bio-samtools 0.6.2 → 2.0.3
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/Gemfile +3 -2
- data/README.md +4 -7
- data/VERSION +1 -1
- data/bio-samtools.gemspec +47 -105
- data/doc/Bio.html +68 -131
- data/doc/Bio/DB.html +51 -111
- data/doc/Bio/DB/Alignment.html +135 -363
- data/doc/Bio/DB/Pileup.html +183 -170
- data/doc/Bio/DB/SAM.html +1396 -820
- data/doc/Bio/DB/SAM/Library.html +73 -123
- data/doc/Bio/DB/SAM/Tools.html +51 -273
- data/doc/Bio/DB/Tag.html +78 -124
- data/doc/Bio/DB/Vcf.html +111 -147
- data/doc/LICENSE_txt.html +113 -148
- data/doc/created.rid +9 -10
- data/doc/fonts.css +167 -0
- data/doc/fonts/Lato-Light.ttf +0 -0
- data/doc/fonts/Lato-LightItalic.ttf +0 -0
- data/doc/fonts/Lato-Regular.ttf +0 -0
- data/doc/fonts/Lato-RegularItalic.ttf +0 -0
- data/doc/fonts/SourceCodePro-Bold.ttf +0 -0
- data/doc/fonts/SourceCodePro-Regular.ttf +0 -0
- data/doc/images/add.png +0 -0
- data/doc/images/arrow_up.png +0 -0
- data/doc/images/delete.png +0 -0
- data/doc/images/tag_blue.png +0 -0
- data/doc/index.html +48 -54
- data/doc/js/darkfish.js +9 -22
- data/doc/js/search.js +20 -5
- data/doc/js/search_index.js +1 -1
- data/doc/rdoc.css +255 -218
- data/doc/table_of_contents.html +256 -137
- data/ext/Rakefile +57 -0
- data/lib/bio-samtools.rb +7 -2
- data/lib/bio/BIOExtensions.rb +89 -0
- data/lib/bio/db/alignment.rb +59 -0
- data/lib/bio/db/fastadb.rb +255 -0
- data/lib/bio/db/pileup.rb +221 -172
- data/lib/bio/db/sam.rb +639 -589
- data/lib/bio/db/sam/{faidx.rb → faidx_old.rb} +0 -0
- data/lib/bio/db/vcf.rb +69 -68
- data/test/.gitignore +1 -0
- data/test/{test_basic.rb → old_test_basic.rb} +33 -1
- data/test/samples/small/dupes.bam +0 -0
- data/test/samples/small/dupes.sam +274 -0
- data/test/samples/small/map_for_reheader.sam +8 -0
- data/test/samples/small/map_to_merge1.bam +0 -0
- data/test/samples/small/map_to_merge1.bam.bai +0 -0
- data/test/samples/small/map_to_merge1.sam +8 -0
- data/test/samples/small/map_to_merge2.bam +0 -0
- data/test/samples/small/map_to_merge2.bam.bai +0 -0
- data/test/samples/small/map_to_merge2.sam +8 -0
- data/test/samples/small/no_md.sam +8 -0
- data/test/samples/small/test_chr.fasta.1.bt2 +0 -0
- data/test/samples/small/test_chr.fasta.2.bt2 +0 -0
- data/test/samples/small/test_chr.fasta.3.bt2 +0 -0
- data/test/samples/small/test_chr.fasta.4.bt2 +0 -0
- data/test/samples/small/test_chr.fasta.rev.1.bt2 +0 -0
- data/test/samples/small/test_chr.fasta.rev.2.bt2 +0 -0
- data/test/samples/small/test_cov.svg +273 -0
- data/test/samples/small/testu.bam.bai +0 -0
- data/test/svg +133 -0
- data/test/test_pileup.rb +84 -0
- data/test/test_sam.rb +331 -0
- data/test/test_vcf.rb +11 -0
- data/{doc → tutorial}/tutorial.html +0 -0
- data/{doc → tutorial}/tutorial.pdf +0 -0
- metadata +56 -114
- data/doc/Bio/DB/SAM/Tools/Bam1CoreT.html +0 -159
- data/doc/Bio/DB/SAM/Tools/Bam1T.html +0 -220
