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

Improve documentation and code of ancestry readers/writers. Solve variants_alt inconsistency. Rename phased to sum_strands and set default to False #12

Merged
merged 21 commits into from
Nov 21, 2024
Merged

Improve documentation and code of ancestry readers/writers. Solve variants_alt inconsistency. Rename phased to sum_strands and set default to False #12

merged 21 commits into from
Nov 21, 2024

Conversation

miriambt
Copy link
Collaborator

No description provided.

@miriambt
Implement save and save_pickle for LocalAncestryObject. Add support f…
adc7c90 
…or .msp.tsv
@miriambt
Improve docstring and code in LAIReader. Add support for .msp.tsv
b5a7db6
@miriambt
Improve docstring and comments. Add expected MSP contnt
576a3c5
@miriambt
Improve local ancestry readers
fb9721a
@miriambt
Improve docstrings in local ancestry readers/writers
f3bae66
@miriambt
Improve flexibility of MSPWriter. Only write available attributes. So…
3494f91 
…lve bug. Improve docstrings
@miriambt
Make chm and lai/samples optional in MSPWriter
9b0c19a
@miriambt
Write missing attributes as NaN for MSP and read as None
d1c1e4e
@miriambt
Improve AdmixtureMappingVCFWriter
8aebefa
@miriambt
Improve global ancestry readers and writers
3d75031
@miriambt
Add save and save_pickle to GlobalAncestryObject. Improve AdmixtureWr…
6edefd5 
…iter
@miriambt
Merge remote-tracking branch 'origin/main' into readers-writers
e1b10b3
@miriambt
Fix inconsistency in variants_alt. (rad allways as 1-dimensional)
7603094
@miriambt
Rename phased to sum_strands. Set defauult to False
be9e7cc
@miriambt
Fix bug accessing variants_alt in BEDWriter
75aaf0c
@miriambt miriambt requested a review from salcc November 20, 2024 13:58
@davidbonet davidbonet requested review from davidbonet and removed request for davidbonet November 20, 2024 15:39
@davidbonet davidbonet self-assigned this Nov 20, 2024
salcc
salcc approved these changes Nov 21, 2024
View reviewed changes
Copy link
Member

@salcc salcc left a comment •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thanks! Everything looks good. The documentation improvements are very nice to have, and finally the SNPObject is truly common for all the formats!

@salcc salcc merged commit ce39cd7 into main Nov 21, 2024
6 checks passed
@salcc salcc deleted the readers-writers branch November 21, 2024 02:18
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@salcc salcc salcc approved these changes

Assignees

@davidbonet davidbonet

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@miriambt @salcc @davidbonet