Merge pull request #107 from SMD-Bioinformatics-Lund/fix-ng50-low-qua…

…l-bug Fix NG50 bug that couldn't process low quality configs
SMD-Bioinformatics-Lund · Jan 8, 2025 · fdca9f6 · fdca9f6
2 parents 4c8d7fc + 015f965
commit fdca9f6
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,8 @@
 
 ### Fixed
 
+ - Fixed NG50 bug that couldn't process "-"
+
 ### Changed
 
 ## [0.11.3]

diff --git a/prp/models/metadata.py b/prp/models/metadata.py
@@ -3,7 +3,7 @@
 from enum import Enum
 from typing import Optional
 
-from pydantic import BaseModel, Field
+from pydantic import BaseModel
 
 from .base import RWModel
 

diff --git a/prp/models/qc.py b/prp/models/qc.py
@@ -7,6 +7,12 @@
 from .typing import TypingSoftware
 
 
+class ValidQualityStr(Enum):
+    """Valid strings for qc entries."""
+
+    LOWCONTIGQUAL = "-"
+
+
 class QcSoftware(Enum):
     """Valid tools."""
 
@@ -24,7 +30,7 @@ class QuastQcResult(BaseModel):
     largest_contig: int
     n_contigs: int
     n50: int
-    ng50: int | None = None
+    ng50: int | ValidQualityStr | None = None
     assembly_gc: float
     reference_gc: float | None = None
     duplication_ratio: float | None = None