From 67a55ed9c6cd5c4ad11adb68ae18949cffcd8f59 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Wed, 24 Aug 2011 21:03:15 +0000
Subject: [PATCH] worked on unit tests for sam.rb
git-svn-id: http://biopieces.googlecode.com/svn/trunk@1499 74ccb610-7750-0410-82ae-013aeee3265d
---
code_ruby/lib/maasha/sam.rb | 5 +++++
1 file changed, 5 insertions(+)
diff --git a/code_ruby/lib/maasha/sam.rb b/code_ruby/lib/maasha/sam.rb
index 92b8d95..0161cd7 100644
--- a/code_ruby/lib/maasha/sam.rb
+++ b/code_ruby/lib/maasha/sam.rb
@@ -318,6 +318,11 @@ class Sam < Filesys
raise SamError, "Bad cigar with internal H: #{cigar}"
end
+ # Check cigar soft clipping only at ends or H.
+ if cigar.gsub(/^[0-9]+H|[0-9]+H$/, "").gsub(/^[0-9]+S|[0-9]+S$/, "").match('S')
+ raise SamError, "Bad cigar with internal S: #{cigar}"
+ end
+
# Check cigar length matches sequence length.
unless cigar == '*' or seq == '*'
cigar_len = 0
--
2.39.5