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‎README.md

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Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
# GenoBoost v1.1.0
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# GenoBoost
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[![GenoBoost](https://github.com/rickyota/genoboost/actions/workflows/genoboost.yml/badge.svg)](https://github.com/rickyota/genoboost/actions/workflows/genoboost.yml)
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[![Release](https://github.com/rickyota/genoboost/actions/workflows/publish.yml/badge.svg)](https://github.com/rickyota/genoboost/actions/workflows/publish.yml)
@@ -22,15 +22,16 @@ $ genoboost train \
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## Table of Contents
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25-
- [GenoBoost v1.1.0](#genoboost-v110)
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- [GenoBoost](#genoboost)
2626
- [Getting Started](#getting-started)
2727
- [Table of Contents](#table-of-contents)
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- [News](#news)
2929
- [Introduction](#introduction)
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- [Users' Guide](#users-guide)
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- [Installation](#installation)
3232
- [Plink1 Input](#plink1-input)
33-
- [Plink2 Input](#plink2-input)
33+
- [Plink2 Input (compile)](#plink2-input-compile)
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- [Plink2 Input (docker)](#plink2-input-docker)
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- [Advanced Install](#advanced-install)
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- [Train GenoBoost Model](#train-genoboost-model)
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- [Simplest Usage](#simplest-usage)
@@ -52,6 +53,8 @@ $ genoboost train \
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## <a name="news"></a>News
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- [v1.2.0](https://github.com/rickyota/genoboost/releases/tag/v1.2.0) (Dec 28, 2024)
57+
- Clean code and remove some requirements for plink2.
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- [v1.1.0](https://github.com/rickyota/genoboost/releases/tag/v1.1.0) (May 23, 2024)
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- Clean code.
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- [v1.0.8](https://github.com/rickyota/genoboost/releases/tag/v1.0.8) (Nov 25, 2023)
@@ -84,11 +87,11 @@ For now, the input genotype format is allowed for plink1 or plink2 only.
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If you want to input plink1, download a compiled program for Linux (tested on Rocky Linux<=8.9), macOS (tested on <=14.3.1), and Windows (not tested) from [here][release]. This should take less than 1 minute.
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#### <a name="install-plink2"></a>Plink2 Input
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#### <a name="install-plink2-compile"></a>Plink2 Input (compile)
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If you want to input plink2 genotype file, you have to compile it by yourself as below. You can use plink1 format as well.
92+
If you want to input plink2 genotype file, you can compile program by yourself as below or [use docker or singularity](#advanced-installation). You can use plink1 format as well.
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First, install `rust` as instructed [here][rust-install], `cmake>=3.14`, and `clang` if not installed. Then,
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First, install `rust` as instructed [here][rust-install] if not installed. Then,
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```bash
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git clone https://github.com/rickyota/genoboost.git
@@ -99,10 +102,6 @@ cp ./projects_rust/target/release/genoboost ./genoboost
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100103
and you can use `genoboost` program. This should take less than 5 minutes.
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102-
#### <a name="install-advanced"></a>Advanced Install
103-
104-
See [Advanced Guide](#advanced-guide) for docker or singularity users.
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106105
Using arm architecture, including Macbook M1 and M2 chips, will stop or slow down the software due to the unavailability of SIMD.
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I plan to deal with it in the future.
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‎lib/pgenlib_rust/Cargo.toml

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Original file line numberDiff line numberDiff line change
@@ -3,13 +3,13 @@ name = "pgenlib_rust"
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version = "0.1.0"
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authors = ["name"]
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edition = "2021"
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build = "build.rs"
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#build = "build.rs"
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#crate-type = ["staticlib"]
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[dependencies]
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libc = "0.2.94"
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cxx = "1.0"
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# for build.rs
1213
[build-dependencies]
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cmake = "0.1.50"
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bindgen = "0.65.1"
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#cmake = "0.1"
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cxx-build = "1.0"
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walkdir = "2"