- data/doc/Bio/DB/SAM/Tools/BamHeaderT.html +0 -249
- data/doc/Bio/DB/SAM/Tools/BamPileup1T.html +0 -159
- data/doc/Bio/DB/SAM/Tools/SamfileT.html +0 -171
- data/doc/Bio/DB/SAM/Tools/SamfileTX.html +0 -159
- data/doc/Bio/DB/SAMException.html +0 -205
- data/doc/LibC.html +0 -155
- data/doc/Pileup.html +0 -571
- data/doc/Vcf.html +0 -473
- data/doc/basic_styles.css +0 -31
- data/doc/classes/Bio.html +0 -139
- data/doc/classes/Bio/DB.html +0 -137
- data/doc/classes/Bio/DB/Alignment.html +0 -441
- data/doc/classes/Bio/DB/Alignment.src/M000012.html +0 -19
- data/doc/classes/Bio/DB/Alignment.src/M000013.html +0 -27
- data/doc/classes/Bio/DB/Alignment.src/M000014.html +0 -45
- data/doc/classes/Bio/DB/Alignment.src/M000015.html +0 -40
- data/doc/classes/Bio/DB/SAM.html +0 -510
- data/doc/classes/Bio/DB/SAM/Library.html +0 -135
- data/doc/classes/Bio/DB/SAM/Library.src/M000006.html +0 -28
- data/doc/classes/Bio/DB/SAM/Tools.html +0 -278
- data/doc/classes/Bio/DB/SAM/Tools.src/M000007.html +0 -20
- data/doc/classes/Bio/DB/SAM/Tools/Bam1CoreT.html +0 -111
- data/doc/classes/Bio/DB/SAM/Tools/Bam1T.html +0 -150
- data/doc/classes/Bio/DB/SAM/Tools/Bam1T.src/M000010.html +0 -20
- data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.html +0 -169
- data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000008.html +0 -19
- data/doc/classes/Bio/DB/SAM/Tools/BamHeaderT.src/M000009.html +0 -18
- data/doc/classes/Bio/DB/SAM/Tools/BamPileup1T.html +0 -111
- data/doc/classes/Bio/DB/SAM/Tools/SamfileT.html +0 -129
- data/doc/classes/Bio/DB/SAM/Tools/SamfileTX.html +0 -111
- data/doc/classes/Bio/DB/SAMException.html +0 -140
- data/doc/classes/Bio/DB/SAMException.src/M000016.html +0 -18
- data/doc/classes/Bio/DB/Sam.src/M000017.html +0 -43
- data/doc/classes/Bio/DB/Sam.src/M000018.html +0 -42
- data/doc/classes/Bio/DB/Sam.src/M000019.html +0 -18
- data/doc/classes/Bio/DB/Sam.src/M000020.html +0 -22
- data/doc/classes/Bio/DB/Sam.src/M000021.html +0 -19
- data/doc/classes/Bio/DB/Sam.src/M000022.html +0 -25
- data/doc/classes/Bio/DB/Sam.src/M000023.html +0 -28
- data/doc/classes/Bio/DB/Sam.src/M000024.html +0 -28
- data/doc/classes/Bio/DB/Sam.src/M000025.html +0 -46
- data/doc/classes/Bio/DB/Sam.src/M000026.html +0 -24
- data/doc/classes/Bio/DB/Sam.src/M000027.html +0 -19
- data/doc/classes/Bio/DB/Sam.src/M000028.html +0 -24
- data/doc/classes/Bio/DB/Sam.src/M000029.html +0 -41
- data/doc/classes/Bio/DB/Sam.src/M000030.html +0 -31
- data/doc/classes/Bio/DB/Sam.src/M000031.html +0 -86
- data/doc/classes/Bio/DB/Sam.src/M000032.html +0 -34
- data/doc/classes/Bio/DB/Tag.html +0 -160
- data/doc/classes/Bio/DB/Tag.src/M000011.html +0 -21
- data/doc/classes/LibC.html +0 -105
- data/doc/classes/Pileup.html +0 -374
- data/doc/classes/Pileup.src/M000001.html +0 -34
- data/doc/classes/Pileup.src/M000002.html +0 -21
- data/doc/classes/Pileup.src/M000003.html +0 -21
