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.

Sign up for GitHub

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

Jump to bottom

vcf_to_hdf5 and variable length strings #153

Closed
alimanfoo opened this issue Jul 2, 2017 · 1 comment
Closed

vcf_to_hdf5 and variable length strings #153

alimanfoo opened this issue Jul 2, 2017 · 1 comment

Comments

@alimanfoo
Copy link
Contributor

alimanfoo commented Jul 2, 2017 •
edited

It appears that HDF5 uses a lot of space to store variable length strings, in the best case 32 bytes of overhead per string, plus the actual data. Also, the actual string data are not compressed. This can lead to very large file sizes for string columns like CHROM, ID, REF, ALT etc., if using object dtype.
@alimanfoo
Copy link
Contributor Author

Resolved in 1.1.7.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@alimanfoo