cleanup of findsim.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 3bd71ac55e2408643ca10ba6d8f3c3ec2786d8e9..ba9ffb0ed255e476e210a3eb7fbcd33f0a4d494c 100644 (file)
--- a/code_ruby/lib/maasha/sam.rb
+++ b/code_ruby/lib/maasha/sam.rb
@@ -63,6 +63,7 @@ class Sam < Filesys
     bp[:STRAND]   = sam[:FLAG].revcomp? ? '-' : '+'
     bp[:S_ID]     = sam[:RNAME]
     bp[:S_BEG]    = sam[:POS]
+    bp[:S_END]    = sam[:POS] + sam[:SEQ].length - 1
     bp[:MAPQ]     = sam[:MAPQ]
     bp[:CIGAR]    = sam[:CIGAR].to_s
 
@@ -475,58 +476,58 @@ class Sam < Filesys
     # Method to test if template have
     # multiple fragments in sequencing.
     def multi?
-      flag & FLAG_MULTI
+      (flag & FLAG_MULTI) == 0
     end
 
     # Method to test if each fragment
     # properly aligned according to the aligner.
     def aligned?
-      flag & FLAG_ALIGNED 
+      (flag & FLAG_ALIGNED) == 0
     end
     
     # Method to test if the fragment was unmapped.
     def unmapped?
-      flag & FLAG_UNMAPPED
+      (flag & FLAG_UNMAPPED) == 0
     end
 
     # Method to test if the next fragment was unmapped.
     def next_unmapped?
-      flag & FLAG_NEXT_UNMAPPED
+      (flag & FLAG_NEXT_UNMAPPED) == 0
     end
 
     # Method to test if the fragment was reverse complemented.
     def revcomp?
-      flag & FLAG_REVCOMP
+      (flag & FLAG_REVCOMP) == 0
     end
 
     # Method to test if the next fragment was reverse complemented.
     def next_revcomp?
-      flag & FLAG_NEXT_REVCOMP
+      (flag & FLAG_NEXT_REVCOMP) == 0
     end
 
     # Method to test if the fragment was first in the template.
     def first?
-      flag & FLAG_FIRST
+      (flag & FLAG_FIRST) == 0
     end
 
     # Method to test if the fragment was last in the template.
     def last?
-      flag & FLAG_LAST
+      (flag & FLAG_LAST) == 0
     end
 
     # Method to test for secondary alignment.
     def secondary_alignment?
-      flag & FLAG_SECONDARY_ALIGNMENT
+      (flag & FLAG_SECONDARY_ALIGNMENT) == 0
     end
 
     # Method to test for quality fail.
     def quality_fail?
-      flag & FLAG_QUALITY_FAIL
+      (flag & FLAG_QUALITY_FAIL) == 0
     end
 
     # Method to test for PCR or optical duplicates.
     def duplicates?
-      flag & FLAG_DUPLICATES
+      (flag & FLAG_DUPLICATES) == 0
     end
   end
 end