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kdm9 / axe

Rapid competitive read demulitplexer. Made with tries.
http://axe-demultiplexer.rtfd.io
GNU General Public License v3.0
23 stars 5 forks source link

Finishes without error on a corrupt gzipped sequence file #5

Closed relshire closed 7 years ago

relshire commented 8 years ago

While working with a corrupt gzipped sequence file, axe-demux 'finished' but did not throw an error or otherwise alert me to a problem. Having fraction of the expected sequences in the summary table did alert me to the problem.

I'm not sure how one would catch this error....

In any case. This works very well. Thank Kevin for making it. This is the first program I've used that takes advantage of the hamming distances that I designed into the molecular part of GBS!

kdm9 commented 8 years ago

Hi Rob,

Thanks for the bug report. That looks like a bug to me, though this could actually be quite low-level (within the C libraries I use for parsing). How is your gzip file corrupted? If you can generate a minimal failing example file, I'll debug this locally. Otherwise I can give you tips on how to debug this at your end.

Cheers, K

relshire commented 8 years ago

Hi Kevin, The files I am working with are around 12G each. The file got corrupted during copying. Not sure what the nature of the corruption is. I've tried to find instructions on how to corrupt a gz file, but only find fixes. :) Happy to take some tips on debugging.

Best,

Rob

kdm9 commented 8 years ago

Hi Rob,

Sorry it's taken a while to get back to you.

Do you have the original files available?

Cheers, K

kdm9 commented 8 years ago

Hi Rob, I just made a gitter chat room for Axe. We can continue the discussion there if you prefer a more real-time discussion.

Cheers, K

relshire commented 8 years ago

HI Kevin,Sorry for the slow reply. I've been at an Open Source // Open Society conference in Wellington. Some cool stuff going on here. Will get back home late in the afternoon tomorrow and will pick up this thread.Best,Rob----- Original Message ----- From: Kevin Murray [mailto:notifications@github.com] To: axe@noreply.github.com Cc: rob@elshire.org,author@noreply.github.com Sent: Mon, 22 Aug 2016 18:45:10 -0700 Subject: Re: [kdmurray91/axe] Finishes without error on a corrupt gzippedsequence file (#5) Hi Rob, I just made a gitter chat room for Axe. We can continue the discussion there if you prefer a more real-time discussion.

Cheers, K

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