class CagnutGatk::Base

Public Instance Methods

analyze_covariates(dirs, order, previous_job_id, input) click to toggle source
# 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) click to toggle source
# 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 = {}) click to toggle source
# 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) click to toggle source
# 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) click to toggle source
# 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) click to toggle source
# 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) click to toggle source
realigner_target_creator(dirs, order, previous_job_id, input = nil) click to toggle source
# 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) click to toggle source
# 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) click to toggle source
# 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) click to toggle source
# 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