class CagnutPicard::Base

Public Instance Methods

add_or_replace_readgroups(dirs, order, previous_job_id = nil, input = nil) click to toggle source
# 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) click to toggle source
# 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) click to toggle source
# 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) click to toggle source
# 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) click to toggle source
# 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) click to toggle source
# 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) click to toggle source
# 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) click to toggle source
# 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) click to toggle source
# 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