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isovic / graphmap

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
https://github.com/lbcb-sci/graphmap2
MIT License
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segmentation fault when using reference with ambiguous characters #54

Closed filicado closed 7 years ago

filicado commented 7 years ago

So I managed to make this reproducible and am happy to share the fastq and reference files and scripts.

It doesn't happen with every ambiguous reference and the error isn't always the same.

isovic commented 7 years ago

That would be great! Can you upload them here (if they are not big?) or email me a download link?

Or - could you test the latest commit to see if it's still happening?

Thank you! Best regards, Ivan.

filicado commented 7 years ago

I will try the latest commit soon. In the meantime I found a simple hack-fix. Adding a single N as the first base of the reference prevents the crash.

isovic commented 7 years ago

Hmm interesting hack :D Not quite sure why it works :D

filicado commented 7 years ago

problem no longer there in the new build, closing. keep up the good work, graphmap is a great tool in our hands!

isovic commented 7 years ago

Thank you very much! :-)

Best regards, Ivan.