Class: Bio::Picard

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/picard.rb,
lib/bio/picard/version.rb

Constant Summary collapse

VERSION = 
"1.131.5"

Instance Method Summary collapse

Constructor Details

#initialize(*java_options) ⇒ Picard

instantiate Picard command tools

Parameters:

  • path (String) —

    path to picard.jar



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# File 'lib/bio/picard.rb', line 9

def initialize(*java_options)
  @java_options = java_options.join(' ')
  @picard = File.join(File.expand_path(File.dirname(__FILE__)), 'picard', 'external', 'picard.jar')
end

Instance Method Details

#run(command, *options) ⇒ Object

run picard tools for command and all options please go to broadinstitute.github.io/picard/command-line-overview.html

Parameters:

  • command (String) —

    Picard command

  • options (Array) —

    of Picard command



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# File 'lib/bio/picard.rb', line 19

def run(command, *options)
  `java #{@java_options == '' ? '' : "#{@java_options.chomp} "}-jar #{@picard} #{command} #{options.flatten.join(' ')}`
end