__author__ = 'mahajrod'

from RouToolPa.Tools.GATK.PrintReads import PrintReads
from RouToolPa.Tools.GATK.CatVariants import CatVariants
from RouToolPa.Tools.GATK.GenotypeGVCFs import GenotypeGVCFs
from RouToolPa.Tools.GATK.IndelRealigner import IndelRealigner
from RouToolPa.Tools.GATK.SelectVariants import SelectVariants
from RouToolPa.Tools.GATK.CombineVariants import CombineVariants
from RouToolPa.Tools.GATK.HaplotypeCaller import HaplotypeCaller
from RouToolPa.Tools.GATK.ValidateVariants import ValidateVariants
from RouToolPa.Tools.GATK.BaseRecalibrator import BaseRecalibrator
from RouToolPa.Tools.GATK.UnifiedGenotyper import UnifiedGenotyper
from RouToolPa.Tools.GATK.AnalyzeCovariates import AnalyzeCovariates
from RouToolPa.Tools.GATK.VariantFiltration import VariantFiltration
from RouToolPa.Tools.GATK.ApplyRecalibration import ApplyRecalibration
from RouToolPa.Tools.GATK.VariantRecalibrator import VariantRecalibrator
from RouToolPa.Tools.GATK.RealignerTargetCreator import RealignerTargetCreator
from RouToolPa.Tools.GATK.FastaAlternateReferenceMaker import FastaAlternateReferenceMaker


PrintReads = PrintReads()
CatVariants = CatVariants()
GenotypeGVCFs = GenotypeGVCFs()
IndelRealigner = IndelRealigner()
SelectVariants = SelectVariants()
CombineVariants = CombineVariants()
HaplotypeCaller = HaplotypeCaller()
ValidateVariants = ValidateVariants()
BaseRecalibrator = BaseRecalibrator()
UnifiedGenotyper = UnifiedGenotyper()
AnalyzeCovariates = AnalyzeCovariates()
VariantFiltration = VariantFiltration()
ApplyRecalibration = ApplyRecalibration()
VariantRecalibrator = VariantRecalibrator()
RealignerTargetCreator = RealignerTargetCreator()
FastaAlternateReferenceMaker = FastaAlternateReferenceMaker()
