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

Debug state is not properly passed to the EventMap in HaplotypeCaller #4943

Closed
ldgauthier opened this issue Jun 25, 2018 · 3 comments
Closed

Debug state is not properly passed to the EventMap in HaplotypeCaller #4943

ldgauthier opened this issue Jun 25, 2018 · 3 comments
Assignees
@MartonKN
Labels
bug HaplotypeCaller learn GATK Suitable for GATK beginners

Comments

@ldgauthier
Copy link
Contributor

ldgauthier commented Jun 25, 2018 •
edited
Loading

The AssemblyResultSet in AssemblyBasedCallerUtils.assembleReads is sup posed to output some stats about the active region (debugDump), but it never appears in the log.

Also debug state is not properly passed to the EventMap.
@ldgauthier
Copy link
Contributor Author

Ohhh, I need to lower the logger output level from the command line. I thought I remembered that there were two args for effective HC debugging and that's the second one.

But the EventMap thing is still true.

@droazen droazen changed the title HC logger output missing Debug state is not properly passed to the EventMap in HaplotypeCaller Jun 25, 2018
@davidbenjamin davidbenjamin added the learn GATK Suitable for GATK beginners label Jun 26, 2018
@davidbenjamin
Copy link
Contributor

@MartonKN You will need to check exactly what @ldgauthier has in mind for this one.

MartonKN added a commit that referenced this issue Nov 28, 2018
@MartonKN
Fixed issue #4943: the debug variable of AsseemblyResultSet wasn't se…
57cf704 
…t anywhere, and therefore the command line argument debug didn't propagate to the function buildEventMapsForHaplotypes in EventMap.java. I added the function setDebug to AssemblyResultSet, and set its value in HaplotypeCallerEngine.
@davidbenjamin davidbenjamin mentioned this issue Nov 29, 2018
Merged
MartonKN added a commit that referenced this issue Nov 30, 2018
@MartonKN
The debug command line argument is now passed correctly in Haplotype …
afc0d22 
…caller -- fixed issue #4943 (#5455)

* Fixed issue #4943: the debug variable of AsseemblyResultSet wasn't set anywhere, and therefore the command line argument debug didn't propagate to the function buildEventMapsForHaplotypes in EventMap.java. I added the function setDebug to AssemblyResultSet, and set its value in HaplotypeCallerEngine.

* Did the same changes to Mutect2Engine.

* Changed where the debug variable is set for AssemblyResultSet. Previously, I set those after initialization in Mutect2Engine and HaplotypeCallerEngine, and now I do it at initialization.
@davidbenjamin
Copy link
Contributor

Closed by #5455.

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

@MartonKN MartonKN

Labels
bug HaplotypeCaller learn GATK Suitable for GATK beginners
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
4 participants
@droazen @MartonKN @ldgauthier @davidbenjamin