Audit htslib error codes

broadinstitute / gamgee

A C++14 library for NGS data formats

http://broadinstitute.github.io/gamgee/

MIT License

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Audit htslib error codes #295

Open jmthibault79 opened 10 years ago

jmthibault79 commented 10 years ago

Many htslib functions return error codes. We often don't check them, and I also just found a place (since fixed) where I did but should not have. We should look at these more closely.

MauricioCarneiro commented 10 years ago

I couldn't agree with this more, but this is not really an action item, more like something we should broadcast in hip chat and enforce in code reviews.

droazen commented 10 years ago

Disagree -- this is an action item. Someone should spend an hour reviewing existing usage of htslib functions that return an error code, and make sure we are not segfaulting on things like file-not-found. This is not hypothetical -- Joel and I have seen gamgee segfault on file-not-found because of this very issue.

MauricioCarneiro commented 10 years ago

alright this ^^ is an action item

spend an hour looking at all usages of htslib functions that return error codes and making sure to handle them appropriately.

droazen commented 10 years ago

Which is pretty much what Joel's original title said :)