Changes to Mutect2 to support Mutect3 #7663
Merged
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
d6e4986 to
1e82224
Compare
|
@davidbenjamin sorry I may not be able to get to it until later this week, is that acceptable? |
|
@takutosato Sure, not a problem! |
takutosato
approved these changes
Mar 21, 2022
src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect2IntegrationTest.java
Show resolved
Hide resolved
...org/broadinstitute/hellbender/tools/walkers/mutect/GetNormalArtifactDataIntegrationTest.java
Show resolved
Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/SomaticGenotypingEngine.java
Show resolved
Hide resolved
...org/broadinstitute/hellbender/tools/walkers/mutect/GetNormalArtifactDataIntegrationTest.java
Outdated
Show resolved
Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/NormalArtifactRecord.java
Outdated
Show resolved
Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect3DatasetEngine.java
Outdated
Show resolved
Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect3DatasetEngine.java
Show resolved
Hide resolved
src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect3DatasetEngine.java
Outdated
Show resolved
Hide resolved
| final boolean hasNormal = normalDepth > 0; | ||
|
|
||
| final List<Label> labels = new ArrayList<>(numAlt); | ||
| final Map<Allele, Integer> altDownsampleMap= new HashMap<>(); |
There was a problem hiding this comment.
A comment describing this map would be very useful for the reader (i.e. me). Namely it contains the target alt counts to downsample to
src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/Mutect3DatasetEngine.java
Outdated
Show resolved
Hide resolved
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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.
@takutosato Are you able to look at this? The two big changes here are 1) data for the M3 normal artifact filter and 2) outputting tensors for M3 as plain text rather than VCF.