gumpy
Advanced tools
| Metadata-Version: 2.1 | ||
| Name: gumpy | ||
| Version: 1.3.5 | ||
| Version: 1.3.6 | ||
| Summary: Genetics with Numpy | ||
@@ -5,0 +5,0 @@ Home-page: https://github.com/oxfordmmm/gumpy |
@@ -83,3 +83,3 @@ """ | ||
| assert len(record.filter.items()) >= 0, "A record has more than 1 filter set!" | ||
| self.filter: str | None | ||
| self.filter: list[str] | None | ||
| if len(record.filter.items()) == 0: | ||
@@ -89,5 +89,5 @@ self.filter = None | ||
| else: | ||
| self.filter = str(record.filter.items()[0][0]) | ||
| self.filter = [str(x) for x in record.filter.keys()] | ||
| self.is_filter_pass = ( | ||
| True if record.filter.items()[0][0] == "PASS" else False | ||
| True if len(self.filter) == 1 and self.filter == ["PASS"] else False | ||
| ) | ||
@@ -162,4 +162,4 @@ | ||
| if self.is_null: | ||
| # Override filter fails on nulls to enforce that they are detected | ||
| if self.is_null and self.filter == ["MIN_FRS"]: | ||
| # Override MIN_FRS filter fails on nulls to enforce that they are detected | ||
| self.is_filter_pass = True | ||
@@ -184,3 +184,3 @@ | ||
| else: | ||
| s += self.filter + "\t" | ||
| s += ",".join(self.filter) + "\t" | ||
| for val in self.values.keys(): | ||
@@ -568,3 +568,3 @@ if val == "POS": | ||
| # We only want to allow these through if the filter fail is MIN_FRS | ||
| if record.filter == "MIN_FRS": | ||
| if record.filter == ["MIN_FRS"]: | ||
| # Allow MIN_FRS | ||
@@ -571,0 +571,0 @@ variant = record.ref |
+1
-1
| Metadata-Version: 2.1 | ||
| Name: gumpy | ||
| Version: 1.3.5 | ||
| Version: 1.3.6 | ||
| Summary: Genetics with Numpy | ||
@@ -5,0 +5,0 @@ Home-page: https://github.com/oxfordmmm/gumpy |
+1
-2
@@ -1,2 +0,1 @@ | ||
| 1.3.5 | ||
| 1.3.6 |
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