class Bio::WS::BAM

Public Class Methods

new(app = nil, params = {}) click to toggle source
Calls superclass method
# File lib/bio-samtools-server/samtools-server.rb, line 7
def initialize(app = nil, params = {})
  super(app)
  @bootstrap = params.fetch(:bootstrap, false)
  @bam_files = Hash.new
end

Public Instance Methods

get_bam(bam,reference) click to toggle source
# File lib/bio-samtools-server/samtools-server.rb, line 13
def get_bam(bam,reference)
  return @bam_files[bam] if @bam_files[bam] 
  
  bam_path = "#{self.settings.folder.to_s}/#{bam}.bam"
  reference_path =  "#{self.settings.reference.to_s}/#{reference}"
  return nil unless File.file?(bam_path)
  @bam_files[bam] = Bio::DB::Sam.new( 
      :fasta =>  reference_path,
      :bam => bam_path
  )
  
  return @bam_files[bam] 
end