Add some more benches (#97)
* Add rev_complement test # Conflicts: # benches/src/lib.rs # benches/wasm-kernel/src/lib.rs * Add redux_regex test. # Conflicts: # benches/wasm-kernel/Cargo.toml * Fmt and return an original header * Use ManuallyDrop * Really initialize lazy static.
This commit is contained in:
Sergey Pepyakin
GitHub
parent
f305b3cd1f
commit
94b797de44
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@ -6,3 +6,4 @@ authors = ["Sergey Pepyakin <s.pepyakin@gmail.com>"]
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[dependencies]
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[dependencies]
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wasmi = { path = ".." }
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wasmi = { path = ".." }
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assert_matches = "1.2"
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assert_matches = "1.2"
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wabt = "0.3"
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@ -4,6 +4,7 @@ extern crate test;
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extern crate wasmi;
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extern crate wasmi;
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#[macro_use]
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#[macro_use]
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extern crate assert_matches;
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extern crate assert_matches;
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extern crate wabt;
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use std::error;
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use std::error;
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use std::fs::File;
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use std::fs::File;
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@ -20,6 +21,9 @@ fn load_from_file(filename: &str) -> Result<Module, Box<error::Error>> {
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Ok(Module::from_buffer(buf)?)
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Ok(Module::from_buffer(buf)?)
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}
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}
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const REVCOMP_INPUT: &'static [u8] = include_bytes!("./revcomp-input.txt");
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const REVCOMP_OUTPUT: &'static [u8] = include_bytes!("./revcomp-output.txt");
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#[bench]
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#[bench]
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fn bench_tiny_keccak(b: &mut Bencher) {
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fn bench_tiny_keccak(b: &mut Bencher) {
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let wasm_kernel = load_from_file(
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let wasm_kernel = load_from_file(
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@ -41,3 +45,234 @@ fn bench_tiny_keccak(b: &mut Bencher) {
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.unwrap();
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.unwrap();
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});
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});
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}
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}
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#[bench]
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fn bench_rev_comp(b: &mut Bencher) {
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let wasm_kernel = load_from_file(
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"./wasm-kernel/target/wasm32-unknown-unknown/release/wasm_kernel.wasm",
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).expect("failed to load wasm_kernel. Is `build.rs` broken?");
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let instance = ModuleInstance::new(&wasm_kernel, &ImportsBuilder::default())
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.expect("failed to instantiate wasm module")
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.assert_no_start();
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// Allocate buffers for the input and output.
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let test_data_ptr: RuntimeValue = {
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let input_size = RuntimeValue::I32(REVCOMP_INPUT.len() as i32);
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assert_matches!(
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instance.invoke_export("prepare_rev_complement", &[input_size], &mut NopExternals),
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Ok(Some(v @ RuntimeValue::I32(_))) => v,
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"",
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)
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};
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// Get the pointer to the input buffer.
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let input_data_mem_offset = assert_matches!(
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instance.invoke_export("rev_complement_input_ptr", &[test_data_ptr], &mut NopExternals),
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Ok(Some(RuntimeValue::I32(v))) => v as u32,
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"",
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);
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// Copy test data inside the wasm memory.
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let memory = instance.export_by_name("memory")
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.expect("Expected export with a name 'memory'")
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.as_memory()
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.expect("'memory' should be a memory instance")
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.clone();
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memory
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.set(input_data_mem_offset, REVCOMP_INPUT)
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.expect("can't load test data into a wasm memory");
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b.iter(|| {
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instance
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.invoke_export("bench_rev_complement", &[test_data_ptr], &mut NopExternals)
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.unwrap();
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});
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// Verify the result.
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let output_data_mem_offset = assert_matches!(
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instance.invoke_export("rev_complement_output_ptr", &[test_data_ptr], &mut NopExternals),
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Ok(Some(RuntimeValue::I32(v))) => v as u32,
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"",
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);
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let result = memory
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.get(output_data_mem_offset, REVCOMP_OUTPUT.len())
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.expect("can't get result data from a wasm memory");
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assert_eq!(&*result, REVCOMP_OUTPUT);
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}
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#[bench]
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fn bench_regex_redux(b: &mut Bencher) {
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let wasm_kernel = load_from_file(
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"./wasm-kernel/target/wasm32-unknown-unknown/release/wasm_kernel.wasm",
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).expect("failed to load wasm_kernel. Is `build.rs` broken?");
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let instance = ModuleInstance::new(&wasm_kernel, &ImportsBuilder::default())
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.expect("failed to instantiate wasm module")
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.assert_no_start();
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// Allocate buffers for the input and output.
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let test_data_ptr: RuntimeValue = {
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let input_size = RuntimeValue::I32(REVCOMP_INPUT.len() as i32);
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assert_matches!(
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instance.invoke_export("prepare_regex_redux", &[input_size], &mut NopExternals),
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Ok(Some(v @ RuntimeValue::I32(_))) => v,
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"",
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)
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};
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// Get the pointer to the input buffer.
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let input_data_mem_offset = assert_matches!(
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instance.invoke_export("regex_redux_input_ptr", &[test_data_ptr], &mut NopExternals),
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Ok(Some(RuntimeValue::I32(v))) => v as u32,
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"",
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);
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// Copy test data inside the wasm memory.
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let memory = instance.export_by_name("memory")
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.expect("Expected export with a name 'memory'")
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.as_memory()
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.expect("'memory' should be a memory instance")
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.clone();
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memory
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.set(input_data_mem_offset, REVCOMP_INPUT)
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.expect("can't load test data into a wasm memory");
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b.iter(|| {
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instance
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.invoke_export("bench_regex_redux", &[test_data_ptr], &mut NopExternals)
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.unwrap();
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});
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}
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#[bench]
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fn fac_recursive(b: &mut Bencher) {
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let wasm = wabt::wat2wasm(
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r#"
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;; Recursive factorial
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(func (export "fac-rec") (param i64) (result i64)
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(if (result i64) (i64.eq (get_local 0) (i64.const 0))
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(then (i64.const 1))
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(else
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(i64.mul (get_local 0) (call 0 (i64.sub (get_local 0) (i64.const 1))))
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)
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)
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)
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"#
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).unwrap();
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let module = Module::from_buffer(&wasm).unwrap();
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let instance = ModuleInstance::new(&module, &ImportsBuilder::default())
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.expect("failed to instantiate wasm module")
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.assert_no_start();
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b.iter(|| {
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let value = instance
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.invoke_export("fac-rec", &[RuntimeValue::I64(25)], &mut NopExternals);
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assert_matches!(value, Ok(Some(RuntimeValue::I64(7034535277573963776))));
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});
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}
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#[bench]
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fn fac_opt(b: &mut Bencher) {
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let wasm = wabt::wat2wasm(
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r#"
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;; Optimized factorial.
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(func (export "fac-opt") (param i64) (result i64)
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(local i64)
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(set_local 1 (i64.const 1))
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(block
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(br_if 0 (i64.lt_s (get_local 0) (i64.const 2)))
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(loop
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(set_local 1 (i64.mul (get_local 1) (get_local 0)))
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(set_local 0 (i64.add (get_local 0) (i64.const -1)))
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(br_if 0 (i64.gt_s (get_local 0) (i64.const 1)))
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)
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)
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(get_local 1)
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)
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"#
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).unwrap();
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let module = Module::from_buffer(&wasm).unwrap();
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let instance = ModuleInstance::new(&module, &ImportsBuilder::default())
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.expect("failed to instantiate wasm module")
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.assert_no_start();
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b.iter(|| {
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let value = instance
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.invoke_export("fac-opt", &[RuntimeValue::I64(25)], &mut NopExternals);
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assert_matches!(value, Ok(Some(RuntimeValue::I64(7034535277573963776))));
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});
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}
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// This is used for testing overhead of a function call
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// is not too large.
