sam update

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1504 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/read_fastq b/bp_bin/read_fastq
index 51dd56b916ffb62f864fa5ca62fee1429c958bfe..923a3b057c7198b9792a799fa82e4b2102d26f8a 100755 (executable)
--- a/bp_bin/read_fastq
+++ b/bp_bin/read_fastq
@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 
-# Copyright (C) 2007-2010 Martin A. Hansen.
+# Copyright (C) 2007-2011 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

diff --git a/code_ruby/test/maasha/test_sam.rb b/code_ruby/test/maasha/test_sam.rb
index 31cb59f167b28f05f39d3c8ecdd9f9b4305df88d..d36e9ad41295259b72515eadf4c9ac55196c9175 100755 (executable)
--- a/code_ruby/test/maasha/test_sam.rb
+++ b/code_ruby/test/maasha/test_sam.rb
@@ -246,19 +246,6 @@ class SamTest < Test::Unit::TestCase
     assert_nothing_raised { sam.each }
   end
 
-  def test_Sam_each_with_bad_cigar_raises
-    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t24\t*\t*\t*\t*\t*\n"))
-    assert_raise(SamError) { sam.each }
-  end
-
-  def test_Sam_each_with_ok_cigar_dont_raise
-    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t24M2I3D\t*\t*\t*\t*\t*\n"))
-    assert_nothing_raised { sam.each }
-
-    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t*\t*\t*\t*\t*\t*\n"))
-    assert_nothing_raised { sam.each }
-  end
-
   def test_Sam_each_with_bad_rnext_raises
     sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t*\t \t*\t*\t*\t*\n"))
     assert_raise(SamError) { sam.each }
@@ -358,50 +345,5 @@ 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_each_with_bad_cigar_hard_clip_raises
-    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t1M1H1M\t*\t*\t\*\tAAA\t*\n"))
-    assert_raise(SamError) { sam.each }
-
-    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t1H1M1H1M\t*\t*\t\*\tAAA\t*\n"))
-    assert_raise(SamError) { sam.each }
-
-    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t1M1H1M1H\t*\t*\t\*\tAAA\t*\n"))
-    assert_raise(SamError) { sam.each }
-  end
-
-  def test_Sam_each_with_ok_cigar_hard_clip_dont_raise
-    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t1H1M\t*\t*\t\*\tA\t*\n"))
-    assert_nothing_raised { sam.each }
-
-    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t1M1H\t*\t*\t\*\tA\t*\n"))
-    assert_nothing_raised { sam.each }
-
-    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t1H1M1H\t*\t*\t\*\tA\t*\n"))
-    assert_nothing_raised { sam.each }
-  end
-
-  def test_Sam_each_with_bad_cigar_soft_clip_raises
-    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t1M1S1M\t*\t*\t\*\tA\t*\n"))
-    assert_raise(SamError) { sam.each }
-  end
-
-  def test_Sam_each_with_ok_cigar_soft_clip_dont_raise
-    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t1S1M\t*\t*\t\*\tAA\t*\n"))
-    assert_nothing_raised { sam.each }
-
-    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t1H1S1M\t*\t*\t\*\tAA\t*\n"))
-    assert_nothing_raised { sam.each }
-  end
-
-  def test_Sam_each_with_bad_cigar_length_raise
-    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t6M\t*\t*\t\*\tAAAAA\t*\n"))
-    assert_raise(SamError) { sam.each }
-  end
-
-  def test_Sam_each_with_ok_cigar_length_dont_raise
-    sam = Sam.new(StringIO.new("*\t*\t*\t*\t*\t6M\t*\t*\t\*\tAAAAAA\t*\n"))
-    assert_nothing_raised { sam.each }
-  end
 end