- data/doc/classes/Pileup.src/M000004.html +0 -21
- data/doc/classes/Pileup.src/M000005.html +0 -31
- data/doc/files/lib/bio-samtools_rb.html +0 -109
- data/doc/files/lib/bio/db/sam/bam_rb.html +0 -108
- data/doc/files/lib/bio/db/sam/faidx_rb.html +0 -108
- data/doc/files/lib/bio/db/sam/library_rb.html +0 -101
- data/doc/files/lib/bio/db/sam/pileup_rb.html +0 -178
- data/doc/files/lib/bio/db/sam/sam_rb.html +0 -113
- data/doc/files/lib/bio/db/sam_rb.html +0 -111
- data/doc/fr_class_index.html +0 -43
- data/doc/fr_file_index.html +0 -33
- data/doc/fr_method_index.html +0 -58
- data/doc/lib/bio-samtools_rb.html +0 -115
- data/doc/lib/bio/db/pileup_rb.html +0 -171
- data/doc/lib/bio/db/sam/bam_rb.html +0 -121
- data/doc/lib/bio/db/sam/faidx_rb.html +0 -117
- data/doc/lib/bio/db/sam/library_rb.html +0 -115
- data/doc/lib/bio/db/sam/pileup_rb.html +0 -171
- data/doc/lib/bio/db/sam/sam_rb.html +0 -121
- data/doc/lib/bio/db/sam/vcf_rb.html +0 -124
- data/doc/lib/bio/db/sam_rb.html +0 -115
- data/doc/lib/bio/db/vcf_rb.html +0 -124
- data/doc/rdoc-style.css +0 -208
- data/lib/bio/db/sam/bam.rb +0 -210
- data/lib/bio/db/sam/sam.rb +0 -86
- data/test/samples/pipe_char/test.bam +0 -0
- data/test/samples/pipe_char/test.bam.bai +0 -0
- data/test/samples/pipe_char/test.tam +0 -10
- data/test/samples/pipe_char/test_chr.fasta +0 -1000
- data/test/samples/pipe_char/test_chr.fasta.fai +0 -1
- data/test/samples/small/test +0 -0
- data/test/samples/small/test.bam +0 -0
- data/test/samples/small/test.fa +0 -20
- data/test/samples/small/test.fai +0 -0
|
@@ -1,19 +0,0 @@
|
|
|
1
|
-
<?xml version="1.0" encoding="iso-8859-1"?>
|
|
2
|
-
<!DOCTYPE html
|
|
3
|
-
PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
|
|
4
|
-
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
5
|
-
|
|
6
|
-
<html>
|
|
7
|
-
<head>
|
|
8
|
-
<title>text= (Bio::DB::SAM::Tools::BamHeaderT)</title>
|
|
9
|
-
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
|
|
10
|
-
<link rel="stylesheet" href="../../../../../.././rdoc-style.css" type="text/css" media="screen" />
|
|
11
|
-
</head>
|
|
12
|
-
<body class="standalone-code">
|
|
13
|
-
<pre><span class="ruby-comment cmt"># File lib/bio/db/sam/sam.rb, line 38</span>
|
|
14
|
-
<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">text=</span>(<span class="ruby-identifier">str</span>)
|
|
15
|
-
<span class="ruby-ivar">@text</span> = <span class="ruby-constant">FFI</span><span class="ruby-operator">::</span><span class="ruby-constant">MemoryPointer</span>.<span class="ruby-identifier">from_string</span>(<span class="ruby-identifier">str</span>)
|
|
16
|
-
<span class="ruby-keyword kw">self</span>[<span class="ruby-identifier">:text</span>] = <span class="ruby-ivar">@text</span>
|
|
17
|
-
<span class="ruby-keyword kw">end</span></pre>
|
|
18
|
-
</body>
|
|
19
|
-
</html>
|
|
@@ -1,18 +0,0 @@
|
|
|
1
