worked on unit tests for sam.rb

[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 3ffc56d361c8c92e474c23a23d0699df0421bcd5..f29e6219fb72cf12ddbfbdeeeb3b1b4f1424218c 100644 (file)
--- a/code_ruby/lib/maasha/sam.rb
+++ b/code_ruby/lib/maasha/sam.rb
@@ -248,19 +248,17 @@ class Sam < Filesys
     seq   = fields[9]
     qual  = fields[10]
 
-    raise SamError, "Bad qname: #{qname}" unless qname =~ /^[!-?A-~]{1,255}$/
-    raise SamError, "Bad flag: #{flag}"   unless (0 .. 2**16 - 1).include? flag
-    raise SamError, "Bad rname: #{rname}" unless rname =~ /^(\*|[!-()+-<>-~][!-~]*)$/
-    raise SamError, "Bad pos: #{pos}"     unless (0 .. 2**29 - 1).include? pos
-    raise SamError, "Bad mapq: #{mapq}"   unless (0 .. 2**8 - 1).include? mapq
-    raise SamError, "Bad cigar: #{cigar}" unless cigar =~ /^(\*|([0-9]+[MIDNSHPX=])+)$/
-    raise SamError, "Bad rnext: #{rnext}" unless rnext =~ /^(\*|=|[!-()+-<>-~][!-~]*)$/
-    raise SamError, "Bad pnext: #{pnext}" unless (0 .. 2**29 - 1).include? pnext
-    raise SamError, "Bad tlen: #{tlen}"   unless (-2**29 + 1 .. 2**29 - 1).include? tlen
-    raise SamError, "Bad seq: #{seq}"     unless seq  =~ /^(\*|[A-Za-z=.]+)$/
-    raise SamError, "Bad qual: #{qual}"   unless qual =~ /^[!-~]+$/
-
+    check_qname(qname)
+    check_flag(flag)
     check_rname(rname)
+    check_pos(pos)
+    check_mapq(mapq)
+    check_cigar(cigar)
+    check_rnext(rnext)
+    check_pnext(pnext)
+    check_tlen(tlen)
+    check_seq(seq)
+    check_qual(qual)
 
     entry = {}
     entry[:QNAME] = qname
@@ -272,16 +270,28 @@ class Sam < Filesys
     entry[:RNEXT] = rnext
     entry[:PNEXT] = pnext
     entry[:TLEN]  = tlen
-    entry[:SEQ]   = seq
+    entry[:SEQ]   = Seq.new(qname, seq)
     entry[:QUAL]  = qual
 
     entry
   end
 
+  # Method to check qname.
+  def check_qname(qname)
+    raise SamError, "Bad qname: #{qname}" unless qname =~ /^[!-?A-~]{1,255}$/
+  end
+
+  # Method to check flag.
+  def check_flag(flag)
+    raise SamError, "Bad flag: #{flag}" unless (0 .. 2**16 - 1).include? flag
+  end
+
   # Method to check if rname, when not '*' and
   # @SQ header lines are present, is located in
   # the header hash.
   def check_rname(rname)
+    raise SamError, "Bad rname: #{rname}" unless rname =~ /^(\*|[!-()+-<>-~][!-~]*)$/
+
     unless @header.empty? or rname == '*'
       unless @header[:SQ][:SN].has_key? rname.to_sym
         raise SamError, "rname not found in header hash: #{rname}"
@@ -289,16 +299,53 @@ class Sam < Filesys
     end
   end
 
+  # Method to check pos.
+  def check_pos(pos)
+    raise SamError, "Bad pos: #{pos}" unless (0 .. 2**29 - 1).include? pos
+  end
+
+  # Method to check mapq.
+  def check_mapq(mapq)
+    raise SamError, "Bad mapq: #{mapq}"   unless (0 .. 2**8 - 1).include? mapq
+  end
+
+  # Method to check cigar.
+  def check_cigar(cigar)
+    raise SamError, "Bad cigar: #{cigar}" unless cigar =~ /^(\*|([0-9]+[MIDNSHPX=])+)$/
+  end
+
   # Method to check if rnext, when not '*' or '='
   # and @SQ header lines are present, is located
   # in the header hash.
   def check_rnext(rnext)
+    raise SamError, "Bad rnext: #{rnext}" unless rnext =~ /^(\*|=|[!-()+-<>-~][!-~]*)$/
+
     unless @header.empty? or rnext == '*' or rnext == '='
       unless @header[:SQ][:SN].has_key? rnext.to_sym
         raise SamError, "rnext not found in header hash: #{rnext}"
       end
     end
   end
+
+  # Method to check pnext.
+  def check_pnext(pnext)
+    raise SamError, "Bad pnext: #{pnext}" unless (0 .. 2**29 - 1).include? pnext
+  end
+
+  # Method to check tlen.
+  def check_tlen(tlen)
+    raise SamError, "Bad tlen: #{tlen}"   unless (-2**29 + 1 .. 2**29 - 1).include? tlen
+  end
+
+  # Method to check seq.
+  def check_seq(seq)
+    raise SamError, "Bad seq: #{seq}"     unless seq  =~ /^(\*|[A-Za-z=.]+)$/
+  end
+
+  # Method to check qual.
+  def check_qual(qual)
+    raise SamError, "Bad qual: #{qual}"   unless qual =~ /^[!-~]+$/
+  end
 end