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brentpbrentp
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add .github/workflow
from @danielecook requires changes to functional tests due to zcat differences on osx
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‎.github/workflows/build.yml‎

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# copied from Daniel Cook's Seq collection
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name: Build
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on:
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- push
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- pull_request
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jobs:
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build:
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [ubuntu-18.04, macos-10.15]
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steps:
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- uses: actions/checkout@v2
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# Caching
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- name: Cache choosenim
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id: cache-choosenim
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uses: actions/cache@v1
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with:
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path: ~/.choosenim
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key: ${{ runner.os }}-choosenim-stable
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- name: Cache nimble
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id: cache-nimble
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uses: actions/cache@v1
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with:
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path: ~/.nimble
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key: ${{ runner.os }}-nimble-stable
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- name: Cache htslib
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id: cache-htslib
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uses: actions/cache@v1
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with:
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path: $HOME/htslib
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key: ${{ runner.os }}-htslib-1.10
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# Setup nim
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- uses: jiro4989/setup-nim-action@v1.0.2
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with:
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nim-version: 1.0.6
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# Install Dependencies
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- name: Install dependencies (Linux)
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if: runner.os == 'Linux'
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run: |
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sudo apt-get update
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sudo apt-get -qy install bwa make build-essential cmake libncurses-dev ncurses-dev libbz2-dev lzma-dev liblzma-dev \
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curl libssl-dev libtool autoconf automake libcurl4-openssl-dev
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# Setup htslib
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- name: Install htslib (linux)
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if: runner.os == 'Linux'
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run: |
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cd
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git clone --recursive https://github.com/samtools/htslib.git
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cd htslib && git checkout 1.10 && autoheader && autoconf && ./configure --enable-libcurl
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cd
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make -j 4 -C htslib
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echo "::set-env name=LD_LIBRARY_PATH::${LD_LIBRARY_PATH}:${HOME}/htslib"
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ls -lh $HOME/htslib/*.so
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- name: Install hstlib (macos)
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if: runner.os == 'macOS'
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run: |
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brew install htslib
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# Build and Test
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- name: Build test executable
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run: nimble build -Y mosdepth.nimble
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- name: "Copy binary"
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run: chmod +x mosdepth && mkdir bin && cp mosdepth bin/mosdepth_debug_${{ matrix.os }}
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- name: "Build and Copy release binary"
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run: nim c -d:danger -d:release -o:bin/mosdepth_${{ matrix.os }} mosdepth
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- name: Functional Tests
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env:
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TERM: "xterm"
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run: |
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bash ./functional-tests.sh
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- name: Unit Tests
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run: |
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nim c -r tests/all.nim
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#- run: nimble test -Y
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- name: Upload Artifact
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if: success()
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uses: actions/upload-artifact@v1.0.0
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with:
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# Artifact name
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name: mosdepth_${{ matrix.os }}
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path: bin

‎README.md‎

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@@ -4,6 +4,7 @@ fast BAM/CRAM depth calculation for **WGS**, **exome**, or **targeted sequencing
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![logo](https://user-images.githubusercontent.com/1739/29678184-da1f384c-88ba-11e7-9d98-df4fe3a59924.png "logo")
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[![Build](https://github.com/brentp/mosdepth/workflows/Build/badge.svg?branch=master)](https://github.com/brentp/mosdepth/actions?query=workflow%3ABuild)
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[![Build Status](https://travis-ci.com/brentp/mosdepth.svg?branch=master)](https://travis-ci.com/brentp/mosdepth)
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[![citation](https://img.shields.io/badge/cite-open%20access-orange.svg)](https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btx699/4583630?guestAccessKey=35b55064-4566-4ab3-a769-32916fa1c6e6)

‎functional-tests.sh‎

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run unordered_bed $exe --by tests/unordered.bed t tests/ovl.bam
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assert_exit_code 0
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assert_equal $(zcat t.regions.bed.gz | wc -l) 2
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assert_equal $(zcat < t.regions.bed.gz | wc -l) 2
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# theres data left in the bam but the region tree is empty...
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run missing_bed_chrom $exe --by tests/missing.bed t tests/ovl.bam
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rm -f t.thresholds.bed.gz*
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run threshold_test $exe --by 100 -T 0,1,2,3,4,5 -c MT t tests/ovl.bam
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assert_equal "$(zcat t.thresholds.bed.gz | tail -n +2 | head -1)" "MT 0 100 unknown 100 80 0 0 0 0"
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assert_equal "0" "$(zcat t.thresholds.bed.gz | tail -n+2 | cut -f 7 | uniq)"
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assert_equal "$(zcat < t.thresholds.bed.gz | tail -n +2 | head -1)" "MT 0 100 unknown 100 80 0 0 0 0"
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assert_equal "0" "$(zcat < t.thresholds.bed.gz | tail -n+2 | cut -f 7 | uniq)"
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assert_exit_code 0
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rm -f t.thresholds.bed.gz*
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run threshold_test_by $exe --by tests/track.bed -T 0,1,2 -c MT t tests/ovl.bam
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assert_equal "$(zcat t.thresholds.bed.gz | tail -n +2)" "MT 2 80 aregion 78 78 0"
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assert_equal "$(zcat < t.thresholds.bed.gz | tail -n +2)" "MT 2 80 aregion 78 78 0"
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assert_exit_code 0
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export MOSDEPTH_Q0=AAA
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run track_header $exe --by tests/track.bed t tests/ovl.bam
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assert_exit_code 0
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assert_equal "$(zcat t.regions.bed.gz)" "MT 2 80 aregion 1.00"
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assert_equal "$(zcat < t.regions.bed.gz)" "MT 2 80 aregion 1.00"
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run track_header_by $exe --by tests/bad.bed t tests/ovl.bam
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assert_exit_code 1
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rm -f t_regions.*
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run overlappingPairs $exe t tests/overlapping-pairs.bam
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assert_equal "$(zcat t.per-base.bed.gz)" "1 0 565173 0
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assert_equal "$(zcat < t.per-base.bed.gz)" "1 0 565173 0
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1 565173 565253 1
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1 565253 249250621 0"
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assert_exit_code 0

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