|
-
<?xml version="1.0" encoding="iso-8859-1"?>
|
|
2
|
-
<!DOCTYPE html
|
|
3
|
-
PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
|
|
4
|
-
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
5
|
-
|
|
6
|
-
<html>
|
|
7
|
-
<head>
|
|
8
|
-
<title>text (Bio::DB::SAM::Tools::BamHeaderT)</title>
|
|
9
|
-
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
|
|
10
|
-
<link rel="stylesheet" href="../../../../../.././rdoc-style.css" type="text/css" media="screen" />
|
|
11
|
-
</head>
|
|
12
|
-
<body class="standalone-code">
|
|
13
|
-
<pre><span class="ruby-comment cmt"># File lib/bio/db/sam/sam.rb, line 42</span>
|
|
14
|
-
<span class="ruby-keyword kw">def</span> <span class="ruby-identifier">text</span>
|
|
15
|
-
<span class="ruby-ivar">@text</span>.<span class="ruby-identifier">get_string</span>(<span class="ruby-value">0</span>)
|
|
16
|
-
<span class="ruby-keyword kw">end</span></pre>
|
|
17
|
-
</body>
|
|
18
|
-
</html>
|
|
@@ -1,111 +0,0 @@
|
|
|
1
|
-
<?xml version="1.0" encoding="iso-8859-1"?>
|
|
2
|
-
<!DOCTYPE html
|
|
3
|
-
PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
|
|
4
|
-
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
5
|
-
|
|
6
|
-
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
|
|
7
|
-
<head>
|
|
8
|
-
<title>Class: Bio::DB::SAM::Tools::BamPileup1T</title>
|
|
9
|
-
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
|
|
10
|
-
<meta http-equiv="Content-Script-Type" content="text/javascript" />
|
|
11
|
-
<link rel="stylesheet" href="../../../../.././rdoc-style.css" type="text/css" media="screen" />
|
|
12
|
-
<script type="text/javascript">
|
|
13
|
-
// <![CDATA[
|
|
14
|
-
|
|
15
|
-
function popupCode( url ) {
|
|
16
|
-
window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
|
|
17
|
-
}
|
|
18
|
-
|
|
19
|
-
function toggleCode( id ) {
|
|
20
|
-
if ( document.getElementById )
|
|
21
|
-
elem = document.getElementById( id );
|
|
22
|
-
else if ( document.all )
|
|
23
|
-
elem = eval( "document.all." + id );
|
|
24
|
-
else
|
|
25
|
-
return false;
|
|
26
|
-
|
|
27
|
-
elemStyle = elem.style;
|
|
28
|
-
|
|
29
|
-
if ( elemStyle.display != "block" ) {
|
|
30
|
-
elemStyle.display = "block"
|
|
31
|
-
} else {
|
|
32
|
-
elemStyle.display = "none"
|
|
33
|
-
}
|
|
34
|
-
|
|
35
|
-
return true;
|
|
36
|
-
}
|
|
37
|
-
|
|
38
|
-
// Make codeblocks hidden by default
|
|
39
|
-
document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
|
|
40
|
-
|
|
41
|
-
// ]]>
|
|
42
|
-
</script>
|
|
43
|
-
|
|
44
|
-
</head>
|
|
45
|
-
<body>
|
|
46
|
-
|
|
47
|
-
|
|
48
|
-
|
|
49
|
-
<div id="classHeader">
|
|
50
|
-
<table class="header-table">
|
|
51
|
-
<tr class="top-aligned-row">
|
|
52
|
-
<td><strong>Class</strong></td>
|
|
53
|
-
<td class="class-name-in-header">Bio::DB::SAM::Tools::BamPileup1T</td>
|
|
54
|
-
</tr>
|
|
55
|
-
<tr class="top-aligned-row">
