Adding AD for scale testing VS 225 add AD #7713
Conversation
RoriCremer
force-pushed
the
rc-vs-225-add-AD
branch
4 times, most recently
from
4b2a3fa
to
2cc5bb5
Compare
RoriCremer
force-pushed
the
rc-vs-225-add-AD
branch
2 times, most recently
from
52e5d86
to
86a8322
Compare
| @@ -261,7 +262,7 @@ def make_extract_table(fq_ranges_dataset, | |||
|
|
|||
| ## TODO -- provide a cmdline arg to override this (so we can simulate smaller datasets) | |||
|
|
|||
| global PET_VET_TABLE_COUNT | |||
| global PET_VET_TABLE_COUNT ## TODO why are we using PET here? | |||
There was a problem hiding this comment.
I think it's just a name, and now it would more accurately be REF_VET_TABLE_COUNT
| Boolean emit_pls = false | ||
| Boolean emit_ads = true | ||
|
|
There was a problem hiding this comment.
nit: I don't think you need to create these as variables since they're pretty straightforward and only used once.
| @@ -32,6 +32,7 @@ public void testDefinedExtractCohortRecord() { | |||
| Assert.assertEquals(allDefinedRecord.getRefAllele(), "CTTT"); | |||
| Assert.assertEquals(allDefinedRecord.getAltAllele(), "C"); | |||
| Assert.assertEquals(allDefinedRecord.getCallGT(), "1/1"); | |||
| // Assert.assertEquals(allDefinedRecord.getCallAD(), "0,1"); // TODO need to add this to the extract Avro! | |||
There was a problem hiding this comment.
Can this be done as part of this PR, since it's directly related to the added functionality?
There was a problem hiding this comment.
The issue is that the data is so old, it's from when we used PET to create a cohort, so I think the whole test needs a lil makeover. If all I need to do is add AD, then I can probably figure something out, but Im wondering if the whole test could use some changes
There was a problem hiding this comment.
Ah, ok — yeah, that sounds like a candidate for a separate ticket.
| Boolean emit_pls | ||
| Boolean emit_ads | ||
|
|
There was a problem hiding this comment.
sorry that I wasn't clear — I don't think these need to be parameterized, I think the "true" and "false" values can just be passed directly in the call to ExtractTask (lines 96 + 97).
RoriCremer
force-pushed
the
rc-vs-225-add-AD
branch
from
2f2ac77
to
2bf4296
Compare
RoriCremer
force-pushed
the
rc-vs-225-add-AD
branch
2 times, most recently
from
fa67243
to
47ba7f6
Compare
RoriCremer
force-pushed
the
rc-vs-225-add-AD
branch
from
47ba7f6
to
1f53709
Compare
This adds call_AD to the prepare step
and in the VCF: