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()