quinlan-lab / vcf2db

create a gemini-compatible database from a VCF
MIT License
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Remove superflous (and possibly dangerous) raise statement #60

Closed lbeltrame closed 2 years ago

lbeltrame commented 5 years ago

When vcf2db hits an exception when inserting multiple records at a time, it catches it then inserts single records, and if an exception occurs, prints the record as bad before raising the exception itself.

However, there are cases where the batch insertion fails, and the individual insertions succeed. In this case the code hits a second raise statement and interrupts loading, even though no error has occurred.

This commit removes the raise statement for these reasons:

Note that this is a workaround more than a fix, since it is unclear why adding record in batch would fail, while individual records would work.

Workarounds issue #59.

lbeltrame commented 2 years ago

Dropping this. I wrote something to replace vcf2db internally which is not as full of problems.