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

refactor/rewrite/extend indexed-fasta stores #1152

Closed
rbuels opened this Issue Aug 1, 2018 · 4 comments

Comments

Projects
None yet
2 participants
@rbuels
Collaborator

rbuels commented Aug 1, 2018

  • add bgzip+fasta support as in #1138
  • pull all low-level parsing code out into node modules that support uncompressed and fai-indexed fasta files, and compressed and .gzi-indexed fasta files

from #1138:

The fasta+fai index is not compressed, might be nice to get the bgzip fasta + the gzi index
Barebones level of gzi index docs here http://www.htslib.org/doc/bgzip.html

@rbuels rbuels added this to the 1.16.0 milestone Aug 1, 2018

@rbuels rbuels added the big task label Aug 1, 2018

@rbuels rbuels assigned cmdcolin and rbuels and unassigned cmdcolin Aug 1, 2018

@rbuels

This comment has been minimized.

Show comment
Hide comment
@rbuels

rbuels Aug 15, 2018

Collaborator

2 new node packages are coming out of this: bgzf-filehandle and another called indexed-fasta that will use bgzf-filehandle (or regular filehandles). bgzf-filehandle is pretty much done, indexed-fasta is the next thing to do on this.

Collaborator

rbuels commented Aug 15, 2018

2 new node packages are coming out of this: bgzf-filehandle and another called indexed-fasta that will use bgzf-filehandle (or regular filehandles). bgzf-filehandle is pretty much done, indexed-fasta is the next thing to do on this.

@rbuels rbuels modified the milestones: 1.15.2, 1.16.0 Aug 15, 2018

@rbuels rbuels assigned cmdcolin and unassigned rbuels Aug 20, 2018

@cmdcolin

This comment has been minimized.

Show comment
Hide comment
@cmdcolin

cmdcolin Aug 22, 2018

Contributor

I have a simple little module now that implements unindexed FASTA, indexed FASTA, and bgzip compressed indexed

Contributor

cmdcolin commented Aug 22, 2018

I have a simple little module now that implements unindexed FASTA, indexed FASTA, and bgzip compressed indexed

@cmdcolin

This comment has been minimized.

Show comment
Hide comment
@cmdcolin

cmdcolin Aug 27, 2018

Contributor

I adopted the twobit tests for indexedfasta so now they should have a similar API and test suite :)

New link https://github.com/GMOD/indexedfasta-js

Contributor

cmdcolin commented Aug 27, 2018

I adopted the twobit tests for indexedfasta so now they should have a similar API and test suite :)

New link https://github.com/GMOD/indexedfasta-js

@cmdcolin

This comment has been minimized.

Show comment
Hide comment
@cmdcolin

cmdcolin Sep 13, 2018

Contributor

The branch has been merged :) Feel free to test and open up new issues if they arise

Contributor

cmdcolin commented Sep 13, 2018

The branch has been merged :) Feel free to test and open up new issues if they arise

@cmdcolin cmdcolin closed this Sep 13, 2018

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