New version of NanoSim-H #19
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Owner
karel-brinda
commented
Aug 30, 2019
•
karel-brinda
commented
- Add R9.4 1D ecoli profile (by @mbhall88)
- Optimization and bug fixing (@ExplodingCabbage)
… of a chromosome
Note that a few lines above, in the case of a circular chromosome, the code gets this right. Specifically, this check uses <= correctly:
if length + ref_pos <= genome_len:
It's only this spot where the logic was wrong and consequently reads that end on the last base of the chromosome weren't allowed.
(Probably not hyperbole. A 100-million base sequence that case_convert was going to take ~ 10 days tp process before now takes <5 seconds.)
add R9.4 1D ecoli profile
Make case_convert about a million times faster for long sequences
…-short-references Fix bugs preventing tool from working on short reference sequences
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.