class CagnutBwa::Util

Attributes

bwa[RW]
config[RW]

Public Class Methods

new(config) click to toggle source
# File lib/cagnut_bwa/util.rb, line 5
def initialize config
  @config = config
  @bwa = CagnutBwa::Base.new
end

Public Instance Methods

aln(dirs, order=1, previous_job_id = nil, filename=nil) click to toggle source
# File lib/cagnut_bwa/util.rb, line 20
def aln dirs, order=1, previous_job_id = nil, filename=nil
  job_name = bwa.aln dirs, order, previous_job_id, filename
  [job_name, order+1]
end
aln_one_fastq(dirs, order=1, filename=nil) click to toggle source
# File lib/cagnut_bwa/util.rb, line 10
def aln_one_fastq dirs, order=1, filename=nil
  job_name = bwa.aln_one_fastq dirs, order, filename
  [job_name, order+1]
end
mem(dirs, order=1, filename = nil) click to toggle source
# File lib/cagnut_bwa/util.rb, line 30
def mem dirs, order=1, filename = nil
  job_name, filename = bwa.mem dirs, order, filename
  [job_name, filename, order+1]
end
samp(dirs, order=1, previous_job_id=nil, filename=nil) click to toggle source
# File lib/cagnut_bwa/util.rb, line 25
def samp dirs, order=1, previous_job_id=nil, filename=nil
  job_name, filename = bwa.samp dirs, order, previous_job_id, filename
  [job_name, filename, order+1]
end
samp_one_fastq(dirs, order=1, previous_job_id=nil, filename=nil) click to toggle source
# File lib/cagnut_bwa/util.rb, line 15
def samp_one_fastq dirs, order=1, previous_job_id=nil, filename=nil
  job_name, filename = bwa.samp_one_fastq dirs, order, previous_job_id, filename
  [job_name, filename, order+1]
end