mutect2 expose param #8447
mutect2 expose param #8447
Conversation
|
@ldgauthier Did you intend to include the |
ldgauthier
force-pushed
the
ldg_mutect2_expose_param
branch
from
9ad6a64
to
fdbaf98
Compare
|
|
||
|
|
||
| @Test | ||
| public void testOldErrorModelBehavior() { |
| */ | ||
| @Advanced | ||
| @Argument(fullName = USER_DEFINED_BASE_QUAL_CORRECTION, optional = true, doc = "Set to zero to turn off the error model changes included in GATK 4.1.9.0.") | ||
| public double userDefinedBaseQualCorrection = 1; |
There was a problem hiding this comment.
I lean toward making this private int activeRegionMultipleSubstitutionBaseQualCorrection = Math.round(10 * Math.log(3)) (maybe make the name a bit more graceful than that). That way 1) setting it to zero is inherently the desired behavior of turning off the change without requiring interpretation as a sentinel value, 2) it eliminates the indirection of the user-defined multiplier and goes straight to the desired variable, 3) it makes the variable an int from the beginning.
There was a problem hiding this comment.
I think I get what you're saying, but in that case it would be public since it's an arg right?
There was a problem hiding this comment.
For sure, I'm not sure why I wrote private.
|
I think I got it right but please double check the actual base qual equation -- back to you @davidbenjamin |
| private static final int ONE_THIRD_QUAL_CORRECTION = 5; | ||
|
|
||
| private static double USER_DEFINED_QUAL_CORRECTION = 1; | ||
| private static double MULTIPLE_SUBSTITUTION_BASE_QUAL_CORRECTION = 5; |
There was a problem hiding this comment.
The constant default isn't needed anymore because now the default is set in the argument collection, right?
| @Argument(fullName = USER_DEFINED_BASE_QUAL_CORRECTION, optional = true, doc = "Set to zero to turn off the error model changes included in GATK 4.1.9.0.") | ||
| public double userDefinedBaseQualCorrection = 1; | ||
| @Argument(fullName = MULTIPLE_SUBSTITUTION_BASE_QUAL_CORRECTION, optional = true, doc = "Set to zero to turn off the error model changes included in GATK 4.1.9.0.") | ||
| public long activeRegionMultipleSubstitutionBaseQualCorrection = Math.round(10 * Math.log(3)); |
There was a problem hiding this comment.
This should be an int.
|
Github actions tests reported job failures from actions build 5822346095
|
|
Addresses #7921 |
Allow users to turn off fix from 4.1.9.0 for consistency's sake
Allow users to turn off Mutect2 error model fix from 4.1.9.0