-
Notifications
You must be signed in to change notification settings - Fork 10
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.
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
graphdump now outputs a specialized gfa called Pufferized #18
Open
fataltes
wants to merge
31
commits into
medvedevgroup:master
Choose a base branch
from
fataltes:pufferize
base: master
Could not load branches
Branch not found: {{ refName }}
Could not load tags
Nothing to show
Are you sure you want to change the base?
Some commits from the old base branch may be removed from the timeline,
and old review comments may become outdated.
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
… (num of preceding/succeeding etc.)
…n of OS made me run these changes. Just wanted to create a binary for it and had to make these changes to make it compatible with the docker os version we're using and stuff
…he first sequence as the starting point of a sequence and the last kmer in the last sequence as the ending point of a sequence outside the while loop that does this for first and last kmers of the intermediate sequences when the seq id changes.
Added the binaryWriter. Added a new type of GFA1 serializer which writes the gfa in binary.
…r based on size rather than capacity.
… the path into a separate binary file.
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Outdated suggestions cannot be applied.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.
Dear @IlyaMinkin and @pashadag ,
I'm Fatemeh, @rob-p's student.
This pull request is regarding the conversation we had about outputting a cdbg with segments having overlap of k-1 instead of k. The series of commits in this pull request handle this case and can be called by the same set of inputs for graphdump with a new type as
pufferized
.All the changes have been pushed to a separate branch
pufferize
.It also takes care of cases that were in general problematic:
palindrome cases in which you have a sequence that is equal to its reverse-complement. In a palindrome case, we will have repeated kmers in the sequence other than the overlapping kmers at the two ends of the sequence. This specific case is important for us because our index builder relies on this specific property of cdbgs that each kmer appears at most once in all the contigs (In twopaco's output, if it is not a boundary kmer). This is specifically taken care of for the
pufferized
type of output. You can apply the change to other output types as well if you think this case should generally be taken care of.graph-dump uses a fixed space size for different inputs that can cause unnecessary overhead for small input files. In this version, the memory consumption can be restricted based on actual number of junctions which is determined in previous step, graphconstruction. In the current implementation, we go one extra pass over the binary input file to determine the number of junctions, but this step can be simply discarded with a minor change in graphconstructor step to store total number of junctions on the disk so that graphdump can read the input in and resize the data structures accordingly.
There is a special case in segment_id_generator that will create different IDs (in absolute) for a segment and its reverse complement that causes to output two different contigs for the segment and its reverse-complement. This also has been resolved by just adding one extra condition to the list of conditions. (I will post it as an issue, so that it's not lost in the list of all the other changes here)
Best,
Fatemeh