fixed method name change

[biopieces.git] / code_ruby / lib / maasha / sam.rb

diff --git a/code_ruby/lib/maasha/sam.rb b/code_ruby/lib/maasha/sam.rb
index 074b999aa58589ea962356655c7f3262ab3b05a3..8772e6382f20913d2fca3c9076b90475d2824564 100644 (file)
--- a/code_ruby/lib/maasha/sam.rb
+++ b/code_ruby/lib/maasha/sam.rb
@@ -76,7 +76,7 @@ class Sam < Filesys
     bp[:SEQ]      = sam[:SEQ].seq
 
     unless sam[:SEQ].qual.nil?
-      bp[:SCORES] = sam[:SEQ].convert_phred2illumina!.qual
+      bp[:SCORES] = sam[:SEQ].qual_convert!(:base_33, :base_64).qual
     end
 
     if sam[:NM] and sam[:NM].to_i > 0
@@ -393,7 +393,7 @@ class Sam < Filesys
     entry[:RNEXT] = rnext
     entry[:PNEXT] = pnext
     entry[:TLEN]  = tlen
-    entry[:SEQ]   = (qual == '*') ? Seq.new(qname, seq) : Seq.new(qname, seq, qual)
+    entry[:SEQ]   = (qual == '*') ? Seq.new(seq_name: qname, seq: seq) : Seq.new(seq_name: qname, seq: seq, qual: qual)
     entry[:QUAL]  = qual
 
     # Optional fields - where some are really important! HATE HATE HATE SAM!!!