Class: CagnutGatk::Base

Inherits:
Object
  • Object
show all
Defined in:
lib/cagnut_gatk/base.rb

Instance Method Summary collapse

Instance Method Details

#analyze_covariates(dirs, order, previous_job_id, input) ⇒ Object 



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# File 'lib/cagnut_gatk/base.rb', line 40

def analyze_covariates dirs, order, previous_job_id, input
  opts = { input: input, dirs: dirs, order: order }
  analyze_covariates = CagnutGatk::AnalyzeCovariates.new opts
  analyze_covariates.run previous_job_id
end

#base_recalibrator(dirs, order, previous_job_id, input, opts) ⇒ Object 



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# File 'lib/cagnut_gatk/base.rb', line 34

def base_recalibrator dirs, order, previous_job_id, input, opts
  opts = { input: input, dirs: dirs, order: order }.merge opts
  base_recalibrator = CagnutGatk::BaseRecalibrator.new opts
  base_recalibrator.run previous_job_id
end

#count_read(dirs, order, previous_job_id, opts = {}) ⇒ Object 



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# File 'lib/cagnut_gatk/base.rb', line 16

def count_read dirs, order, previous_job_id, opts = {}
  opts = { dirs: dirs, order: order }.merge opts
  count_read = CagnutGatk::CountRead.new opts
  count_read.run previous_job_id
end

#depth_of_coverage(dirs, order, previous_job_id, input, opts) ⇒ Object 



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# File 'lib/cagnut_gatk/base.rb', line 52

def depth_of_coverage dirs, order, previous_job_id, input, opts
  opts = { input: input, dirs: dirs, order: order }.merge opts
  depth_of_coverage = CagnutGatk::DepthOfCoverage.new opts
  depth_of_coverage.run previous_job_id
end

#haplotype_caller(dirs, order, previous_job_id, input) ⇒ Object 



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# File 'lib/cagnut_gatk/base.rb', line 58

def haplotype_caller dirs, order, previous_job_id, input
  opts = { input: input, dirs: dirs, order: order }
  haplotype_caller = CagnutGatk::HaplotypeCaller.new opts
  haplotype_caller.run previous_job_id
end

#indel_realigner(dirs, order, previous_job_id, input, interval_list) ⇒ Object 



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# File 'lib/cagnut_gatk/base.rb', line 28

def indel_realigner dirs, order, previous_job_id, input, interval_list
  opts = { input: input, interval_list: interval_list, dirs: dirs, order: order }
  indel_realigner = CagnutGatk::IndelRealigner.new opts
  indel_realigner.run previous_job_id
end

#print_reads(dirs, order, previous_job_id, input) ⇒ Object 



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# File 'lib/cagnut_gatk/base.rb', line 46

def print_reads dirs, order, previous_job_id, input
  opts = { input: input, dirs: dirs, order: order}
  print_reads = CagnutGatk::PrintReads.new opts
  print_reads.run previous_job_id
end

#realigner_target_creator(dirs, order, previous_job_id, input = nil) ⇒ Object 



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# File 'lib/cagnut_gatk/base.rb', line 22

def realigner_target_creator dirs, order, previous_job_id, input = nil
  opts = { input: input, dirs: dirs, order: order }
  realigner_target_creator = CagnutGatk::RealignerTargetCreator.new opts
  realigner_target_creator.run previous_job_id
end

#unified_genotyper(dirs, order, previous_job_id, input) ⇒ Object 



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# File 'lib/cagnut_gatk/base.rb', line 64

def unified_genotyper dirs, order, previous_job_id, input
  opts = { input: input, dirs: dirs, order: order }
  unifiedgenotyper = CagnutGatk::UnifiedGenotyper.new opts
  unifiedgenotyper.run previous_job_id
end

#variant_eval(dirs, order, previous_job_id, input) ⇒ Object 



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# File 'lib/cagnut_gatk/base.rb', line 76

def variant_eval dirs, order, previous_job_id, input
  opts = { input: input, dirs: dirs, order: order }
  variant_eval = CagnutGatk::VariantEval.new opts
  variant_eval.run previous_job_id
end

#variant_filtration(dirs, order, previous_job_id, input) ⇒ Object 



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# File 'lib/cagnut_gatk/base.rb', line 70

def variant_filtration dirs, order, previous_job_id, input
  opts = { input: input, dirs: dirs, order: order }
  variant_filtration = CagnutGatk::VariantFiltration.new opts
  variant_filtration.run previous_job_id
end