Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

False-positive kmer hits #14

Open
masakistan opened this issue Jul 13, 2018 · 2 comments · May be fixed by #15
Open

False-positive kmer hits #14

masakistan opened this issue Jul 13, 2018 · 2 comments · May be fixed by #15

Comments

@masakistan
Copy link

Thanks for the great software package, it's been great to use.

It is my understanding that the BFT shouldn't return false-positive kmer hits, is this correct?

If I'm correct, I think I've come across a bug. I'm adding only canonical kmers from two different genomes with k=90 to a BFT. When I query a particular kmer, I get a hit saying that it appears in both genomes but when I grep for the kmer in the kmer count dumps it only appears in one of the genomes.

The data files can be accessed here. The file contains:

  • BY4741_Toronto_2012.dump.sorted - kmers to add to BFT
  • EC1118.dump.sorted - kmers to add to BFT
  • query_list.txt - list of query files
  • query.txt - problematic kmer query

The problematic kmer is AAAGAAAAAGGGGAAGAAATGGGCGAGGTAGCAAACGTAAATGAAATTCCGGTCAAGATAAGAAATCATAAGTATCCTGCGAAAGAACAT

Thanks for your help! Please let me know if you require any additional information or if I can do anything.
@GuillaumeHolley
Copy link
Owner

Hey Stanley,

Thanks for opening this issue and sorry that I answer so late (I am not actively working on the project). I will look into the matter as soon as I can ;)

Guillaume

@masakistan
Copy link
Author

No worries, I appreciate the response and the great software package.

Please let me know if there is anything I can do to help.

@masakistan masakistan linked a pull request Sep 7, 2018 that will close this issue
Open
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging a pull request may close this issue.

fixed traversal masakistan/BloomFilterTrie
2 participants
@GuillaumeHolley @masakistan