_bucket_all_b s: (bindash_bucket s "1") (bindash_bucket s "8") (bindash_bucket s "16") (bindash_bucket s "32")
bindash_bucket_all: (bindash_bucket_all_b "128") (bindash_bucket_all_b "1024") (bindash_bucket_all_b "8192") (bindash_bucket_all_b "32768")
bindash_bucket_all_s b: (bindash_bucket "128" b) (bindash_bucket "1024" b) (bindash_bucket "8192" b) (bindash_bucket "32768" b)


bindashrs s:
    ./bindash-rs -t 6 -k 31 --sketch_size {{s}} -q {{input}}_files -r {{input}}_files --stats {{stats}} -o {{output}}/bindashrs_s{{s}}.dist


bindashrs_all: (bindashrs "128") (bindashrs "1024") (bindashrs "8192") (bindashrs "32768")