Class: CagnutPicard::Base

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

Instance Method Summary collapse

Instance Method Details

#add_or_replace_readgroups(dirs, order, previous_job_id = nil, input = nil) ⇒ Object 



14
15
16
17
 
# 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) ⇒ Object 



24
25
26
27
 
# 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) ⇒ Object 



39
40
41
42
 
# 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) ⇒ Object 



44
45
46
47
 
# 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) ⇒ Object 



54
55
56
57
 
# 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) ⇒ Object 



19
20
21
22
 
# 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) ⇒ Object 



29
30
31
32
 
# 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) ⇒ Object 



34
35
36
37
 
# 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) ⇒ Object 



49
50
51
52
 
# 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