remove prefix on snarl intermediate file input and output of stoat vcf - #59
Open
Plogeur wants to merge 3 commits into
Open
remove prefix on snarl intermediate file input and output of stoat vcf#59Plogeur wants to merge 3 commits into
Plogeur wants to merge 3 commits into
Conversation
jmonlong
reviewed
Apr 7, 2026
| // JEAN would reduce memory to write the collection while genotyping the snarls, one chr at a time, appending to the output file (or in separate chr files). | ||
| auto start_writegt_timer = std::chrono::high_resolution_clock::now(); | ||
| snarl_collection.write_snarl_data_collection(*gt_writer); | ||
| snarl_collection.write_snarl_data_collection(*gt_writer, remove_prefix_str); |
Member
There was a problem hiding this comment.
This one is not needed because we should already have homogenized the path names earlier (snarl_collection.genotype_snarls_by_chr_from_vcf).
jmonlong
reviewed
Apr 7, 2026
| snarl_writer.reset(new StdWriter(snarls_filename)); | ||
| } | ||
|
|
||
| // equivalent to what was done before in stoat vcf: enumerate all walks through a snarl |
Member
There was a problem hiding this comment.
If we want to remove the prefix in the intermediate file, we should do it around here. Otherwise, another approach, would be to keep the "real" path names in those file and just remove the prefix on the fly when reading/matching the VCF records (somewhere around snarl_collection.genotype_snarls_by_chr_from_vcf).
… decomposition are done in the same time that genotyping
Member
|
Let me know when this is ready to review. |
This file contains hidden or 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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
PR Log Entry
Whoever merges this PR should copy the following bullet points to the PR Log:
Linked to this issue: Deal with reference path prefixes #36
Add new option on stoat vcf that remove the snarl chromosome prefix for both case :
Description