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

CRAM layout can get messed up #1271

Closed
cmdcolin opened this Issue Nov 29, 2018 · 4 comments

Comments

Projects
None yet
2 participants
@cmdcolin
Copy link
Contributor

cmdcolin commented Nov 29, 2018

The layout of CRAM features can get messed up possibly near block boundaries?

screenshot-localhost-2018 11 29-09-16-28
See the screenshot there are "holes" in the layout

pseudomonas2.tar.gz

To reproduce I uploaded a sample data directory. Start at the start of the chromosome and then scroll to the end of the data and the layout will be weird and mouseovers will not work at the end right where the features end

Tested on 1.15.3 and dev branch. The same thing does not appear to happen with BAM versions of the same file

@cmdcolin cmdcolin added the bug label Nov 29, 2018

@rbuels rbuels added this to the 1.16.0 milestone Nov 30, 2018

@rbuels

This comment has been minimized.

Copy link
Collaborator

rbuels commented Nov 30, 2018

@cmdcolin try it in 1.15.0

@cmdcolin

This comment has been minimized.

Copy link
Contributor

cmdcolin commented Nov 30, 2018

I tested in 1.15.0 and it still exhibited problem, and the BAM for same file works fine

@cmdcolin

This comment has been minimized.

Copy link
Contributor

cmdcolin commented Nov 30, 2018

Now, the interesting thing is i think it is due to ID collisions. If I make a simple hashmap collision detector e.g.

    if(totalMap[feature.id()] && totalMap[feature.id()]!=feature.get('start')+','+feature.get('end')) {
        console.log('collision',totalMap[feature.id()],'t1',feature.get('start')+','+feature.get('end'));
    }
    else {
        totalMap[feature.id()]=feature.get('start')+','+feature.get('end');
    }

Then this outputs a lot of collisions in the areas that the layout is bad

@cmdcolin

This comment has been minimized.

Copy link
Contributor

cmdcolin commented Nov 30, 2018

The reason that it is not the thing where we have broken features is becauuse the IDs are not inconsistent across blocks, but instead collide

@rbuels rbuels closed this Dec 7, 2018

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment