lib/cheripic/regions.rb in cheripic-1.0.0 vs lib/cheripic/regions.rb in cheripic-1.1.0

@@ -2,35 +2,51 @@
 require 'bio-samtools'
 require 'forwardable'
 
 module Cheripic
 
+  # Custom error handling for Regions class
   class RegionsError < CheripicError; end
 
+  # An application of Bio::DB::Fasta object that lets to extract selected regions of the fasta entries
+  #
+  # @!attribute [r] reference_db
+  #   @return [Bio::DB::Fasta::FastaFile] indexed fasta object
+  # @!attribute [r] id_len
+  #   @return [Hash] a hash of fasta entry ids as keys and sequence length as values
   class Regions
 
     include Enumerable
     extend Forwardable
     def_delegators :@id_len, :each, :each_key, :each_value, :length, :[]
-    attr_accessor :reference_db, :id_len
+    attr_reader :reference_db, :id_len
 
+    # creates a Regions object using fasta
+    #
+    # @param assembly [String] path to a fasta file
     def initialize(assembly)
       @reference_db = Bio::DB::Fasta::FastaFile.new({:fasta=>assembly})
       @id_len = {}
       self.get_id_len
     end
 
+    # A method to extract fasta entry ids and length and make a hash
+    #
+    # @return [Hash] a hash of fasta entry ids as keys and sequence length as values
     def get_id_len
       @reference_db.load_fai_entries
       @reference_db.index.entries.each_entry do | entry |
         @id_len[entry.id] = entry.length
       end
     end
 
-    # for each id and position returns left and right sequence
-    # of pre-selected length
+    # A method to returns left and right sequence of specified length, for a provided id and position
+    # @note this method excludes the base at the position provided
+    # @param id [String]
+    # @param pos [Integer]
+    # @return [Array<String>]
     def fetch_seq(id, pos)
-      limit = Options.params.sel_seq_len + 1
+      limit = Options.sel_seq_len + 1
       len = @id_len[id]
       low = pos-limit <= 0 ? 0 : pos-limit
       high = pos+limit >= len ? len : pos+limit
       region = Bio::DB::Fasta::Region.parse_region("#{id}:#{low}-#{pos-1}")
       seq_left = @reference_db.fetch_sequence(region)