make test expected to fail?

genome / pindel

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

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make test expected to fail? #42

Open dtrudg opened 8 years ago

dtrudg commented 8 years ago

I'm installing pindel on our HPC cluster and on running the make test it fails with TargetOutput/colowobd15_D and ActualOutput/colowobd15_D not identical.

Just want to check if make test is expected to succeed? I note in the git repo the TargetOutput hasn't been updated for several years, while the code has.

The program appears to run OK.

EWLameijer commented 8 years ago

Hi David,

my apologies for this very late reply. I'm not sure if the answer I can give is satisfactory: basically, I myself have made a cleaned-up branch https://github.com/genome/pindel/tree/removing_and_changing_deprecated_files with a separate test script https://github.com/genome/pindel/blob/removing_and_changing_deprecated_files/devtools/run_regressiontests.sh

At least that test should work!

I'll ask Kai if I can merge it in.

Best regards,

Eric-Wubbo

dtrudg commented 8 years ago

No need to apologise. Thanks for the info!