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#[bench]
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fn recursive_ok(b: &mut Bencher) {
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let wasm = wabt::wat2wasm(
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r#"
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(module
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(func $call (export "call") (param i32) (result i32)
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block (result i32)
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get_local 0
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get_local 0
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i32.eqz
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br_if 0
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i32.const 1
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i32.sub
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call $call
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end
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)
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)
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"#
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).unwrap();
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let module = Module::from_buffer(&wasm).unwrap();
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let instance = ModuleInstance::new(&module, &ImportsBuilder::default())
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.expect("failed to instantiate wasm module")
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.assert_no_start();
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b.iter(|| {
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let value = instance
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.invoke_export("call", &[RuntimeValue::I32(8000)], &mut NopExternals);
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assert_matches!(value, Ok(Some(RuntimeValue::I32(0))));
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});
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}
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#[bench]
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fn recursive_trap(b: &mut Bencher) {
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let wasm = wabt::wat2wasm(
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r#"
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(module
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(func $call (export "call") (param i32) (result i32)
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block (result i32)
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get_local 0
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get_local 0
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i32.eqz
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br_if 0
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i32.const 1
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i32.sub
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call $call
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end
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unreachable
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)
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)
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"#
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).unwrap();
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let module = Module::from_buffer(&wasm).unwrap();
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let instance = ModuleInstance::new(&module, &ImportsBuilder::default())
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.expect("failed to instantiate wasm module")
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.assert_no_start();
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b.iter(|| {
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let value = instance
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.invoke_export("call", &[RuntimeValue::I32(1000)], &mut NopExternals);
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assert_matches!(value, Err(_));
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});
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}
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@ -0,0 +1,171 @@
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>ONE Homo sapiens alu
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GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGA
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TCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACT
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AAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAG
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GCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCG
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CCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAGGCCGGGCGCGGT
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GGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGGTCA
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GGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAA
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TTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAG
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AATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCA
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GCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAGGCCGGGCGCGGTGGCTCACGCCTGT
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AATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACC
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AGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTG
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GTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACC
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CGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAG
