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CI testing (test.yaml) (#8)
* Update Cargo.lock * Bump version * Add some sanity checks * Add GH Actions release and test workflows * Update license * Update README
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‎.github/workflows/release.yaml

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on:
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push:
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# Sequence of patterns matched against refs/tags
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tags:
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- 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
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name: Build and Upload Release
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env:
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CARGO_INCREMENTAL: 0
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jobs:
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linux:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout git repository
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uses: actions/checkout@master
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- name: Login to GitHub Package Registry
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run: docker login docker.pkg.github.com -u 10xbuild -p ${{secrets.GH_PAT}}
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- name: Make release build
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run: >
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docker run -v ${{github.workspace}}:/root
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-e GITHUB_SHA -e GITHUB_REF
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docker.pkg.github.com/10xdev/toolchain-scripts/toolchain:latest
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/bin/bash -lec '
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cargo build --release;
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target/release/subset-bam --help | grep -q subset-bam;
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readelf -V target/release/subset-bam;
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';
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mkdir ${{runner.temp}}/artifacts;
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cp -a target/release/subset-bam ${{runner.temp}}/artifacts/subset-bam-linux
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- name: Upload build artifact
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uses: actions/upload-artifact@v1
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with:
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name: subset-bam
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path: ${{runner.temp}}/artifacts
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macos:
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runs-on: macos-latest
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env:
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MACOSX_DEPLOYMENT_TARGET: 10.7
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steps:
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- name: Checkout git repository
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uses: actions/checkout@master
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- name: Make release build
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run: |
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cargo build --release
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target/release/subset-bam --help | grep -q subset-bam
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mkdir ${{runner.temp}}/artifacts
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cp -a target/release/subset-bam ${{runner.temp}}/artifacts/subset-bam-macos
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- name: Upload build artifact
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uses: actions/upload-artifact@v1
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with:
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name: subset-bam
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path: ${{runner.temp}}/artifacts
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setup-release:
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needs: [linux, macos]
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runs-on: ubuntu-latest
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steps:
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- uses: actions/download-artifact@v1
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with:
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name: subset-bam
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path: ${{runner.temp}}/artifacts
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- run: ls ${{runner.temp}}/artifacts
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- name: Create Release
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id: create_release
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uses: actions/create-release@v1
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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with:
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tag_name: ${{ github.ref }}
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release_name: Release ${{ github.ref }}
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draft: false
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prerelease: false
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- name: Upload Linux
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id: upload-linux-release
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uses: actions/upload-release-asset@v1
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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with:
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upload_url: ${{ steps.create_release.outputs.upload_url }}
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asset_path: ${{runner.temp}}/artifacts/subset-bam-linux
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asset_name: subset-bam_linux
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asset_content_type: application/octet-stream
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- name: Upload Mac
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id: upload-mac-release
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uses: actions/upload-release-asset@v1
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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with:
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upload_url: ${{ steps.create_release.outputs.upload_url }}
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asset_path: ${{runner.temp}}/artifacts/subset-bam-macos
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asset_name: subset-bam_macos
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asset_content_type: application/octet-stream

‎.github/workflows/test.yaml

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name: Test subset-bam
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on:
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pull_request:
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push:
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branches:
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- master
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env:
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CARGO_INCREMENTAL: 0
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jobs:
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test-mac:
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# This job runs on MacOS Catalina
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runs-on: macos-latest
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steps:
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- name: rust version
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run: rustup default 1.44.0
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- name: add rustfmt
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run: rustup component add rustfmt
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- name: Checkout subset-bam master
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uses: actions/checkout@master
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- name: Check Rust formatting
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run: cargo fmt -- --check
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- name: build-subset-bam
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run: cargo build --release
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- name: unit tests
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run: cargo test --release -- --nocapture
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test-linux:
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# This job runs on Linux
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runs-on: ubuntu-latest
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steps:
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- name: rust version
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run: rustup default 1.44.0
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- name: add rustfmt
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run: rustup component add rustfmt
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- name: Checkout subset-bam master
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uses: actions/checkout@master
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- name: Check Rust formatting
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run: cargo fmt -- --check
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- name: build-subset-bam
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run: cargo build --release
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- name: unit tests
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run: cargo test --release -- --nocapture

‎Cargo.lock

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‎Cargo.toml

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rayon = "*"
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ring = "0.14.6"
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data-encoding = "*"
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faccess="0.2.3"
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[profile.release]
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debug = 1

‎LICENSE

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The MIT License (MIT)
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Copyright (c) 2018 10x Genomics, Inc.
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Copyright (c) 2020 10x Genomics, Inc.
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal

‎README.md

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# subset-bam
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`subset-bam` is a tool to subset a 10x Genomics BAM file based on a tag, most commonly the cell barcode tag.
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`subset-bam` is a tool to subset a 10x Genomics BAM file based on a tag, most commonly the cell barcode tag. The latest version is `v1.1.0` and can be found [on the releases page](https://github.com/10XGenomics/subset-bam/releases).
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## Overview of how it works
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`subset-bam` is a simple tool implemented in Rust that takes a 10x Genomics BAM file, a CSV file defining the subset of cells you want to isolate, and produces a new BAM file with only alignments associated with those cells.

‎src/main.rs

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extern crate terminal_size;
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#[macro_use]
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extern crate log;
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extern crate faccess;
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extern crate human_panic;
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use clap::{App, Arg};
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use faccess::{AccessMode, PathExt};
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use failure::Error;
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use rayon::prelude::*;
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use rust_htslib::bam;
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fn get_args() -> clap::App<'static, 'static> {
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let args = App::new("subset-bam")
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.set_term_width(if let Some((Width(w), _)) = terminal_size() { w as usize } else { 120 })
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.version("1.0.0")
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.author("Ian Fiddes <ian.fiddes@10xgenomics.com>")
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.version("1.1.0")
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.author("Ian Fiddes <ian.fiddes@10xgenomics.com>, Wyatt McDonnell <wyatt.mcdonnell@10xgenomics.com>")
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.about("Subsetting 10x Genomics BAM files")
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.arg(Arg::with_name("bam")
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.short("b")

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