‎lib/pgenlib_rust/build.rs

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// https://rendered-obsolete.github.io/2018/09/30/rust-ffi-ci.html
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use walkdir::WalkDir;
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3-
// later: https://rust-lang.github.io/rust-bindgen/non-system-libraries.html
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// if you have .o : https://rust-lang.github.io/rust-bindgen/tutorial-3.html
3+
fn main() {
4+
let dirs = ["./lib/pgenlib/"];
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// exclude src/unuse
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//let dirs = [
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// "./lib/pgenlib/src/",
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// "./lib/pgenlib/src/include/",
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// "./lib/pgenlib/src/simde/",
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// "./lib/pgenlib/src/simde/x86",
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// "./lib/pgenlib/src/simde/x86/avx512",
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//];
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6-
// unnecessary?
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//extern crate bindgen;
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//use bindgen;
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// all files with .cc or .cpp
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let cpps: Vec<String> = dirs
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.map(|dir| {
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WalkDir::new(dir)
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.into_iter()
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.map(|x| x.unwrap().path().display().to_string())
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})
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.into_iter()
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.flatten()
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.filter(|x| x.ends_with(".cpp") || x.ends_with(".cc"))
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.collect();
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use std::env;
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use std::path::PathBuf;
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// cannot print in build.rs
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//println!("cpps: {:?}", cpps);
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use bindgen::CargoCallbacks;
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use cmake;
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// how to add openmp?
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// https://users.rust-lang.org/t/binding-openmp-c-function/40196/4
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fn main() {
32+
// should be .rs with #[cxx::bridge]
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cxx_build::bridge("src/lib.rs")
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.files(&cpps)
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.flag_if_supported("-fopenmp")
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.compile("pgenlib-bridge");
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//.flag_if_supported("-static")
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// cmake
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let dst = cmake::build("src/pgenlib");
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println!("cargo:rustc-link-search=native={}", dst.display());
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println!("cargo:rustc-link-lib=dylib=stdc++");
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// ok?
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// should be same as project name in CMakeLists.txt
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println!("cargo:rustc-link-lib=static=pgenlib");
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// [ref](https://stackoverflow.com/questions/50642574/how-can-i-specify-linker-flags-arguments-in-a-build-script)
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// seems not necessary
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//.flag_if_supported("-std=c++")
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//.flag_if_supported("-std=c++11")
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// seems not necessary
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//.flag_if_supported("-lgomp")
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// arg for rustc compile
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// This is same as
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// $ export RUSTFLAGS='-C link-args=-fopenmp'
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// Better use build.rs to make build.sh simple
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//
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println!("cargo:rustc-link-arg=-fopenmp");
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// seems not necessary
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// [ref](https://github.com/rust-lang/cc-rs/issues/266)
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//println!("cargo:rustc-link-lib=gomp");
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println!("cargo:rustc-link-lib=gomp");
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// added 230823
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// [ref](https://github.com/rust-or/highs-sys/blob/master/build.rs)
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//println!("cargo:rustc-link-lib=dylib=gomp");
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// binding
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let bindings = bindgen::Builder::default()
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.header("src/pgenlib/pgenlibr_wrapc.hpp")
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.parse_callbacks(Box::new(CargoCallbacks))
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.clang_arg("-xc++")
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.clang_arg("-std=c++11")
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.clang_arg("-stdlib=libc++")
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.allowlist_file("src/pgenlib/pgenlibr_wrapc.hpp")
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.generate()
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.expect("Unable to generate bindings");
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//let bindings = bindgen::Builder::default()
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// .header("src/pgenlib/pgenlibr_wrapc.h")
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// .parse_callbacks(Box::new(CargoCallbacks))
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// .clang_arg("-xc++")
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// .clang_arg("-std=c++11")
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// .allowlist_file("src/pgenlib/pgenlibr_wrapc.h")
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// .generate()
53-
// .expect("Unable to generate bindings");
54-
55-
let out_path = PathBuf::from(env::var("OUT_DIR").unwrap());
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bindings
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.write_to_file(out_path.join("bindings.rs"))
58-
.expect("Couldn't write bindings");
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println!("cargo:rerun-if-changed=src/lib.rs");
58+
// all cpp and h
59+
dirs.map(|dir| {
60+
WalkDir::new(dir)
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.into_iter()
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.map(|x| x.unwrap().path().display().to_string())
63+
})
64+
.into_iter()
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.flatten()
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.filter(|x| {
67+
x.ends_with(".cpp") || x.ends_with(".cc") || x.ends_with(".hpp") || x.ends_with(".h")
68+
})
69+
.for_each(|x| println!("cargo:rerun-if-changed={:?}", x));
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}
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‎lib/pgenlib_rust/lib/pgenlib/LICENSE

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GNU LESSER GENERAL PUBLIC LICENSE
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Version 3, 29 June 2007
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Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
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Everyone is permitted to copy and distribute verbatim copies
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of this license document, but changing it is not allowed.
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This version of the GNU Lesser General Public License incorporates
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the terms and conditions of version 3 of the GNU General Public
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License, supplemented by the additional permissions listed below.
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0. Additional Definitions.
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As used herein, "this License" refers to version 3 of the GNU Lesser
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General Public License, and the "GNU GPL" refers to version 3 of the GNU
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General Public License.
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"The Library" refers to a covered work governed by this License,
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other than an Application or a Combined Work as defined below.
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An "Application" is any work that makes use of an interface provided
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by the Library, but which is not otherwise based on the Library.
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Defining a subclass of a class defined by the Library is deemed a mode
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of using an interface provided by the Library.
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A "Combined Work" is a work produced by combining or linking an
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Application with the Library. The particular version of the Library
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with which the Combined Work was made is also called the "Linked
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Version".
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The "Minimal Corresponding Source" for a Combined Work means the
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Corresponding Source for the Combined Work, excluding any source code
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for portions of the Combined Work that, considered in isolation, are
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based on the Application, and not on the Linked Version.
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The "Corresponding Application Code" for a Combined Work means the
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You may convey a covered work under sections 3 and 4 of this License
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‎lib/pgenlib_rust/lib/pgenlib/Makefile

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#
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# Makefile to compile PGEN library
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#
4+
AR ?= ar
5+
CXX ?= g++
6+
CXXFLAGS = -O3 -Wall -std=c++11
7+
CFLAGS =
8+
9+
OBJECTS = $(patsubst %.cc,%.o,$(wildcard ./include/*.cc)) $(patsubst %.cpp,%.o,$(wildcard *.cpp)) $(patsubst %.cc,%.o,$(wildcard *.cc))
10+
INC = -I./simde/ -I./include/
11+
12+
pgenlib.a: ${OBJECTS}
13+
${AR} rcs $@ $^
14+
15+
%.o: %.cpp
16+
${CXX} ${CXXFLAGS} -o $@ -c $< ${INC}
17+
18+
%.o: %.cc
19+
${CXX} ${CXXFLAGS} -o $@ -c $< ${INC}
20+
21+
clean:
22+
rm -f *.o *.a ./include/*.o

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