wrong sign

bpblanken · bpblanken · commit facc30331369 · 2024-08-29T20:15:19.000-04:00
diff --git a/v03_pipeline/lib/tasks/validate_callset.py b/v03_pipeline/lib/tasks/validate_callset.py
@@ -107,7 +107,7 @@ def update_table(self, mt: hl.MatrixTable) -> hl.MatrixTable:
             # alleles.  gVCFs may contain GQ or AD at sites without actual variant
             # calls.
             mt = mt.filter_rows(
-                mt.alleles[1] == '<NON_REF>',
+                mt.alleles[1] != '<NON_REF>',
             )
 
         if not self.skip_validation and self.dataset_type.can_run_validation:

Original file line number	Diff line number	Diff line change
`@@ -107,7 +107,7 @@ def update_table(self, mt: hl.MatrixTable) -> hl.MatrixTable:`
`107`	`107`	`# alleles. gVCFs may contain GQ or AD at sites without actual variant`
`108`	`108`	`# calls.`
`109`	`109`	`mt = mt.filter_rows(`
`110`		`- mt.alleles[1] == '<NON_REF>',`
	`110`	`+ mt.alleles[1] != '<NON_REF>',`
`111`	`111`	`)`
`112`	`112`
`113`	`113`	`if not self.skip_validation and self.dataset_type.can_run_validation:`