class CagnutPicard::Util

Attributes

config[RW]
picard[RW]

Public Class Methods

new(config) click to toggle source
# 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) click to toggle source
# 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) click to toggle source
# 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) click to toggle source
# 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) click to toggle source
# 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) click to toggle source
# 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) click to toggle source
# 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) click to toggle source
# 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) click to toggle source
# 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) click to toggle source
# 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) click to toggle source
# 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