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AGCGAGACTCCGTCTCAAAAAGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTT
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TGGGAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACA
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TGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCT
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GTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGG
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TTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGT
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CTCAAAAAGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGG
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CGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCG
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TCTCTACTAAAAATACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTA
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CTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCG
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AGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAGGCCG
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GGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACC
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TGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAA
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TACAAAAATTAGCCGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGA
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GGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACT
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GCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAGGCCGGGCGCGGTGGCTC
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ACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACCTGAGGTCAGGAGT
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TCGAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGC
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CGGGCGTGGTGGCGCGCGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCG
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CTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTG
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GGCGACAGAGCGAGACTCCG
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>TWO IUB ambiguity codes
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cttBtatcatatgctaKggNcataaaSatgtaaaDcDRtBggDtctttataattcBgtcg
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tactDtDagcctatttSVHtHttKtgtHMaSattgWaHKHttttagacatWatgtRgaaa
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NtactMcSMtYtcMgRtacttctWBacgaaatatagScDtttgaagacacatagtVgYgt
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cattHWtMMWcStgttaggKtSgaYaaccWStcgBttgcgaMttBYatcWtgacaYcaga
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gtaBDtRacttttcWatMttDBcatWtatcttactaBgaYtcttgttttttttYaaScYa
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HgtgttNtSatcMtcVaaaStccRcctDaataataStcYtRDSaMtDttgttSagtRRca
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tttHatSttMtWgtcgtatSSagactYaaattcaMtWatttaSgYttaRgKaRtccactt
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tattRggaMcDaWaWagttttgacatgttctacaaaRaatataataaMttcgDacgaSSt
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acaStYRctVaNMtMgtaggcKatcttttattaaaaagVWaHKYagtttttatttaacct
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tacgtVtcVaattVMBcttaMtttaStgacttagattWWacVtgWYagWVRctDattBYt
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gtttaagaagattattgacVatMaacattVctgtBSgaVtgWWggaKHaatKWcBScSWa
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accRVacacaaactaccScattRatatKVtactatatttHttaagtttSKtRtacaaagt
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RDttcaaaaWgcacatWaDgtDKacgaacaattacaRNWaatHtttStgttattaaMtgt
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tgDcgtMgcatBtgcttcgcgaDWgagctgcgaggggVtaaScNatttacttaatgacag
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cccccacatYScaMgtaggtYaNgttctgaMaacNaMRaacaaacaKctacatagYWctg
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ttWaaataaaataRattagHacacaagcgKatacBttRttaagtatttccgatctHSaat
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actcNttMaagtattMtgRtgaMgcataatHcMtaBSaRattagttgatHtMttaaKagg
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YtaaBataSaVatactWtataVWgKgttaaaacagtgcgRatatacatVtHRtVYataSa
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KtWaStVcNKHKttactatccctcatgWHatWaRcttactaggatctataDtDHBttata
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aaaHgtacVtagaYttYaKcctattcttcttaataNDaaggaaaDYgcggctaaWSctBa
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aNtgctggMBaKctaMVKagBaactaWaDaMaccYVtNtaHtVWtKgRtcaaNtYaNacg
|
||||||
|
gtttNattgVtttctgtBaWgtaattcaagtcaVWtactNggattctttaYtaaagccgc
|
||||||
|
tcttagHVggaYtgtNcDaVagctctctKgacgtatagYcctRYHDtgBattDaaDgccK
|
||||||
|
tcHaaStttMcctagtattgcRgWBaVatHaaaataYtgtttagMDMRtaataaggatMt
|
||||||
|
ttctWgtNtgtgaaaaMaatatRtttMtDgHHtgtcattttcWattRSHcVagaagtacg
|
||||||
|
ggtaKVattKYagactNaatgtttgKMMgYNtcccgSKttctaStatatNVataYHgtNa
|
||||||
|
BKRgNacaactgatttcctttaNcgatttctctataScaHtataRagtcRVttacDSDtt
|
||||||
|
aRtSatacHgtSKacYagttMHtWataggatgactNtatSaNctataVtttRNKtgRacc
|
||||||
|
tttYtatgttactttttcctttaaacatacaHactMacacggtWataMtBVacRaSaatc
|
||||||
|
cgtaBVttccagccBcttaRKtgtgcctttttRtgtcagcRttKtaaacKtaaatctcac
|
||||||
|
aattgcaNtSBaaccgggttattaaBcKatDagttactcttcattVtttHaaggctKKga
|
||||||
|
tacatcBggScagtVcacattttgaHaDSgHatRMaHWggtatatRgccDttcgtatcga
|
||||||
|
aacaHtaagttaRatgaVacttagattVKtaaYttaaatcaNatccRttRRaMScNaaaD
|
||||||
|
gttVHWgtcHaaHgacVaWtgttScactaagSgttatcttagggDtaccagWattWtRtg
|
||||||
|
ttHWHacgattBtgVcaYatcggttgagKcWtKKcaVtgaYgWctgYggVctgtHgaNcV
|
||||||
|
taBtWaaYatcDRaaRtSctgaHaYRttagatMatgcatttNattaDttaattgttctaa
|
||||||
|
ccctcccctagaWBtttHtBccttagaVaatMcBHagaVcWcagBVttcBtaYMccagat
|
||||||
|
gaaaaHctctaacgttagNWRtcggattNatcRaNHttcagtKttttgWatWttcSaNgg
|
||||||
|
gaWtactKKMaacatKatacNattgctWtatctaVgagctatgtRaHtYcWcttagccaa
|
||||||
|
