polymarker.rb in bio-polyploid-tools-0.2.3

- old
+ new

@@ -85,11 +85,11 @@
 snps = Array.new
 
 #0. Load the fasta index 
 fasta_reference_db = nil
 if fasta_reference
-  fasta_reference_db = Bio::DB::Fasta::FastaFile.new(fasta_reference)
+  fasta_reference_db = Bio::DB::Fasta::FastaFile.new({:fasta=>fasta_reference})
   fasta_reference_db.load_fai_entries
   p "Fasta reference: #{fasta_reference}"
 end
 
 
@@ -139,10 +139,10 @@
 contigs_f = File.open(temp_contigs, "w")
 filename=path_to_contigs 
 puts filename
 target=filename
 
-fasta_file = Bio::DB::Fasta::FastaFile.new(target)
+fasta_file = Bio::DB::Fasta::FastaFile.new({:fasta=>target})
 fasta_file.load_fai_entries
 
 found_cointigs = Set.new
 Bio::DB::Exonerate.align({:query=>temp_fasta_query, :target=>target, :model=>model}) do |aln|
   if aln.identity > min_identity