class CagnutGatk::Base
Public Instance Methods
analyze_covariates(dirs, order, previous_job_id, input)
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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)
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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 = {})
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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