Ref validator refactoring

bedboss/refgenome_validator/__init__.py

@@ -1,4 +1,2 @@
 from bedboss.refgenome_validator.genome_model import GenomeModel
-from bedboss.refgenome_validator.refgenomevalidator import RefValidator
-
-# __all__ = ["GenomeModel"]
+from bedboss.refgenome_validator.refgenomevalidator import ReferenceValidator

bedboss/refgenome_validator/models.py

@@ -0,0 +1,47 @@
+from pydantic import BaseModel, ConfigDict
+from typing import Union
+
+
+class ChromNameStats(BaseModel):
+    xs: float = 0.0
+    q_and_m: float = 0.0
+    q_and_not_m: float = 0.0
+    not_q_and_m: float = 0.0
+    jaccard_index: float = 0.0
+    jaccard_index_binary: float = 0.0
+    passed_chrom_names: bool = False
+
+
+class ChromLengthStats(BaseModel):
+    oobr: Union[float, None] = None
+    beyond_range: bool = False
+    num_of_chrom_beyond: int = 0
+    percentage_bed_chrom_beyond: float = 0.0
+    percentage_genome_chrom_beyond: float = 0.0
+
+
+class SequenceFitStats(BaseModel):
+    sequence_fit: Union[float, None] = None
+
+
+class RatingModel(BaseModel):
+    assigned_points: int
+    tier_ranking: int
+    # model_config = ConfigDict(extra="forbid")
+
+
+class CompatibilityStats(BaseModel):
+    chrom_name_stats: ChromNameStats
+    chrom_length_stats: ChromLengthStats
+    chrom_sequence_fit_stats: SequenceFitStats
+    igd_stats: Union[dict, None] = None
+    compatibility: Union[RatingModel, None] = None
+
+    model_config = ConfigDict(extra="forbid")
+
+
+class CompatibilityConcise(BaseModel):
+    xs: float = 0.0
+    oobr: Union[float, None] = None
+    sequence_fit: Union[float, None] = None
+    compatibility: Union[RatingModel, None] = None