tYttWttaWSSttaHcaaaaagVacVgtaVaRMgattaVcDactttcHHggHRtgNcctt
|
||||||
|
tYatcatKgctcctctatVcaaaaKaaaagtatatctgMtWtaaaacaStttMtcgactt
|
||||||
|
taSatcgDataaactaaacaagtaaVctaggaSccaatMVtaaSKNVattttgHccatca
|
||||||
|
cBVctgcaVatVttRtactgtVcaattHgtaaattaaattttYtatattaaRSgYtgBag
|
||||||
|
aHSBDgtagcacRHtYcBgtcacttacactaYcgctWtattgSHtSatcataaatataHt
|
||||||
|
cgtYaaMNgBaatttaRgaMaatatttBtttaaaHHKaatctgatWatYaacttMctctt
|
||||||
|
ttVctagctDaaagtaVaKaKRtaacBgtatccaaccactHHaagaagaaggaNaaatBW
|
||||||
|
attccgStaMSaMatBttgcatgRSacgttVVtaaDMtcSgVatWcaSatcttttVatag
|
||||||
|
ttactttacgatcaccNtaDVgSRcgVcgtgaacgaNtaNatatagtHtMgtHcMtagaa
|
||||||
|
attBgtataRaaaacaYKgtRccYtatgaagtaataKgtaaMttgaaRVatgcagaKStc
|
||||||
|
tHNaaatctBBtcttaYaBWHgtVtgacagcaRcataWctcaBcYacYgatDgtDHccta
|
||||||
|
>THREE Homo sapiens frequency
|
||||||
|
aacacttcaccaggtatcgtgaaggctcaagattacccagagaacctttgcaatataaga
|
||||||
|
atatgtatgcagcattaccctaagtaattatattctttttctgactcaaagtgacaagcc
|
||||||
|
ctagtgtatattaaatcggtatatttgggaaattcctcaaactatcctaatcaggtagcc
|
||||||
|
atgaaagtgatcaaaaaagttcgtacttataccatacatgaattctggccaagtaaaaaa
|
||||||
|
tagattgcgcaaaattcgtaccttaagtctctcgccaagatattaggatcctattactca
|
||||||
|
tatcgtgtttttctttattgccgccatccccggagtatctcacccatccttctcttaaag
|
||||||
|
gcctaatattacctatgcaaataaacatatattgttgaaaattgagaacctgatcgtgat
|
||||||
|
tcttatgtgtaccatatgtatagtaatcacgcgactatatagtgctttagtatcgcccgt
|
||||||
|
gggtgagtgaatattctgggctagcgtgagatagtttcttgtcctaatatttttcagatc
|
||||||
|
gaatagcttctatttttgtgtttattgacatatgtcgaaactccttactcagtgaaagtc
|
||||||
|
atgaccagatccacgaacaatcttcggaatcagtctcgttttacggcggaatcttgagtc
|
||||||
|
taacttatatcccgtcgcttactttctaacaccccttatgtatttttaaaattacgttta
|
||||||
|
ttcgaacgtacttggcggaagcgttattttttgaagtaagttacattgggcagactcttg
|
||||||
|
acattttcgatacgactttctttcatccatcacaggactcgttcgtattgatatcagaag
|
||||||
|
ctcgtgatgattagttgtcttctttaccaatactttgaggcctattctgcgaaatttttg
|
||||||
|
ttgccctgcgaacttcacataccaaggaacacctcgcaacatgccttcatatccatcgtt
|
||||||
|
cattgtaattcttacacaatgaatcctaagtaattacatccctgcgtaaaagatggtagg
|
||||||
|
ggcactgaggatatattaccaagcatttagttatgagtaatcagcaatgtttcttgtatt
|
||||||
|
aagttctctaaaatagttacatcgtaatgttatctcgggttccgcgaataaacgagatag
|
||||||
|
attcattatatatggccctaagcaaaaacctcctcgtattctgttggtaattagaatcac
|
||||||
|
acaatacgggttgagatattaattatttgtagtacgaagagatataaaaagatgaacaat
|
||||||
|
tactcaagtcaagatgtatacgggatttataataaaaatcgggtagagatctgctttgca
|
||||||
|
attcagacgtgccactaaatcgtaatatgtcgcgttacatcagaaagggtaactattatt
|
||||||
|
aattaataaagggcttaatcactacatattagatcttatccgatagtcttatctattcgt
|
||||||
|
tgtatttttaagcggttctaattcagtcattatatcagtgctccgagttctttattattg
|
||||||
|
ttttaaggatgacaaaatgcctcttgttataacgctgggagaagcagactaagagtcgga
|
||||||
|
gcagttggtagaatgaggctgcaaaagacggtctcgacgaatggacagactttactaaac
|
||||||
|
caatgaaagacagaagtagagcaaagtctgaagtggtatcagcttaattatgacaaccct
|
||||||
|
taatacttccctttcgccgaatactggcgtggaaaggttttaaaagtcgaagtagttaga
|
||||||
|
ggcatctctcgctcataaataggtagactactcgcaatccaatgtgactatgtaatactg
|
||||||
|
ggaacatcagtccgcgatgcagcgtgtttatcaaccgtccccactcgcctggggagacat
|
||||||
|
gagaccacccccgtggggattattagtccgcagtaatcgactcttgacaatccttttcga
|
||||||
|
ttatgtcatagcaatttacgacagttcagcgaagtgactactcggcgaaatggtattact
|
||||||
|
aaagcattcgaacccacatgaatgtgattcttggcaatttctaatccactaaagcttttc
|
||||||
|
cgttgaatctggttgtagatatttatataagttcactaattaagatcacggtagtatatt
|
||||||
|
gatagtgatgtctttgcaagaggttggccgaggaatttacggattctctattgatacaat
|
||||||
|
ttgtctggcttataactcttaaggctgaaccaggcgtttttagacgacttgatcagctgt
|
||||||
|
tagaatggtttggactccctctttcatgtcagtaacatttcagccgttattgttacgata
|
||||||
|
tgcttgaacaatattgatctaccacacacccatagtatattttataggtcatgctgttac
|
||||||
|
ctacgagcatggtattccacttcccattcaatgagtattcaacatcactagcctcagaga
|
||||||
|
tgatgacccacctctaataacgtcacgttgcggccatgtgaaacctgaacttgagtagac
|
||||||
|
gatatcaagcgctttaaattgcatataacatttgagggtaaagctaagcggatgctttat
|
||||||
|
ataatcaatactcaataataagatttgattgcattttagagttatgacacgacatagttc
|
||||||
|
actaacgagttactattcccagatctagactgaagtactgatcgagacgatccttacgtc
|
||||||
|
gatgatcgttagttatcgacttaggtcgggtctctagcggtattggtacttaaccggaca
|
||||||
|
ctatactaataacccatgatcaaagcataacagaatacagacgataatttcgccaacata
|
||||||
|
tatgtacagaccccaagcatgagaagctcattgaaagctatcattgaagtcccgctcaca
|
||||||
|
atgtgtcttttccagacggtttaactggttcccgggagtcctggagtttcgacttacata
|
||||||
|
aatggaaacaatgtattttgctaatttatctatagcgtcatttggaccaatacagaatat
|
||||||
|
tatgttgcctagtaatccactataacccgcaagtgctgatagaaaatttttagacgattt
|
||||||
|
ataaatgccccaagtatccctcccgtgaatcctccgttatactaattagtattcgttcat
|
||||||
|
acgtataccgcgcatatatgaacatttggcgataaggcgcgtgaattgttacgtgacaga
|
||||||
|
gatagcagtttcttgtgatatggttaacagacgtacatgaagggaaactttatatctata
|
||||||
|
gtgatgcttccgtagaaataccgccactggtctgccaatgatgaagtatgtagctttagg
|
||||||
|
tttgtactatgaggctttcgtttgtttgcagagtataacagttgcgagtgaaaaaccgac
|
||||||
|
gaatttatactaatacgctttcactattggctacaaaatagggaagagtttcaatcatga
|
||||||
|
gagggagtatatggatgctttgtagctaaaggtagaacgtatgtatatgctgccgttcat
|
||||||
|
tcttgaaagatacataagcgataagttacgacaattataagcaacatccctaccttcgta
|
||||||
|
acgatttcactgttactgcgcttgaaatacactatggggctattggcggagagaagcaga
|
||||||
|
tcgcgccgagcatatacgagacctataatgttgatgatagagaaggcgtctgaattgata
|
||||||
|
catcgaagtacactttctttcgtagtatctctcgtcctctttctatctccggacacaaga
|
||||||
|
attaagttatatatatagagtcttaccaatcatgttgaatcctgattctcagagttcttt
|
||||||
|
ggcgggccttgtgatgactgagaaacaatgcaatattgctccaaatttcctaagcaaatt
|
||||||
|
ctcggttatgttatgttatcagcaaagcgttacgttatgttatttaaatctggaatgacg
|
||||||
|
gagcgaagttcttatgtcggtgtgggaataattcttttgaagacagcactccttaaataa
|
||||||
|
tatcgctccgtgtttgtatttatcgaatgggtctgtaaccttgcacaagcaaatcggtgg
|
||||||
|
tgtatatatcggataacaattaatacgatgttcatagtgacagtatactgatcgagtcct
|
||||||
|
ctaaagtcaattacctcacttaacaatctcattgatgttgtgtcattcccggtatcgccc
|
||||||
|
gtagtatgtgctctgattgaccgagtgtgaaccaaggaacatctactaatgcctttgtta
|
||||||
|
ggtaagatctctctgaattccttcgtgccaacttaaaacattatcaaaatttcttctact
|
||||||
|
tggattaactacttttacgagcatggcaaattcccctgtggaagacggttcattattatc
|
||||||
|
ggaaaccttatagaaattgcgtgttgactgaaattagatttttattgtaagagttgcatc
|
||||||
|
tttgcgattcctctggtctagcttccaatgaacagtcctcccttctattcgacatcgggt
|
||||||
|
