class CagnutPicard::Base
Public Instance Methods
add_or_replace_readgroups(dirs, order, previous_job_id = nil, input = nil)
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# File lib/cagnut_picard/base.rb, line 14 def add_or_replace_readgroups dirs, order, previous_job_id = nil, input = nil opts = { input: input, dirs: dirs, order: order } CagnutPicard::AddOrReplaceReadGroups.new(opts).run previous_job_id end
build_bam_index(dirs, order, previous_job_id, input)
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# File lib/cagnut_picard/base.rb, line 24 def build_bam_index dirs, order, previous_job_id, input opts = { input: input, dirs: dirs, order: order } CagnutPicard::BuildBamIndex.new(opts).run previous_job_id end
collect_gc_bias_metrics(dirs, order, previous_job_id, input)
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# File lib/cagnut_picard/base.rb, line 39 def collect_gc_bias_metrics dirs, order, previous_job_id, input opts = { input: input, dirs: dirs, order: order } CagnutPicard::CollectGcBiasMetrics.new(opts).run previous_job_id end
collect_insert_size_metrics(dirs, order, previous_job_id, input)
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# File lib/cagnut_picard/base.rb, line 44 def collect_insert_size_metrics dirs, order, previous_job_id, input opts = { input: input, dirs: dirs, order: order } CagnutPicard::CollectInsertSizeMetrics.new(opts).run previous_job_id end
collect_multiple_metrics(dirs, order, previous_job_id, input)
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# File lib/cagnut_picard/base.rb, line 54 def collect_multiple_metrics dirs, order, previous_job_id, input opts = { input: input, dirs: dirs, order: order } CagnutPicard::CollectMultipleMetrics.new(opts).run previous_job_id end
markdup(dirs, order, previous_job_id, input = nil)
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# File lib/cagnut_picard/base.rb, line 19 def markdup dirs, order, previous_job_id, input = nil opts = { input: input, dirs: dirs, order: order } CagnutPicard::Markdup.new(opts).run previous_job_id end
mean_quality_by_cycle(dirs, order, previous_job_id, input)
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# File lib/cagnut_picard/base.rb, line 29 def mean_quality_by_cycle dirs, order, previous_job_id, input opts = { input: input, dirs: dirs, order: order } CagnutPicard::MeanQualityByCycle.new(opts).run previous_job_id end
quality_score_distribution(dirs, order, previous_job_id, input)
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# File lib/cagnut_picard/base.rb, line 34 def quality_score_distribution dirs, order, previous_job_id, input opts = { input: input, dirs: dirs, order: order } CagnutPicard::QualityScoreDistribution.new(opts).run previous_job_id end
sort_sam(dirs, order, previous_job_id, input = nil)
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# File lib/cagnut_picard/base.rb, line 49 def sort_sam dirs, order, previous_job_id, input = nil opts = { input: input, dirs: dirs, order: order } CagnutPicard::SortSam.new(opts).run previous_job_id end