.travis.yml

dist: bionic
language: c
before_install:
    - base=$(pwd)
    - git clone --recursive https://github.com/samtools/htslib.git
    - cd htslib && git checkout 1.10 && autoheader && autoconf && ./configure --enable-libcurl
    - cd ..
    - make -j 4 -C htslib

    - curl https://nim-lang.org/choosenim/init.sh -sSf > init.sh && sh init.sh -y
    - export PATH=/home/travis/.nimble/bin:$PATH

install:
    - nimble install -y
script:
    - export LD_LIBRARY_PATH=$TRAVIS_BUILD_DIR/htslib/
    - ./strling -h
    - nimble test -y

# Download stuff for end to end tests
    - mkdir -p run_tests
    - cd run_tests
    - wget -O data.zip https://ndownloader.figshare.com/articles/11367851?private_link=207b2a78ddcbdb28781b
    - unzip data.zip
    - rm data.zip

    - wget -O chr4.fa.gz https://hgdownload.soe.ucsc.edu/goldenPath/hg38/chromosomes/chr4.fa.gz
    - gzip -d chr4.fa.gz

# End-to-end test single
    - mkdir -p single
    - ../strling extract -f chr4.fa -g chr4.fa.str -v CANVAS.chr4-39348425_AAGGG_0_400.bam single/CANVAS.chr4-39348425_AAGGG_0_400.str.bin
    - ../strling call -v -o single/CANVAS.chr4-39348425_AAGGG_0_400 CANVAS.chr4-39348425_AAGGG_0_400.bam single/CANVAS.chr4-39348425_AAGGG_0_400.str.bin

# End-to-end test joint
    - mkdir -p joint
    - for i in *.bam; do ../strling extract -f chr4.fa -g chr4.fa.str -v $i joint/$i.str.bin; done
    - ../strling merge -f chr4.fa -v -o joint/strling joint/*.bin
    - for i in *.bam; do ../strling call -v -b joint/strling-bounds.txt -o joint/$i $i joint/$i.str.bin; done

after_script:
# View output files
    - head single/*.txt
    - head joint/strling-bounds.txt
    - head joint/*.txt