From ab27a5274bf40c61fa32065454f038a7f92d0e10 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Mon, 5 Sep 2011 13:34:21 +0000
Subject: [PATCH] polishing on sam.rb

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1515 74ccb610-7750-0410-82ae-013aeee3265d
---
 code_ruby/lib/maasha/sam.rb       | 21 ++++++++++++++-------
 code_ruby/test/maasha/test_sam.rb | 18 ++++++++++++++++++
 2 files changed, 32 insertions(+), 7 deletions(-)

diff --git a/code_ruby/lib/maasha/sam.rb b/code_ruby/lib/maasha/sam.rb
index a122cc7..7f4712b 100644
--- a/code_ruby/lib/maasha/sam.rb
+++ b/code_ruby/lib/maasha/sam.rb
@@ -59,12 +59,12 @@ class Sam < Filesys
     bp = {}
 
     bp[:REC_TYPE] = 'SAM'
-    bp[:Q_ID]   = sam[:QNAME]
-    bp[:STRAND] = sam[:FLAG].revcomp? ? '-' : '+'
-    bp[:S_ID]   = sam[:RNAME]
-    bp[:S_BEG]  = sam[:POS]
-    bp[:MAPQ]   = sam[:MAPQ]
-    bp[:CIGAR]  = sam[:CIGAR]
+    bp[:Q_ID]     = sam[:QNAME]
+    bp[:STRAND]   = sam[:FLAG].revcomp? ? '-' : '+'
+    bp[:S_ID]     = sam[:RNAME]
+    bp[:S_BEG]    = sam[:POS]
+    bp[:MAPQ]     = sam[:MAPQ]
+    bp[:CIGAR]    = sam[:CIGAR].to_s
 
     unless sam[:RNEXT] == '*'
       bp[:Q_ID2]  = sam[:RNEXT]
@@ -85,7 +85,14 @@ class Sam < Filesys
     bp
   end
 
-  # Create align descriptors according to the KISS format description:
+  # Class method to convert a Biopiece record
+  # into a SAM entry.
+  def self.to_sam(bp)
+    "FISK"
+  end
+
+  # Create alignment descriptors according to the KISS
+  # format description:
   # http://code.google.com/p/biopieces/wiki/KissFormat
   def self.align_descriptors(sam)
     offset     = 0
diff --git a/code_ruby/test/maasha/test_sam.rb b/code_ruby/test/maasha/test_sam.rb
index d36e9ad..d02d710 100755
--- a/code_ruby/test/maasha/test_sam.rb
+++ b/code_ruby/test/maasha/test_sam.rb
@@ -345,5 +345,23 @@ class SamTest < Test::Unit::TestCase
     sam = Sam.new(StringIO.new("@SQ\tSN:ref\tLN:45\n*\t*\t*\t*\t*\t*\tref\t*\t\*\t*\t*\n"))
     assert_nothing_raised { sam.each }
   end
+
+  def test_Sam_to_bp_returns_correctly
+    string = "ID00036734\t0\tgi48994873\t366089\t37\t37M1I62M\t*\t0\t0\tGTTCCGCTATCGGCTGAATTTGATTGCGAGTGAGATATTTTATGCCAGCCAGCCAGACGCAGACGCGCCGAGACAGAACTTAATGGGCCCGCTAACAGCG\t*\tXT:A:U\tNM:i:1\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:1\tXG:i:1\tMD:Z:99\n"
+
+    sam = Sam.new(StringIO.new(string))
+
+    sam.each do |s|
+      assert_equal("SAM", Sam.to_bp(s)[:REC_TYPE])
+      assert_equal("ID00036734", Sam.to_bp(s)[:Q_ID])
+      assert_equal("-", Sam.to_bp(s)[:STRAND])
+        assert_equal("gi48994873", Sam.to_bp(s)[:S_ID])
+      assert_equal(366089, Sam.to_bp(s)[:S_BEG])
+      assert_equal(37, Sam.to_bp(s)[:MAPQ])
+      assert_equal("37M1I62M", Sam.to_bp(s)[:CIGAR])
+      assert_equal("GTTCCGCTATCGGCTGAATTTGATTGCGAGTGAGATATTTTATGCCAGCCAGCCAGACGCAGACGCGCCGAGACAGAACTTAATGGGCCCGCTAACAGCG", Sam.to_bp(s)[:SEQ])
+      assert_equal("37:->T", Sam.to_bp(s)[:ALIGN])
+    end
+  end
 end
 
-- 
2.39.2