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from typing import Optional
from pydantic import BaseSettings, Field
import os
class EnvBeagle(BaseSettings):
vcf: str = Field(description='Path to the target vcf file')
samples: Optional[str] = Field(default=None,
description='Path to VCF with other samples for conform checks, not required if '
'target VCF contains data for at least 20 individuals')
conform: str = Field(description='Path to conform .jar file')
beagle: str = Field(description='Path to beagle .jar file')
ref: str = Field(description='Path to folder with reference genome:'
' .vcf.gz files are expected to start with "chr1."..."chr22.", "chrX."')
maps: str = Field(description='Path to folder with PLINK format genetic maps, files are expected to start with'
'"plink.chr1.", ..."plink.chr22.", "plink.chrX."')
gb: int = Field(description='Number of gigabytes for running beagle')
class Config:
env_file = os.path.dirname(os.path.abspath(__file__))+"/.env_paths"
IMPUTATION_SETTINGS = EnvBeagle()
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