ccttcgtacatgtctttgcgatgtaataattaggttcggagtgtggccttaatgggtgca
|
||||||
|
actaggaatacaacgcaaatttgctgacatgatagcaaatcggtatgccggcaccaaaac
|
||||||
|
gtgctccttgcttagcttgtgaatgagactcagtagttaaataaatccatatctgcaatc
|
||||||
|
gattccacaggtattgtccactatctttgaactactctaagagatacaagcttagctgag
|
||||||
|
accgaggtgtatatgactacgctgatatctgtaaggtaccaatgcaggcaaagtatgcga
|
||||||
|
gaagctaataccggctgtttccagctttataagattaaaatttggctgtcctggcggcct
|
||||||
|
cagaattgttctatcgtaatcagttggttcattaattagctaagtacgaggtacaactta
|
||||||
|
tctgtcccagaacagctccacaagtttttttacagccgaaacccctgtgtgaatcttaat
|
||||||
|
atccaagcgcgttatctgattagagtttacaactcagtattttatcagtacgttttgttt
|
||||||
|
ccaacattacccggtatgacaaaatgacgccacgtgtcgaataatggtctgaccaatgta
|
||||||
|
ggaagtgaaaagataaatat
|
||||||
|
|
@ -0,0 +1,171 @@
|
||||||
|
>ONE Homo sapiens alu
|
||||||
|
CGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAC
|
||||||
|
CTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACA
|
||||||
|
GGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCAT
|
||||||
|
GTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAA
|
||||||
|
AGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCTTTTTGAGACGGAGTCTCGCTC
|
||||||
|
TGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGG
|
||||||
|
GTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACC
|
||||||
|
ACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTG
|
||||||
|
GTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTA
|
||||||
|
CAGGCGTGAGCCACCGCGCCCGGCCTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCT
|
||||||
|
GGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTC
|
||||||
|
TCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGCTAAT
|
||||||
|
TTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCT
|
||||||
|
GACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCA
|
||||||
|
CCGCGCCCGGCCTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGC
|
||||||
|
GCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCC
|
||||||
|
TCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTA
|
||||||
|
GTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGAT
|
||||||
|
CCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCT
|
||||||
|
TTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTC
|
||||||
|
ACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTG
|
||||||
|
GGATTACAGGCGCGCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGT
|
||||||
|
TTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGG
|
||||||
|
CCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCTTTTTGAGACGGAG
|
||||||
|
TCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCG
|
||||||
|
CCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGC
|
||||||
|
GCGCCACCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGG
|
||||||
|
CCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGC
|
||||||
|
TGGGATTACAGGCGTGAGCCACCGCGCCCGGCCTTTTTGAGACGGAGTCTCGCTCTGTCG
|
||||||
|
CCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCA
|
||||||
|
AGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCACCACGCC
|
||||||
|
CGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTC
|
||||||
|
GAACTCCTGACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGC
|
||||||
|
GTGAGCCACCGCGCCCGGCC
|
||||||
|
>TWO IUB ambiguity codes
|
||||||
|
TAGGDHACHATCRGTRGVTGAGWTATGYTGCTGTCABACDWVTRTAAGAVVAGATTTNDA
|
||||||
|
GASMTCTGCATBYTTCAAKTTACMTATTACTTCATARGGYACMRTGTTTTYTATACVAAT
|
||||||
|
TTCTAKGDACKADACTATATNTANTCGTTCACGBCGYSCBHTANGGTGATCGTAAAGTAA
|
||||||
|
CTATBAAAAGATSTGWATBCSGAKHTTABBAACGTSYCATGCAAVATKTSKTASCGGAAT
|
||||||
|
WVATTTNTCCTTCTTCTTDDAGTGGTTGGATACVGTTAYMTMTBTACTTTHAGCTAGBAA
|
||||||
|
AAGAGKAAGTTRATWATCAGATTMDDTTTAAAVAAATATTKTCYTAAATTVCNKTTRACG
|
||||||
|
ADTATATTTATGATSADSCAATAWAGCGRTAGTGTAAGTGACVGRADYGTGCTACHVSDT
|
||||||
|
CTVCARCSYTTAATATARAAAATTTAATTTACDAATTGBACAGTAYAABATBTGCAGBVG
|
||||||
|
TGATGGDCAAAATBNMSTTABKATTGGSTCCTAGBTTACTTGTTTAGTTTATHCGATSTA
|
||||||
|
AAGTCGAKAAASTGTTTTAWAKCAGATATACTTTTMTTTTGBATAGAGGAGCMATGATRA
|
||||||
|
AAGGNCAYDCCDDGAAAGTHGBTAATCKYTBTACBGTBCTTTTTGDTAASSWTAAWAARA
|
||||||
|
TTGGCTAAGWGRADTYACATAGCTCBTAGATAWAGCAATNGTATMATGTTKMMAGTAWTC
|
||||||
|
CCNTSGAAWATWCAAAAMACTGAADNTYGATNAATCCGAYWNCTAACGTTAGAGDTTTTC
|
||||||
|
ATCTGGKRTAVGAABVCTGWGBTCTDVGKATTBTCTAAGGVADAAAVWTCTAGGGGAGGG
|
||||||
|
TTAGAACAATTAAHTAATNAAATGCATKATCTAAYRTDTCAGSAYTTYHGATRTTWAVTA
|
||||||
|
BGNTCDACAGBCCRCAGWCRTCABTGMMAWGMCTCAACCGATRTGBCAVAATCGTDWDAA
|
||||||
|
CAYAWAATWCTGGTAHCCCTAAGATAACSCTTAGTGSAACAWTBGTCDTTDGACWDBAAC
|
||||||
|
HTTTNGSKTYYAAYGGATNTGATTTAARTTAMBAATCTAAGTBTCATYTAACTTADTGTT
|
||||||
|
TCGATACGAAHGGCYATATACCWDTKYATDCSHTDTCAAAATGTGBACTGSCCVGATGTA
|
||||||
|
TCMMAGCCTTDAAABAATGAAGAGTAACTHATMGVTTAATAACCCGGTTVSANTGCAATT
|
||||||
|
GTGAGATTTAMGTTTAMAAYGCTGACAYAAAAAGGCACAMYTAAGVGGCTGGAABVTACG
|
||||||
|
GATTSTYGTBVAKTATWACCGTGTKAGTDTGTATGTTTAAAGGAAAAAGTAACATARAAA
|
||||||
|
GGTYCAMNYAAABTATAGNTSATANAGTCATCCTATWADKAACTRGTMSACDGTATSAYT
|
||||||
|
AAHSHGTAABYGACTYTATADTGSTATAGAGAAATCGNTAAAGGAAATCAGTTGTNCYMV
|
||||||
|
TNACDRTATBNATATASTAGAAMSCGGGANRCKKMCAAACATTNAGTCTRMAATBMTACC
|
||||||
|
CGTACTTCTBGDSYAATWGAAAATGACADDCHAKAAAYATATTKTTTTCACANACWAGAA
|
||||||
|
AKATCCTTATTAYKHKCTAAACARTATTTTDATBTVWCYGCAATACTAGGKAAASTTDGA
|
||||||
|
MGGCHTTHAATVCAHDRYAGGRCTATACGTCMAGAGAGCTBTHGNACARTCCBDCTAAGA
|
||||||
|
GCGGCTTTARTAAAGAATCCNAGTAWBTGACTTGAATTACWTVACAGAAABCAATNAAAC
|
||||||
|
CGTNTRANTTGAYCMAWBADTANABRGGTKTHTWTAGTTVCTMBKTAGMTVKCCAGCANT
|
||||||
|
TVAGSWTTAGCCGCRHTTTCCTTHNTATTAAGAAGAATAGGMTRAARTCTABGTACDTTT
|
||||||
|
TATAAVDHAHTATAGATCCTAGTAAGYTWATDWCATGAGGGATAGTAAMDMNGBASTWAM
|
||||||
|
TSTATRBAYDABATGTATATYCGCACTGTTTTAACMCWBTATAWAGTATBTSTATVTTAR
|
||||||
|
CCTMTTAAKADATCAACTAATYTSVTAKGDATTATGCKTCAYCAKAATACTTKAANGAGT
|
||||||
|
ATTSDAGATCGGAAATACTTAAYAAVGTATMCGCTTGTGTDCTAATYTATTTTATTTWAA
|
||||||
|
CAGWRCTATGTAGMTGTTTGTTYKTNGTTKTCAGAACNTRACCTACKTGSRATGTGGGGG
|
||||||
|
CTGTCATTAAGTAAATNGSTTABCCCCTCGCAGCTCWHTCGCGAAGCAVATGCKACGHCA
|
||||||
|
ACAKTTAATAACASAAADATTWNYTGTAATTGTTCGTMHACHTWATGTGCWTTTTGAAHY
|
||||||
|
ACTTTGTAYAMSAAACTTAADAAATATAGTABMATATYAATGSGGTAGTTTGTGTBYGGT
|
||||||
|
