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gmarcais / Jellyfish

A fast multi-threaded k-mer counter
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Parser interprets empty read as end-of-file #55

Closed rob-p closed 8 years ago

rob-p commented 8 years ago

Hi Guillaume,

@roryk noticed this issue in RapMap (https://github.com/COMBINE-lab/RapMap/issues/19), and has a nice sample dataset to reproduce it. Basically, when a read is empty, but not the actual end of the file, the parser thinks it's done. Is there an easy way to change the parser logic to account for this situation?

--Rob

gmarcais commented 8 years ago

Indeed, that is not good. I'll fix it ASAP.

gmarcais commented 8 years ago

Can you try the develop branch? The issue should be fixed.

rob-p commented 8 years ago

That was fast! I'll test it out as soon as I get into work.

rob-p commented 8 years ago

Here I betray my strong CMake bias — what magical invocations must I make to generate a proper configure script? I tried aclocal && autoconf && automake --add-missing.

gmarcais commented 8 years ago

The magic call is:

echo abracadabra; autoreconf -fi
rob-p commented 8 years ago

ahhh, see I was missing the abracadabra incantation! Any interest in building a tagged tarball (i.e. with a stable GitHub url) that already has the ./configure script ready to go? Right now I'm pulling from https://github.com/gmarcais/Jellyfish/archive/develop.zip , which, I imagine, is subject to change in content ;P.

gmarcais commented 8 years ago

I will do that. I was hoping to get a feed back from you that it indeed fixed the problem before generating a new version and upload it to the releases.

rob-p commented 8 years ago

I can confirm that this does, indeed, fix the problem (using Rory's test data). The parser now returns (and RapMap now reports) having observed 5 reads, instead of 0, which is correct.

gmarcais commented 8 years ago

OK, the new distribution tarball is ready in the releases(https://github.com/gmarcais/Jellyfish/releases).

Thanks for the bug report.

rob-p commented 8 years ago

Fantastic. Thanks, Guillaume!

roryk commented 8 years ago

Thanks!

mr-c commented 8 years ago

Is it known how far back this bug has existed?