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allow-file-overwriting flag not working for "examine edpl" #21
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Hi @bowmanjeffs, thanks for reporting this! The Can you please share your Cheers and so long |
Lucas, here you go! Thanks for taking a look. 2111SR_20211107_40_16_40m_900mL_S8_L001.12SV5.exp.Bacillariophyta_2836.jplace.zip |
thank you for sharing the file! I see: your placement file only has a single pquery, with a single placement location, that is, a single branch that it has been placed on. Hence, a measure such as the EDPL, which measures the expected distance between the different placement locations of a pquery, will just output nothing, as there is only a single location, so nothing to compute a distance between. Hence, for that particular test file, the output is expected to be N/A. Still, that bug should not occur, and instead a proper warning or N/A as output should be produced. I'll fix that soon™ - but in the meantime, I thought it might be useful for you to know that this file does not have a meaningful EDPL :-) Cheers and so long |
Thanks Lucas! This runs in a loop with many library subsets placing to many trees, so that's expected for some of them. I should have anticipated that :). That particular result is captured as NaN by default. Best, |
Okay, fixed in the latest commit. Instead of the program throwing an exception, it now issues a warning about the situation, but still produces a valid (yet mostly empty) histogram. Closing the issue for now - feel free to re-open should you have any further trouble with this! |
Hello, reporting possible bug:
gappa examine edpl --allow-file-overwriting --out-dir test --file-prefix test --jplace-path test/test.jplace
returns the error:
It seems that perhaps the command is not recognizing the
--allow-file-overwriting
flag? An identically structured command forexamine assign
works as expected.The text was updated successfully, but these errors were encountered: