def read_cases(db: MongoAdapter = Depends(database)):
"""Return counts of SNV and SV variants in database"""
nr_cases_snvs = db.nr_cases(snv_cases=True, sv_cases=False)
nr_cases_svs = db.nr_cases(snv_cases=False, sv_cases=True)
return dict(
nr_cases_snvs=nr_cases_snvs,
nr_cases_svs=nr_cases_svs,
)
def read_variant(variant_id: str, db: MongoAdapter = Depends(database)):
variant = db.get_variant({"_id": variant_id})
if not variant:
raise HTTPException(status_code=status.HTTP_404_NOT_FOUND,
detail=f"Variant {variant_id} not found")
variant["total"] = db.nr_cases(snv_cases=True, sv_cases=False)
return variant
def read_sv(
chrom: str,
pos: int,
end: int,
sv_type: str,
db: MongoAdapter = Depends(database),
end_chrom: str = None,
):
structural_variant = db.get_structural_variant({
"chrom": chrom,
"end_chrom": end_chrom or chrom,
"sv_type": sv_type,
"pos": pos,
"end": end,
})
if not structural_variant:
raise HTTPException(status_code=status.HTTP_404_NOT_FOUND,
detail="Variant not found")
structural_variant["total"] = db.nr_cases(snv_cases=False, sv_cases=True)
return structural_variant