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

feat: improve partitioning of credible sets #900

Open
wants to merge 1 commit into
base: dev
Choose a base branch
from

Conversation

d0choa
Copy link
Collaborator

@d0choa d0choa commented Nov 5, 2024

The current credible sets after validation are completely shuffled. This can have a performance cost in all downstream processes.

In [7]: cs.select("chromosome", "position").show()
+----------+---------+
|chromosome| position|
+----------+---------+
|         2|151525381|
|         1|162388605|
|        10|102449815|
|         2| 47169327|
|        21| 42298501|
|         8| 85157259|
|         1| 11838976|
|        20| 45919050|
|         2|106566631|
|        16| 14889311|
|         1| 17005181|
|         2| 99176335|
|         1|149185498|
|         X|  1661217|
|         X|   312722|
|        11|   807149|
|        10| 79836221|
|         2| 73063040|
|        14| 55647604|
|         5| 43001499|
+----------+---------+
only showing top 20 rows

To improve the partitioning, this PR implements partitioning by range using chromosome and position.

The benefits on performance still need to be evaluated

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants