class CagnutPicard::Util
Attributes
config[RW]
picard[RW]
Public Class Methods
new(config)
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# File lib/cagnut_picard/util.rb, line 5 def initialize config @config = config @picard = CagnutPicard::Base.new end
Public Instance Methods
add_or_replace_readgroups(dirs, order, previous_job_id, filename)
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# File lib/cagnut_picard/util.rb, line 10 def add_or_replace_readgroups dirs, order, previous_job_id, filename job_name, filename = picard.add_or_replace_readgroups dirs, order, previous_job_id, filename [job_name, filename, order+1] end
build_bam_index(dirs, order=1, previous_job_id=nil, filename=nil)
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# File lib/cagnut_picard/util.rb, line 20 def build_bam_index dirs, order=1, previous_job_id=nil, filename=nil job_name = picard.build_bam_index dirs, order, previous_job_id, filename [job_name, order+1] end
collect_gc_bias_metrics(dirs, order, previous_job_id, filename)
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# File lib/cagnut_picard/util.rb, line 42 def collect_gc_bias_metrics dirs, order, previous_job_id, filename picard.collect_gc_bias_metrics dirs, order, previous_job_id, filename order+1 end
collect_insert_size_metrics(dirs, order, previous_job_id, filename)
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# File lib/cagnut_picard/util.rb, line 47 def collect_insert_size_metrics dirs, order, previous_job_id, filename picard.collect_insert_size_metrics dirs, order, previous_job_id, filename order+1 end
collect_multiple_metrics(dirs, order=1, previous_job_id, filename)
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# File lib/cagnut_picard/util.rb, line 57 def collect_multiple_metrics dirs, order=1, previous_job_id, filename picard.collect_multiple_metrics dirs, order, previous_job_id, filename order+1 end
markdup(dirs, order=1, previous_job_id=nil, filename=nil)
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# File lib/cagnut_picard/util.rb, line 15 def markdup dirs, order=1, previous_job_id=nil, filename=nil job_name, filename = picard.markdup dirs, order, previous_job_id, filename [job_name, filename, order+1] end
mean_quality_by_cycle(dirs, order, previous_job_id, filename)
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# File lib/cagnut_picard/util.rb, line 32 def mean_quality_by_cycle dirs, order, previous_job_id, filename picard.mean_quality_by_cycle dirs, order, previous_job_id, filename order+1 end
picard_qc_metrics(dirs, order, previous_job_id, filename)
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# File lib/cagnut_picard/util.rb, line 25 def picard_qc_metrics dirs, order, previous_job_id, filename order = mean_quality_by_cycle dirs, order, previous_job_id, filename order = quality_score_distribution dirs, order, previous_job_id, filename order = collect_gc_bias_metrics dirs, order, previous_job_id, filename collect_insert_size_metrics dirs, order, previous_job_id, filename end
quality_score_distribution(dirs, order, previous_job_id, filename)
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# File lib/cagnut_picard/util.rb, line 37 def quality_score_distribution dirs, order, previous_job_id, filename picard.quality_score_distribution dirs, order, previous_job_id, filename order+1 end
sort_sam(dirs, order=1, previous_job_id, filename)
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# File lib/cagnut_picard/util.rb, line 52 def sort_sam dirs, order=1, previous_job_id, filename job_name, filename = picard.sort_sam dirs, order, previous_job_id, filename [job_name, filename, order+1] end