added provisional write sam support

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2093 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_ruby/lib/maasha/sam.rb b/code_ruby/lib/maasha/sam.rb
index ba9ffb0ed255e476e210a3eb7fbcd33f0a4d494c..5ef7de5fbd99a134bff197070402c5fc7b2b5af8 100644 (file)
--- a/code_ruby/lib/maasha/sam.rb
+++ b/code_ruby/lib/maasha/sam.rb
@@ -1,4 +1,4 @@
-# Copyright (C) 2007-2011 Martin A. Hansen.
+# Copyright (C) 2007-2013 Martin A. Hansen.
 
 # This program is free software; you can redistribute it and/or
 # modify it under the terms of the GNU General Public License
@@ -80,16 +80,40 @@ class Sam < Filesys
     end
 
     if sam.has_key? :NM and sam[:NM].to_i > 0
+      bp[:NM] = sam[:NM]
+      bp[:MD] = sam[:MD]
       bp[:ALIGN] = self.align_descriptors(sam)
     end
 
     bp
   end
 
-  # Class method to convert a Biopiece record
-  # into a SAM entry.
-  def self.to_sam(bp)
-    "FISK" # FIXME
+  # Class method to create a new SAM entry from a Biopiece record.
+  # FIXME
+  def self.new_bp(bp)
+    qname = bp[:Q_ID]
+    flag  = 0
+    rname = bp[:S_ID]
+    pos   = bp[:S_BEG]
+    mapq  = bp[:MAPQ]
+    cigar = bp[:CIGAR]
+    rnext = bp[:Q_ID2]  || '*'
+    pnext = bp[:S_BEG2] || 0
+    tlen  = bp[:TLEN]   || 0
+    seq   = bp[:SEQ]
+    qual  = bp[:SCORES] || '*'
+    nm    = "NM:i:#{bp[:NM]}" if bp[:NM]
+    md    = "MD:Z:#{bp[:MD]}" if bp[:MD]
+
+    flag |= FLAG_REVCOMP if bp[:STRAND] == '+'
+
+    if qname && flag && rname && pos && mapq && cigar && rnext && pnext && tlen && seq && qual
+      ary = [qname, flag, rname, pos, mapq, cigar, rnext, pnext, tlen, seq, qual]
+      ary << nm if nm
+      ary << md if md
+      
+      ary.join("\t")
+    end
   end
 
   # Create alignment descriptors according to the KISS