Skip to content
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

Add CSI index support for BAM and VCF #1086

Merged
merged 21 commits into from Jul 5, 2018

Conversation

Projects
None yet
4 participants
@cmdcolin
Copy link
Contributor

cmdcolin commented Jul 2, 2018

This adds support for using CSI indexes on BAM and VCF

This allows doing coordinates of over a gigabase (or specifically 2^30 which is 1073741824)

It seems effective! The 64-bit bit manipulations are done using some floating point math specifically multiplying by two and dividing by two. A proper 64 bit math library could potentially be implemented.

Ref #926

@wafflebot wafflebot bot added the in progress label Jul 2, 2018

cmdcolin added some commits Jul 2, 2018

@rbuels rbuels merged commit 34bbb6c into dev Jul 5, 2018

2 checks passed

continuous-integration/travis-ci/pr The Travis CI build passed
Details
continuous-integration/travis-ci/push The Travis CI build passed
Details

@wafflebot wafflebot bot removed the in progress label Jul 5, 2018

@rbuels

This comment has been minimized.

Copy link
Collaborator

rbuels commented Jul 5, 2018

This looks good! My only gripe is that it's implemented in the old dojo style, so we are going to have to put in some extra work later to move it out into a node module.

@thomasvangurp

This comment has been minimized.

Copy link

thomasvangurp commented Jul 10, 2018

Would it be possible to support this for GFF3Tabix as well? this might allow for more informative feature density plots as you can set the step size for the index...

@nathanhaigh

This comment has been minimized.

Copy link
Contributor

nathanhaigh commented Jul 10, 2018

@thomasvangurp Hopefully #1105 delivers support for CSI indexed GFF3Tabix.

@rbuels rbuels added this to the 1.15.0 milestone Jul 10, 2018

@cmdcolin cmdcolin deleted the csi_index branch Jul 11, 2018

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
You can’t perform that action at this time.