This repository has been archived by the owner on Mar 16, 2022. It is now read-only.
Fix fetch_reads #493
Open
Fix fetch_reads #493
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
From DNANexus, privately.
pb-cdunn
force-pushed
the
fetch_reads
branch
from
07d2f10 to
2891801
Compare
This is for a different problem, discussed between Jason and Dario. I am not certain of the problem yet. From Jason's email: For FALCON-unzip, you can comment out the following lines in graph_to_contig.py to avoid the seg fault. The FALCON-Unzip will run. Your a_ctg.fa will have some duplicates but it will not affects downstream in general. The detail of a_tig is not used in Unzip process as it replaces it with phased haplotigs. Ok, the root cause is that there is a very long bubble. The alternative path is > 500kb. The internal aligner used is not designed for handling such long sequences. In a halpoid genome, this is not supposed to happened. However, in Cab-Suv genome, we might generate big bubble in the graph level. One proposed fix is to cap the size of sequence sent to the internal aligner now.
pb-cdunn
force-pushed
the
master
branch
2 times, most recently
from
baf9db6 to
58083fe
Compare
Sign up for free
to subscribe to this conversation on GitHub.
Already have an account?
Sign in.
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Outdated suggestions cannot be applied.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.
From DNANexus, privately.
Jason, this was the most recent code exchanged. It has not caused me any problems, but I have not looked into this matter very deeply either.