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

Edge list writer still unspecified. Edge list generator undergoing interface overhaul. , #129

Closed
MatthewRalston opened this issue Mar 24, 2024 · 1 comment · Fixed by #124
Closed

Edge list writer still unspecified. Edge list generator undergoing interface overhaul. , #129

MatthewRalston opened this issue Mar 24, 2024 · 1 comment · Fixed by #124
Assignees
@MatthewRalston
Labels
bug Something isn't working documentation Improvements or additions to documentation
Milestone
edge list tuple

Comments

@MatthewRalston
Copy link
Owner

the feature branch graph_algo is tested/was developed on single sequence .fasta files. When multiple sequences are present in the input, the relationship between the last k-mer of the n'th sequence and the first k-mer of the n+1 sequence does not hold. Currently, it throws an error and exits. Will support in next bugfix.
@MatthewRalston MatthewRalston added bug Something isn't working documentation Improvements or additions to documentation labels Mar 24, 2024
@MatthewRalston MatthewRalston added this to the edge list tuple milestone Mar 24, 2024
@MatthewRalston MatthewRalston self-assigned this Mar 24, 2024
@MatthewRalston
Copy link
Owner Author

The idea centers around not k1 and k2 (for neighbor generation... has not been deprecated?) but around pair[0][1:] and pair[1][:-1]

MatthewRalston added a commit that referenced this issue Mar 25, 2024
@MatthewRalston
Closes #129. Addresses the adjacency issue in multi-sequence .fa and …
443c2af 
….fq files with improved logging, logs a warning about the observed inconsistencies and note about plausible origin from .fa/.fq input.
@MatthewRalston MatthewRalston linked a pull request Mar 25, 2024 that will close this issue
3-tuple i think #124
Merged
MatthewRalston added a commit that referenced this issue Mar 26, 2024
@MatthewRalston
Closes #129. Adds docstrings to several submodules. Condenses the Seq…
a109718 
…Parser class into the parse submodule. wakka wakka!
@MatthewRalston MatthewRalston changed the title graph algo fails on .fastq input (not yet supported) Edge list writer still unspecified. Edge list generator undergoing interface overhaul. ... Splitting duties of summary phase output, Apr 3, 2024
@MatthewRalston MatthewRalston changed the title Edge list writer still unspecified. Edge list generator undergoing interface overhaul. ... Splitting duties of summary phase output, Edge list writer still unspecified. Edge list generator undergoing interface overhaul. , Apr 3, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@MatthewRalston MatthewRalston

Labels
bug Something isn't working documentation Improvements or additions to documentation
Projects
Assembly algorithm (0.7.7+)
Status: Done
Milestone
edge list tuple
Development

Successfully merging a pull request may close this issue.

3-tuple i think MatthewRalston/kmerdb
1 participant
@MatthewRalston