TWSGSVGWMATTDMTCCWWCABTCSVACAGBAATGTTKATBGTCAATAATCTTCTTAAAC
|
||||||
|
ARVAATHAGYBWCTRWCABGTWWAATCTAAGTCASTAAAKTAAGVKBAATTBGABACGTA
|
||||||
|
AGGTTAAATAAAAACTRMDTWBCTTTTTAATAAAAGATMGCCTACKAKNTBAGYRASTGT
|
||||||
|
ASSTCGTHCGAAKTTATTATATTYTTTGTAGAACATGTCAAAACTWTWTHGKTCCYAATA
|
||||||
|
AAGTGGAYTMCYTAARCSTAAATWAKTGAATTTRAGTCTSSATACGACWAKAASATDAAA
|
||||||
|
TGYYACTSAACAAHAKTSHYARGASTATTATTHAGGYGGASTTTBGAKGATSANAACACD
|
||||||
|
TRGSTTRAAAAAAAACAAGARTCVTAGTAAGATAWATGVHAAKATWGAAAAGTYAHVTAC
|
||||||
|
TCTGRTGTCAWGATRVAAKTCGCAAVCGASWGGTTRTCSAMCCTAACASGWKKAWDAATG
|
||||||
|
ACRCBACTATGTGTCTTCAAAHGSCTATATTTCGTVWAGAAGTAYCKGARAKSGKAGTAN
|
||||||
|
TTTCYACATWATGTCTAAAADMDTWCAATSTKDACAMAADADBSAAATAGGCTHAHAGTA
|
||||||
|
CGACVGAATTATAAAGAHCCVAYHGHTTTACATSTTTATGNCCMTAGCATATGATAVAAG
|
||||||
|
>THREE Homo sapiens frequency
|
||||||
|
ATATTTATCTTTTCACTTCCTACATTGGTCAGACCATTATTCGACACGTGGCGTCATTTT
|
||||||
|
GTCATACCGGGTAATGTTGGAAACAAAACGTACTGATAAAATACTGAGTTGTAAACTCTA
|
||||||
|
ATCAGATAACGCGCTTGGATATTAAGATTCACACAGGGGTTTCGGCTGTAAAAAAACTTG
|
||||||
|
TGGAGCTGTTCTGGGACAGATAAGTTGTACCTCGTACTTAGCTAATTAATGAACCAACTG
|
||||||
|
ATTACGATAGAACAATTCTGAGGCCGCCAGGACAGCCAAATTTTAATCTTATAAAGCTGG
|
||||||
|
AAACAGCCGGTATTAGCTTCTCGCATACTTTGCCTGCATTGGTACCTTACAGATATCAGC
|
||||||
|
GTAGTCATATACACCTCGGTCTCAGCTAAGCTTGTATCTCTTAGAGTAGTTCAAAGATAG
|
||||||
|
TGGACAATACCTGTGGAATCGATTGCAGATATGGATTTATTTAACTACTGAGTCTCATTC
|
||||||
|
ACAAGCTAAGCAAGGAGCACGTTTTGGTGCCGGCATACCGATTTGCTATCATGTCAGCAA
|
||||||
|
ATTTGCGTTGTATTCCTAGTTGCACCCATTAAGGCCACACTCCGAACCTAATTATTACAT
|
||||||
|
CGCAAAGACATGTACGAAGGACCCGATGTCGAATAGAAGGGAGGACTGTTCATTGGAAGC
|
||||||
|
TAGACCAGAGGAATCGCAAAGATGCAACTCTTACAATAAAAATCTAATTTCAGTCAACAC
|
||||||
|
GCAATTTCTATAAGGTTTCCGATAATAATGAACCGTCTTCCACAGGGGAATTTGCCATGC
|
||||||
|
TCGTAAAAGTAGTTAATCCAAGTAGAAGAAATTTTGATAATGTTTTAAGTTGGCACGAAG
|
||||||
|
GAATTCAGAGAGATCTTACCTAACAAAGGCATTAGTAGATGTTCCTTGGTTCACACTCGG
|
||||||
|
TCAATCAGAGCACATACTACGGGCGATACCGGGAATGACACAACATCAATGAGATTGTTA
|
||||||
|
AGTGAGGTAATTGACTTTAGAGGACTCGATCAGTATACTGTCACTATGAACATCGTATTA
|
||||||
|
ATTGTTATCCGATATATACACCACCGATTTGCTTGTGCAAGGTTACAGACCCATTCGATA
|
||||||
|
AATACAAACACGGAGCGATATTATTTAAGGAGTGCTGTCTTCAAAAGAATTATTCCCACA
|
||||||
|
CCGACATAAGAACTTCGCTCCGTCATTCCAGATTTAAATAACATAACGTAACGCTTTGCT
|
||||||
|
GATAACATAACATAACCGAGAATTTGCTTAGGAAATTTGGAGCAATATTGCATTGTTTCT
|
||||||
|
CAGTCATCACAAGGCCCGCCAAAGAACTCTGAGAATCAGGATTCAACATGATTGGTAAGA
|
||||||
|
CTCTATATATATAACTTAATTCTTGTGTCCGGAGATAGAAAGAGGACGAGAGATACTACG
|
||||||
|
AAAGAAAGTGTACTTCGATGTATCAATTCAGACGCCTTCTCTATCATCAACATTATAGGT
|
||||||
|
CTCGTATATGCTCGGCGCGATCTGCTTCTCTCCGCCAATAGCCCCATAGTGTATTTCAAG
|
||||||
|
CGCAGTAACAGTGAAATCGTTACGAAGGTAGGGATGTTGCTTATAATTGTCGTAACTTAT
|
||||||
|
CGCTTATGTATCTTTCAAGAATGAACGGCAGCATATACATACGTTCTACCTTTAGCTACA
|
||||||
|
AAGCATCCATATACTCCCTCTCATGATTGAAACTCTTCCCTATTTTGTAGCCAATAGTGA
|
||||||
|
AAGCGTATTAGTATAAATTCGTCGGTTTTTCACTCGCAACTGTTATACTCTGCAAACAAA
|
||||||
|
CGAAAGCCTCATAGTACAAACCTAAAGCTACATACTTCATCATTGGCAGACCAGTGGCGG
|
||||||
|
TATTTCTACGGAAGCATCACTATAGATATAAAGTTTCCCTTCATGTACGTCTGTTAACCA
|
||||||
|
TATCACAAGAAACTGCTATCTCTGTCACGTAACAATTCACGCGCCTTATCGCCAAATGTT
|
||||||
|
CATATATGCGCGGTATACGTATGAACGAATACTAATTAGTATAACGGAGGATTCACGGGA
|
||||||
|
GGGATACTTGGGGCATTTATAAATCGTCTAAAAATTTTCTATCAGCACTTGCGGGTTATA
|
||||||
|
GTGGATTACTAGGCAACATAATATTCTGTATTGGTCCAAATGACGCTATAGATAAATTAG
|
||||||
|
CAAAATACATTGTTTCCATTTATGTAAGTCGAAACTCCAGGACTCCCGGGAACCAGTTAA
|
||||||
|
ACCGTCTGGAAAAGACACATTGTGAGCGGGACTTCAATGATAGCTTTCAATGAGCTTCTC
|
||||||
|
ATGCTTGGGGTCTGTACATATATGTTGGCGAAATTATCGTCTGTATTCTGTTATGCTTTG
|
||||||
|
ATCATGGGTTATTAGTATAGTGTCCGGTTAAGTACCAATACCGCTAGAGACCCGACCTAA
|
||||||
|
GTCGATAACTAACGATCATCGACGTAAGGATCGTCTCGATCAGTACTTCAGTCTAGATCT
|
||||||
|
GGGAATAGTAACTCGTTAGTGAACTATGTCGTGTCATAACTCTAAAATGCAATCAAATCT
|
||||||
|
TATTATTGAGTATTGATTATATAAAGCATCCGCTTAGCTTTACCCTCAAATGTTATATGC
|
||||||
|
AATTTAAAGCGCTTGATATCGTCTACTCAAGTTCAGGTTTCACATGGCCGCAACGTGACG
|
||||||
|
TTATTAGAGGTGGGTCATCATCTCTGAGGCTAGTGATGTTGAATACTCATTGAATGGGAA
|
||||||
|
GTGGAATACCATGCTCGTAGGTAACAGCATGACCTATAAAATATACTATGGGTGTGTGGT
|
||||||
|
AGATCAATATTGTTCAAGCATATCGTAACAATAACGGCTGAAATGTTACTGACATGAAAG
|
||||||
|
AGGGAGTCCAAACCATTCTAACAGCTGATCAAGTCGTCTAAAAACGCCTGGTTCAGCCTT
|
||||||
|
AAGAGTTATAAGCCAGACAAATTGTATCAATAGAGAATCCGTAAATTCCTCGGCCAACCT
|
||||||
|
CTTGCAAAGACATCACTATCAATATACTACCGTGATCTTAATTAGTGAACTTATATAAAT
|
||||||
|
ATCTACAACCAGATTCAACGGAAAAGCTTTAGTGGATTAGAAATTGCCAAGAATCACATT
|
||||||
|
CATGTGGGTTCGAATGCTTTAGTAATACCATTTCGCCGAGTAGTCACTTCGCTGAACTGT
|
||||||
|
CGTAAATTGCTATGACATAATCGAAAAGGATTGTCAAGAGTCGATTACTGCGGACTAATA
|
||||||
|
ATCCCCACGGGGGTGGTCTCATGTCTCCCCAGGCGAGTGGGGACGGTTGATAAACACGCT
|
||||||
|
GCATCGCGGACTGATGTTCCCAGTATTACATAGTCACATTGGATTGCGAGTAGTCTACCT
|
||||||
|
ATTTATGAGCGAGAGATGCCTCTAACTACTTCGACTTTTAAAACCTTTCCACGCCAGTAT
|
||||||
|
TCGGCGAAAGGGAAGTATTAAGGGTTGTCATAATTAAGCTGATACCACTTCAGACTTTGC
|
||||||
|
TCTACTTCTGTCTTTCATTGGTTTAGTAAAGTCTGTCCATTCGTCGAGACCGTCTTTTGC
|
||||||
|
AGCCTCATTCTACCAACTGCTCCGACTCTTAGTCTGCTTCTCCCAGCGTTATAACAAGAG
|
||||||
|
GCATTTTGTCATCCTTAAAACAATAATAAAGAACTCGGAGCACTGATATAATGACTGAAT
|
||||||
|
TAGAACCGCTTAAAAATACAACGAATAGATAAGACTATCGGATAAGATCTAATATGTAGT
|
||||||
|
GATTAAGCCCTTTATTAATTAATAATAGTTACCCTTTCTGATGTAACGCGACATATTACG
|
||||||
|
ATTTAGTGGCACGTCTGAATTGCAAAGCAGATCTCTACCCGATTTTTATTATAAATCCCG
|
||||||
|
TATACATCTTGACTTGAGTAATTGTTCATCTTTTTATATCTCTTCGTACTACAAATAATT
|
||||||
|
AATATCTCAACCCGTATTGTGTGATTCTAATTACCAACAGAATACGAGGAGGTTTTTGCT
|
||||||
|
TAGGGCCATATATAATGAATCTATCTCGTTTATTCGCGGAACCCGAGATAACATTACGAT
|
||||||
|
GTAACTATTTTAGAGAACTTAATACAAGAAACATTGCTGATTACTCATAACTAAATGCTT
|
||||||
|
GGTAATATATCCTCAGTGCCCCTACCATCTTTTACGCAGGGATGTAATTACTTAGGATTC
|
||||||
|
ATTGTGTAAGAATTACAATGAACGATGGATATGAAGGCATGTTGCGAGGTGTTCCTTGGT
|
||||||
|
ATGTGAAGTTCGCAGGGCAACAAAAATTTCGCAGAATAGGCCTCAAAGTATTGGTAAAGA
|
||||||
|
AGACAACTAATCATCACGAGCTTCTGATATCAATACGAACGAGTCCTGTGATGGATGAAA
|
||||||
|
GAAAGTCGTATCGAAAATGTCAAGAGTCTGCCCAATGTAACTTACTTCAAAAAATAACGC
|
||||||
|
TTCCGCCAAGTACGTTCGAATAAACGTAATTTTAAAAATACATAAGGGGTGTTAGAAAGT
|
||||||
|
AAGCGACGGGATATAAGTTAGACTCAAGATTCCGCCGTAAAACGAGACTGATTCCGAAGA
|
