.travis.yml

language: python
sudo: false

python:
  - "3.8"


install:
  - pip install coverage
  - pip install -e . 

script:
  - coverage run amplicov/amplicov --help
  - coverage run amplicov/amplicov --version
  - coverage run amplicov/amplicov --bed tests/input.bed --cov tests/coverage.txt --prefix output --outdir tests/output 
  - coverage run amplicov/amplicov --bed tests/input.bed --bam tests/input.bam --prefix output --outdir tests/output 
  - coverage run amplicov/amplicov --bedpe tests/input.bedpe --pp --bam tests/input.bam --prefix output --outdir tests/output 
  - coverage run amplicov/amplicov --depth_lines 5 10 20 50 --mincov 10 --gff tests/input.gff  --bed tests/input.bed --bam tests/input.bam --prefix output --outdir tests/output 
  - coverage run amplicov/amplicov -r "NC_045512_2" --gff tests/input.gff  --bed tests/input.bed --bam tests/input.bam --prefix output --outdir tests/output 

after_success:
  - bash <(curl -s https://codecov.io/bash)