Integration test files

Johan_DahlbergJohan_Dahlberg Posts: 88Member ✭✭✭

Is there any where I can find the integration test file with the md5sum "45d97df6d291695b92668e8a55c54cd0", which is used in the DataProcessingPipelineTest class? Since my tests fail with another md5sum calculated I would be interested to know what the differences between the files are.

Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,195Administrator, GATK Developer admin
    Answer ✓

    Better news: this is already on the todo list of one of our developers. I can't give you an ETA but I expect it will happen fairly soon.

    Geraldine Van der Auwera, PhD

Answers

  • Johan_DahlbergJohan_Dahlberg Posts: 88Member ✭✭✭

    Never mind. I managed to run run the tests from the master-branch, so I can generate the files there and then find the problem in my devel-branch. Sorry for the bother.

  • Johan_DahlbergJohan_Dahlberg Posts: 88Member ✭✭✭

    As it turns out, the md5s were failing on the master branch as well. My guess is that this is due to me using a different bwa version, causing the header to look different. But right now I have note way to confirm that, so I would still be very happy if there was a way for me to access the file corresponding to the md5sums: 45d97df6d291695b92668e8a55c54cd0 and 9fca827ecc8436465b831bb6f879357a. Is this possible?

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,195Administrator, GATK Developer admin

    Hi Johan,

    Unfortunately we don't have anything set up to share the test files at the moment, but I'll discuss it with the group to see if that's something we could do.

    Geraldine Van der Auwera, PhD

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,195Administrator, GATK Developer admin
    Answer ✓

    Better news: this is already on the todo list of one of our developers. I can't give you an ETA but I expect it will happen fairly soon.

    Geraldine Van der Auwera, PhD

  • Johan_DahlbergJohan_Dahlberg Posts: 88Member ✭✭✭

    Great. Thank you. :)

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