Class: CagnutPicard::Util

Inherits:
Object
  • Object
show all
Defined in:
lib/cagnut_picard/util.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(config) ⇒ Util

Returns a new instance of Util.



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# File 'lib/cagnut_picard/util.rb', line 5

def initialize config
  @config = config
  @picard = CagnutPicard::Base.new
end

Instance Attribute Details

#config ⇒ Object

Returns the value of attribute config.



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# File 'lib/cagnut_picard/util.rb', line 3

def config
  @config
end

#picard ⇒ Object

Returns the value of attribute picard.



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# File 'lib/cagnut_picard/util.rb', line 3

def picard
  @picard
end

Instance Method Details

#add_or_replace_readgroups(dirs, order, previous_job_id, filename) ⇒ Object 



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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) ⇒ Object 



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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) ⇒ Object 



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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) ⇒ Object 



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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) ⇒ Object 



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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) ⇒ Object 



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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) ⇒ Object 



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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) ⇒ Object 



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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) ⇒ Object 



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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) ⇒ Object 



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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