module CagnutSamtools::CheckTools
Public Instance Methods
check_samtools(path)
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# File lib/cagnut_samtools/check_tools.rb, line 9 def check_samtools path check_tool_ver 'Samtools' do `#{path} --version 2>&1| grep samtools | cut -f2 -d ' '` if path end end
check_samtools_index(ref_path)
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# File lib/cagnut_samtools/check_tools.rb, line 15 def check_samtools_index ref_path puts 'Checking Samtools Reference Index Files...' tool = 'Samtools Index' file = "#{ref_path}.fai" command = "#{@config['tools']['samtools']} faidx #{ref_path}" check_ref_related file, tool, command end
check_tool(tools_path, refs)
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Calls superclass method
# File lib/cagnut_samtools/check_tools.rb, line 3 def check_tool tools_path, refs super if defined?(super) ver = check_samtools tools_path['samtools'] check_samtools_index refs['ref_fasta'] if !ver.blank? end