||||||
|
TTGTTCGTGGATCTGGTCATGACTTTCACTGAGTAAGGAGTTTCGACATATGTCAATAAA
|
||||||
|
CACAAAAATAGAAGCTATTCGATCTGAAAAATATTAGGACAAGAAACTATCTCACGCTAG
|
||||||
|
CCCAGAATATTCACTCACCCACGGGCGATACTAAAGCACTATATAGTCGCGTGATTACTA
|
||||||
|
TACATATGGTACACATAAGAATCACGATCAGGTTCTCAATTTTCAACAATATATGTTTAT
|
||||||
|
TTGCATAGGTAATATTAGGCCTTTAAGAGAAGGATGGGTGAGATACTCCGGGGATGGCGG
|
||||||
|
CAATAAAGAAAAACACGATATGAGTAATAGGATCCTAATATCTTGGCGAGAGACTTAAGG
|
||||||
|
TACGAATTTTGCGCAATCTATTTTTTACTTGGCCAGAATTCATGTATGGTATAAGTACGA
|
||||||
|
ACTTTTTTGATCACTTTCATGGCTACCTGATTAGGATAGTTTGAGGAATTTCCCAAATAT
|
||||||
|
ACCGATTTAATATACACTAGGGCTTGTCACTTTGAGTCAGAAAAAGAATATAATTACTTA
|
||||||
|
GGGTAATGCTGCATACATATTCTTATATTGCAAAGGTTCTCTGGGTAATCTTGAGCCTTC
|
||||||
|
ACGATACCTGGTGAAGTGTT
|
||||||
|
|
@ -8,7 +8,8 @@ crate-type = ["cdylib"]
|
||||||
|
|
||||||
[dependencies]
|
[dependencies]
|
||||||
tiny-keccak = "1.4.2"
|
tiny-keccak = "1.4.2"
|
||||||
rlibc = "1.0"
|
regex = "0.2.10"
|
||||||
|
lazy_static = "1.0"
|
||||||
|
|
||||||
[profile.release]
|
[profile.release]
|
||||||
panic = "abort"
|
panic = "abort"
|
||||||
|
|
|
||||||
|
|
@ -1,21 +1,13 @@
|
||||||
#![no_std]
|
|
||||||
#![feature(lang_items)]
|
|
||||||
#![feature(core_intrinsics)]
|
|
||||||
#![feature(panic_implementation)]
|
|
||||||
|
|
||||||
extern crate rlibc;
|
|
||||||
extern crate tiny_keccak;
|
extern crate tiny_keccak;
|
||||||
|
extern crate regex;
|
||||||
|
#[macro_use]
|
||||||
|
extern crate lazy_static;
|
||||||
|
|
||||||
|
use std::mem::ManuallyDrop;
|
||||||
use tiny_keccak::Keccak;
|
use tiny_keccak::Keccak;
|
||||||
|
|
||||||
#[no_mangle]
|
mod rev_complement;
|
||||||
#[panic_implementation]
|
mod regex_redux;
|
||||||
pub fn panic_fmt(_info: &::core::panic::PanicInfo) -> ! {
|
|
||||||
use core::intrinsics;
|
|
||||||
unsafe {
|
|
||||||
intrinsics::abort();
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
pub struct TinyKeccakTestData {
|
pub struct TinyKeccakTestData {
|
||||||
data: &'static [u8],
|
data: &'static [u8],
|
||||||
|
|
@ -48,3 +40,84 @@ pub extern "C" fn bench_tiny_keccak(test_data: *const TinyKeccakTestData) {
|
||||||
keccak.finalize((*test_data).result);
|
keccak.finalize((*test_data).result);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
pub struct RevComplementTestData {
|
||||||
|
input: ManuallyDrop<Box<[u8]>>,
|
||||||
|
output: ManuallyDrop<Box<[u8]>>,
|
||||||
|
}
|
||||||
|
|
||||||
|
#[no_mangle]
|
||||||
|
pub extern "C" fn prepare_rev_complement(size: usize) -> *mut RevComplementTestData {
|
||||||
|
let input = vec![0; size];
|
||||||
|
let output = vec![0; size];
|
||||||
|
|
||||||
|
let test_data = Box::new(
|
||||||
|
RevComplementTestData {
|
||||||
|
input: ManuallyDrop::new(input.into_boxed_slice()),
|
||||||
|
output: ManuallyDrop::new(output.into_boxed_slice()),
|
||||||
|
}
|
||||||
|
);
|
||||||
|
|
||||||
|
// Basically leak the pointer to the test data. This shouldn't be harmful since `prepare` is called
|
||||||
|
// only once per bench run (not for the iteration), and afterwards whole memory instance is discarded.
|
||||||
|
Box::into_raw(test_data)
|
||||||
|
}
|
||||||
|
|
||||||
|
#[no_mangle]
|
||||||
|
pub extern "C" fn rev_complement_input_ptr(test_data: *mut RevComplementTestData) -> *mut u8 {
|
||||||
|
unsafe {
|
||||||
|
(*test_data).input.as_mut_ptr()
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
#[no_mangle]
|
||||||
|
pub extern "C" fn rev_complement_output_ptr(test_data: *mut RevComplementTestData) -> *const u8 {
|
||||||
|
unsafe {
|
||||||
|
(*test_data).output.as_ptr()
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
#[no_mangle]
|
||||||
|
pub extern "C" fn bench_rev_complement(test_data: *mut RevComplementTestData) {
|
||||||
|
unsafe {
|
||||||
|
let result = rev_complement::run(&*(*test_data).input);
|
||||||
|
(*test_data).output.copy_from_slice(&result);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
pub struct RegexReduxTestData {
|
||||||
|
input: ManuallyDrop<Box<[u8]>>,
|
||||||
|
output: Option<usize>,
|
||||||
|
}
|
||||||
|
|
||||||
|
#[no_mangle]
|
||||||
|
pub extern "C" fn prepare_regex_redux(size: usize) -> *mut RegexReduxTestData {
|
||||||
|
regex_redux::prepare();
|
||||||
|
|
||||||
|
let input = vec![0; size];
|
||||||
|
let test_data = Box::new(
|
||||||
|
RegexReduxTestData {
|
||||||
|
input: ManuallyDrop::new(input.into_boxed_slice()),
|
||||||
|
output: None,
|
||||||
|
}
|
||||||
|
);
|
||||||
|
|
||||||
|
// Basically leak the pointer to the test data. This shouldn't be harmful since `prepare` is called
|
||||||
|
// only once per bench run (not for the iteration), and afterwards whole memory instance is discarded.
|
||||||
|
Box::into_raw(test_data)
|
||||||
|
}
|
||||||
|
|
||||||
|
#[no_mangle]
|
||||||
|
pub extern "C" fn regex_redux_input_ptr(test_data: *mut RegexReduxTestData) -> *mut u8 {
|
||||||
|
unsafe {
|
||||||
|
(*test_data).input.as_mut_ptr()
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
#[no_mangle]
|
||||||
|
pub extern "C" fn bench_regex_redux(test_data: *mut RegexReduxTestData) {
|
||||||
|
unsafe {
|
||||||
|
let result = regex_redux::run(&*(*test_data).input);
|
||||||
|
(*test_data).output = Some(result);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
|
||||||
|
|
@ -0,0 +1,17 @@
|
||||||
|
//! Initially it supposed to be like [1]. However it turned out
|
||||||
|
//! that executing this code in wasmi way too slow.
|
||||||
|
//!
|
||||||
|
//! [1]: https://benchmarksgame-team.pages.debian.net/benchmarksgame/program/regexredux-rust-2.html
|
||||||
|
|
||||||
|
lazy_static! {
|
||||||
|
static ref REGEX: ::regex::bytes::Regex =
|
||||||
|
{ ::regex::bytes::Regex::new("agggtaa[cgt]|[acg]ttaccct").unwrap() };
|
||||||
|
}
|
||||||
|
|
||||||
|
pub fn prepare() {
|
||||||
|
::lazy_static::initialize(®EX);
|
||||||
|
}
|
||||||
|
|
||||||
|
pub fn run(seq: &[u8]) -> usize {
|
||||||
|
REGEX.find_iter(seq).count()
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,164 @@
|
||||||
|
// Adapted version from benchmarks game. In particular
|
||||||
|
// rayon is removed.
