Open
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Since no info file is generated after completing imputation on other servers (such as ChinaMAP Imputation Server), if the genotyped status in the dose file is "TYPED_ONLY", the file does not contain R2. As a result, make_info.py would set it to -1, causing the program to terminate. Therefore, this modification primarily addresses this issue by avoiding exit() when the genotyped status is "TYPED_ONLY" and R2 is -1.
Additionally, since the script will print out which variants are in this situation during the process, a logging feature has been added to the script to write to a log file.