.travis.yml

language: perl

sudo: false

perl:
    - "5.14"

install:
    - "export PATH=$PWD:$PATH"

script:
    - "! samclip"
    - "samclip --version"
    - "samclip --help"
    - "! samclip --doesnotexist"
    - "samclip --ref doesnotexist 2>&1 | grep ERROR"
    - "samclip --ref test.fna 2>&1 | grep ERROR"
    - "touch empty.fai"
    - "wc -l test.sam | grep 254"
    - "grep -c -E '[0-9]+S' test.sam"
    - "grep -c '>' test.fna | grep '^4$'"
    - "samclip --ref empty.fai 2>&1 | grep ERROR"
    - "samclip --ref empty.fai /dev/null 2>&1 | grep 'Found 0 seq'"
    - "samclip --ref test.fna /dev/null 2>&1 | grep 'Found 4 seq'"
    - "samclip --ref test.fna < test.sam 2>&1 > /dev/null | grep Done"
    - "samclip --ref test.fna < test.sam 2>&1 > /dev/null | grep 'Header contained 5 lines'"
    - "samclip --max 0 --ref test.fna test.sam 2>&1 > /dev/null | grep Done"
    - "samclip --invert --ref test.fna test.sam 2>&1 > /dev/null | grep Done"
    - "samclip --progress 50 --ref test.fna test.sam 2>&1 > /dev/null | grep 'Processed 150 records'"