Feature: My bootstrapped app kinda works
  In order to get going on coding my awesome app
  I want to have aruba and cucumber setup
  So I don't have to do it myself

  Background:
    Given a file named "hg19/unmasked/chr1.fa" with:
      """
      >chr1
      AATCACACGTGCAGGAACCCTTTTCCAAAGGAGGGTCACGCTCACAGCTT
      CTGGAGTAGGACATGGACTTGTCTTTTTGGAGGCCCATCCTCAACGCACC
      ACAGTTGACTACATCAAGGTCTGCCTCTGATCTGGTGGGAGTGCTGGGTG
      GTCTGTCTCCACCAGCACTTTGTGGGTGGGCTCTGTCCCCAGGAAATGCT
      C
      """
    And a file named "hg19/snp/chr1.subst.fa" with:
      """
      AATCACACGTGCAGGAACCCTTTTCCAAAGGAGGGTCACGCTCACAGCTT
      CTGGAGTAGGACATGGACTTGTCTTTTTGGAGGCCCATCCTCAACGCACC
      ACAGTTGACTACATCAAGGTCTGCCTCTGATCTGGTGGGAGTGCTGGGTG
      GTCTGTCTCCACCAGCACTTTGTGGGTGGGCTCTGTCCCCAGGAAATGCT
      C
      """

  Scenario: Basic UI
    When I get help for "fasta_read"
    Then the exit status should be 0
      And the banner should be present
      And the banner should include the version
      And the banner should document that this app takes options
      And the following options should be documented:
        |--version|
        |--snp    |
        |--output |
        |-o       |
      And the banner should document that this app's arguments are
        |assembly  |which is required|
        |chromosome|which is required|
        |cstart    |which is required|
        |cend      |which is required|

  Scenario Outline: files with one line stream
    Given a file named "hg19/unmasked/chr1.fa" with:
      """
      >chr1
      AATCACACGTGCAGGAACCCTTTTCCAAAGGAGGGTCACGCTCACAGCTT
      CTGGAGTAGGACATGGACTTGTCTTTTTGGAGGCCCATCCTCAACGCACC
      ACAGTTGACTACATCAAGGTCTGCCTCTGATCTGGTGGGAGTGCTGGGTG
      GTCTGTCTCCACCAGCACTTTGTGGGTGGGCTCTGTCCCCAGGAAATGCT
      C
      """
    And a file named "hg19/snp/chr1.subst.fa" with:
      """
      >chr1
      AATCACACGTGCAGGAACCCTTTTCCAAAGGAGGGTCACGCTCACAGCTT
      CTGGAGTAGGACATGGACTTGTCTTTTTGGAGGCCCATCCTCAACGCACC
      ACAGTTGACTACATCAAGGTCTGCCTCTGATCTGGTGGGAGTGCTGGGTG
      GTCTGTCTCCACCAGCACTTTGTGGGTGGGCTCTGTCCCCAGGAAATGCT
      C
      """
    When I successfully run `fasta_read <options>`
    Then the output should contain "<output>"

    Scenarios: unmasked
      |options        |output                   |
      |hg19 chr1 0 200|AATCACACGTGCAGGAACCCTTTTCCAAAGGAGGGTCACGCTCACAGCTTCTGGAGTAGGACATGGACTTGTCTTTTTGGAGGCCCATCCTCAACGCACCACAGTTGACTACATCAAGGTCTGCCTCTGATCTGGTGGGAGTGCTGGGTGGTCTGTCTCCACCAGCACTTTGTGGGTGGGCTCTGTCCCCAGGAAATGCT|
    Scenarios: snp
      |options            |output    |
      |hg19 chr1 0 200 --snp|AATCACACGTGCAGGAACCCTTTTCCAAAGGAGGGTCACGCTCACAGCTTCTGGAGTAGGACATGGACTTGTCTTTTTGGAGGCCCATCCTCAACGCACCACAGTTGACTACATCAAGGTCTGCCTCTGATCTGGTGGGAGTGCTGGGTGGTCTGTCTCCACCAGCACTTTGTGGGTGGGCTCTGTCCCCAGGAAATGCT|

  Scenario: Export to file
    When I successfully run `fasta_read hg19 chr1 0 200 --output=out.txt`
    Then the file "out.txt" should contain:
    """
    AATCACACGTGCAGGAACCCTTTTCCAAAGGAGGGTCACGCTCACAGCTTCTGGAGTAGGACATGGACTTGTCTTTTTGGAGGCCCATCCTCAACGCACCACAGTTGACTACATCAAGGTCTGCCTCTGATCTGGTGGGAGTGCTGGGTGGTCTGTCTCCACCAGCACTTTGTGGGTGGGCTCTGTCCCCAGGAAATGCT
    """

  Scenario Outline: Painful path
    When I run `fasta_read <options>`
    Then the stderr should contain "<output>"
    Scenarios: incorrect assembly/chromosome
      |options                      |output                                                  |
      |foo chr12 0 3 --log-level=debug |the 'foo' assembly doesn't exist in directory structure |
      |hg19 chr99 0 3 --log-level=debug|the 'chr99' chromosome doesn't exist in directory structure|