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zwdzwd / transvar

TransVar - multiway annotator for precision medicine
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some error message in the info field are not self-explanatory #29

Open DavidTamborero opened 5 years ago

DavidTamborero commented 5 years ago

Hi there,

when inputing a cdna change to transvar with an incorrect reference nucleotide sequence, as e.g. ./transvar canno -i 'PALB2:c.172_175delTTGA' --ensembl (instead of PALB2:c.172_175delTTGT) I realized that transvar returns an empty record with a 'no_valid_transcript_found' message in the INFO field

I m a bit rusty in the use of Transvar, but I assume that the INFO field is intended to contain the errors/warnings as approppriate. If so, maybe you can consider another type of message (ignore this issue otherwise!)

thanks again for such a great tool and your work! best d

zwdzwd commented 5 years ago

Thanks for the feedback! I am in the middle of providing an option --ignore so that checks upon provided reference and actual reference is lifted. This will appear in the future version.

DavidTamborero commented 5 years ago

thanks for your answer! note that the --ignore option can be indeed useful for certain use cases, but the objective of this issue (sorry if this was not clear) was to point out that when the reference provided is not mtching the reference genome, the warning in the INFO field is not self-explanatory (i.e. the message should better say, instead of 'no valid transcript found', something as e.g. 'the reference provided does not match with the reference genome' to better understand what happened)

thanks! d