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KarchinLab / open-cravat

A modular annotation tool for genomic variants
MIT License
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Hyphen in vcf file cause error. #105

Closed Alex-Karmazin closed 1 year ago

Alex-Karmazin commented 2 years ago

When vcf file contain hyphen it cause this error: 2022/04/19 14:45:00 cravat.aggregator Traceback (most recent call last): File "C:\ProgramData\Anaconda3\envs\openCravatPlugin\lib\site-packages\cravat\aggregator.py", line 155, in run self.cursor.execute(update_template, ins_vals) sqlite3.OperationalError: near "-": syntax error

Line that cause error is:

INFO=

When I change hyphen to underscore there is no error.

kmoad commented 1 year ago

Sorry for the late response. A solution for this is in the queue. Likely, the solution will be to automatically convert hyphens to underscores.

kmoad commented 1 year ago

This is fixed in vcf-converter version 2.2.1. INFO fields with a dash in the name are converted internally to an underscore. They will still show up with a dash in the GUI.

https://github.com/KarchinLab/open-cravat-modules-karchinlab/commit/b6d11dfb0ae6b030bf7cc8f0768cd33932e96b30