From 4456ec65a7c2050c3c9494ed4ec0fc97897fb8a2 Mon Sep 17 00:00:00 2001 From: martinahansen Date: Wed, 31 Aug 2011 13:14:11 +0000 Subject: [PATCH] sam update git-svn-id: http://biopieces.googlecode.com/svn/trunk@1504 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/read_fastq | 2 +- code_ruby/test/maasha/test_sam.rb | 58 ------------------------------- 2 files changed, 1 insertion(+), 59 deletions(-) diff --git a/bp_bin/read_fastq b/bp_bin/read_fastq index 51dd56b..923a3b0 100755 --- 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 31cb59f..d36e9ad 100755 --- 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 -- 2.39.2