|
||||||
|
//
|
||||||
|
// https://benchmarksgame-team.pages.debian.net/benchmarksgame/program/revcomp-rust-3.html
|
||||||
|
|
||||||
|
// The Computer Language Benchmarks Game
|
||||||
|
// https://salsa.debian.org/benchmarksgame-team/benchmarksgame/
|
||||||
|
//
|
||||||
|
// contributed by the Rust Project Developers
|
||||||
|
// contributed by Cristi Cobzarenco
|
||||||
|
// contributed by TeXitoi
|
||||||
|
// contributed by Matt Brubeck
|
||||||
|
|
||||||
|
use std::io::BufRead;
|
||||||
|
use std::mem::replace;
|
||||||
|
use std::{cmp, io};
|
||||||
|
|
||||||
|
/// Lookup table to find the complement of a single FASTA code.
|
||||||
|
fn build_table() -> [u8; 256] {
|
||||||
|
let mut table = [0; 256];
|
||||||
|
for (i, x) in table.iter_mut().enumerate() {
|
||||||
|
*x = match i as u8 as char {
|
||||||
|
'A' | 'a' => 'T',
|
||||||
|
'C' | 'c' => 'G',
|
||||||
|
'G' | 'g' => 'C',
|
||||||
|
'T' | 't' => 'A',
|
||||||
|
'U' | 'u' => 'A',
|
||||||
|
'M' | 'm' => 'K',
|
||||||
|
'R' | 'r' => 'Y',
|
||||||
|
'W' | 'w' => 'W',
|
||||||
|
'S' | 's' => 'S',
|
||||||
|
'Y' | 'y' => 'R',
|
||||||
|
'K' | 'k' => 'M',
|
||||||
|
'V' | 'v' => 'B',
|
||||||
|
'H' | 'h' => 'D',
|
||||||
|
'D' | 'd' => 'H',
|
||||||
|
'B' | 'b' => 'V',
|
||||||
|
'N' | 'n' => 'N',
|
||||||
|
i => i,
|
||||||
|
} as u8;
|
||||||
|
}
|
||||||
|
table
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Utilities for splitting chunks off of slices.
|
||||||
|
trait SplitOff {
|
||||||
|
fn split_off_left(&mut self, n: usize) -> Self;
|
||||||
|
fn split_off_right(&mut self, n: usize) -> Self;
|
||||||
|
}
|
||||||
|
impl<'a, T> SplitOff for &'a mut [T] {
|
||||||
|
/// Split the left `n` items from self and return them as a separate slice.
|
||||||
|
fn split_off_left(&mut self, n: usize) -> Self {
|
||||||
|
let n = cmp::min(self.len(), n);
|
||||||
|
let data = replace(self, &mut []);
|
||||||
|
let (left, data) = data.split_at_mut(n);
|
||||||
|
*self = data;
|
||||||
|
left
|
||||||
|
}
|
||||||
|
/// Split the right `n` items from self and return them as a separate slice.
|
||||||
|
fn split_off_right(&mut self, n: usize) -> Self {
|
||||||
|
let len = self.len();
|
||||||
|
let n = cmp::min(len, n);
|
||||||
|
let data = replace(self, &mut []);
|
||||||
|
let (data, right) = data.split_at_mut(len - n);
|
||||||
|
*self = data;
|
||||||
|
right
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Length of a normal line including the terminating \n.
|
||||||
|
const LINE_LEN: usize = 61;
|
||||||
|
|
||||||
|
/// Compute the reverse complement for two contiguous chunks without line breaks.
|
||||||
|
fn reverse_chunks(left: &mut [u8], right: &mut [u8], table: &[u8; 256]) {
|
||||||
|
for (x, y) in left.iter_mut().zip(right.iter_mut().rev()) {
|
||||||
|
*y = table[replace(x, table[*y as usize]) as usize];
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Compute the reverse complement on chunks from opposite ends of a sequence.
|
||||||
|
///
|
||||||
|
/// `left` must start at the beginning of a line. If there are an odd number of
|
||||||
|
/// bytes, `right` will initially be 1 byte longer than `left`; otherwise they
|
||||||
|
/// will have equal lengths.
|
||||||
|
fn reverse_complement_left_right(
|
||||||
|
mut left: &mut [u8],
|
||||||
|
mut right: &mut [u8],
|
||||||
|
trailing_len: usize,
|
||||||
|
table: &[u8; 256],
|
||||||
|
) {
|
||||||
|
// Each iteration swaps one line from the start of the sequence with one
|
||||||
|
// from the end.
|
||||||
|
while left.len() > 0 || right.len() > 0 {
|
||||||
|
// Get the chunk up to the newline in `right`.
|
||||||
|
let mut a = left.split_off_left(trailing_len);
|
||||||
|
let mut b = right.split_off_right(trailing_len);
|
||||||
|
right.split_off_right(1); // Skip the newline in `right`.
|
||||||
|
|
||||||
|
// If we've reached the middle of the sequence here and there is an
|
||||||
|
// odd number of bytes remaining, the odd one will be on the right.
|
||||||
|
if b.len() > a.len() {
|
||||||
|
let mid = b.split_off_left(1);
|
||||||
|
mid[0] = table[mid[0] as usize];
|
||||||
|
}
|
||||||
|
|
||||||
|
reverse_chunks(a, b, table);
|
||||||
|
|
||||||
|
// Get the chunk up to the newline in `left`.
|
||||||
|
let n = LINE_LEN - 1 - trailing_len;
|
||||||
|
a = left.split_off_left(n);
|
||||||
|
b = right.split_off_right(n);
|
||||||
|
left.split_off_left(1); // Skip the newline in `left`.
|
||||||
|
|
||||||
|
// If we've reached the middle of the sequence and there is an odd
|
||||||
|
// number of bytes remaining, the odd one will now be on the left.
|
||||||
|
if a.len() > b.len() {
|
||||||
|
let mid = a.split_off_right(1);
|
||||||
|
mid[0] = table[mid[0] as usize]
|
||||||
|
}
|
||||||
|
|
||||||
|
reverse_chunks(a, b, table);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Compute the reverse complement of one sequence.
|
||||||
|
fn reverse_complement(seq: &mut [u8], table: &[u8; 256]) {
|
||||||
|
let len = seq.len() - 1;
|
||||||
|
let seq = &mut seq[..len]; // Drop the last newline
|
||||||
|
let trailing_len = len % LINE_LEN;
|
||||||
|
let (left, right) = seq.split_at_mut(len / 2);
|
||||||
|
reverse_complement_left_right(left, right, trailing_len, table);
|
||||||
|
}
|
||||||
|
|
||||||
|
/// Read sequences from stdin and print the reverse complement to stdout.
|
||||||
|
pub fn run(input: &[u8]) -> Vec<u8> {
|
||||||
|
let mut buf = Vec::with_capacity(input.len());
|
||||||
|
|
||||||
|
let mut input = io::Cursor::new(input);
|
||||||
|
|
||||||
|
// Read the first header line.
|
||||||
|
input.read_until(b'\n', &mut buf).unwrap();
|
||||||
|
|
||||||
|
// Read sequence data line-by-line, splitting on headers.
|
||||||
|
let mut line_start = buf.len();
|
||||||
|
let mut seq_start = line_start;
|
||||||
|
let mut seqs = vec![];
|
||||||
|
while input.read_until(b'\n', &mut buf).unwrap() > 0 {
|
||||||
|
if buf[line_start] == b'>' {
|
||||||
|
// Found the start of a new sequence.
|
||||||
|
seqs.push(seq_start..line_start);
|
||||||
|
seq_start = buf.len();
|
||||||
|
}
|
||||||
|
line_start = buf.len();
|
||||||
|
}
|
||||||
|
seqs.push(seq_start..buf.len());
|
||||||
|
|
||||||
|
// Compute the reverse complements of each sequence.
|
||||||
|
let table = build_table();
|
||||||
|
for seq in seqs {
|
||||||
|
reverse_complement(&mut buf[seq], &table);
|
||||||
|
}
|
||||||
|
|
||||||
|
buf
|
||||||
|
}
|
||||||
Loading…
Reference in New Issue