|
|
56
|
-
<td><strong>In:</strong></td>
|
|
57
|
-
<td>
|
|
58
|
-
<a href="../../../../../files/lib/bio/db/sam/bam_rb.html">
|
|
59
|
-
lib/bio/db/sam/bam.rb
|
|
60
|
-
</a>
|
|
61
|
-
<br />
|
|
62
|
-
</td>
|
|
63
|
-
</tr>
|
|
64
|
-
|
|
65
|
-
<tr class="top-aligned-row">
|
|
66
|
-
<td><strong>Parent:</strong></td>
|
|
67
|
-
<td>
|
|
68
|
-
FFI::Struct
|
|
69
|
-
</td>
|
|
70
|
-
</tr>
|
|
71
|
-
</table>
|
|
72
|
-
</div>
|
|
73
|
-
<!-- banner header -->
|
|
74
|
-
|
|
75
|
-
<div id="bodyContent">
|
|
76
|
-
|
|
77
|
-
|
|
78
|
-
|
|
79
|
-
<div id="contextContent">
|
|
80
|
-
|
|
81
|
-
|
|
82
|
-
|
|
83
|
-
</div>
|
|
84
|
-
|
|
85
|
-
|
|
86
|
-
</div>
|
|
87
|
-
|
|
88
|
-
|
|
89
|
-
<!-- if includes -->
|
|
90
|
-
|
|
91
|
-
<div id="section">
|
|
92
|
-
|
|
93
|
-
|
|
94
|
-
|
|
95
|
-
|
|
96
|
-
|
|
97
|
-
|
|
98
|
-
|
|
99
|
-
|
|
100
|
-
<!-- if method_list -->
|
|
101
|
-
|
|
102
|
-
|
|
103
|
-
</div>
|
|
104
|
-
|
|
105
|
-
|
|
106
|
-
<div id="validator-badges">
|
|
107
|
-
<p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
|
|
108
|
-
</div>
|
|
109
|
-
|
|
110
|
-
</body>
|
|
111
|
-
</html>
|
|
@@ -1,129 +0,0 @@
|
|
|
1
|
-
<?xml version="1.0" encoding="iso-8859-1"?>
|
|
2
|
-
<!DOCTYPE html
|
|
3
|
-
PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
|
|
4
|
-
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
5
|
-
|
|
6
|
-
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
|
|
7
|
-
<head>
|
|
8
|
-
<title>Class: Bio::DB::SAM::Tools::SamfileT</title>
|
|
9
|
-
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
|
|
10
|
-
<meta http-equiv="Content-Script-Type" content="text/javascript" />
|
|
11
|
-
<link rel="stylesheet" href="../../../../.././rdoc-style.css" type="text/css" media="screen" />
|
|
12
|
-
<script type="text/javascript">
|
|
13
|
-
// <![CDATA[
|
|
14
|
-
|
|
15
|
-
function popupCode( url ) {
|
|
16
|
-
window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
|
|
17
|
-
}
|
|
18
|
-
|
|
19
|
-
function toggleCode( id ) {
|
|
20
|
-
if ( document.getElementById )
|
|
21
|
-
elem = document.getElementById( id );
|
|
22
|
-
else if ( document.all )
|
|
23
|
-
elem = eval( "document.all." + id );
|
|
24
|
-
else
|
|
25
|
-
return false;
|
|
26
|
-
|
|
27
|
-
elemStyle = elem.style;
|
|
28
|
-
|
|
29
|
-
if ( elemStyle.display != "block" ) {
|
|
30
|
-
elemStyle.display = "block"
|
|
31
|
-
} else {
|
|
32
|
-
elemStyle.display = "none"
|
|
33
|
-
}
|
|
34
|
-
|
|
35
|
-
return true;
|
|
36
|
-
}
|
|
37
|
-
|
|
38
|
-
// Make codeblocks hidden by default
|
|
39
|
-
document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
|
|
40
|
-
|
|
41
|
-
// ]]>
|
|
42
|
-
</script>
|
|
43
|
-
|
|
44
|
-
</head>
|
|
45
|
-
<body>
|
|
46
|
-
|
|
47
|
-
|
|
48
|
-
|
|
49
|
-
<div id="classHeader">
|
|
50
|
-
<table class="header-table">
|
|
51
|
-
<tr class="top-aligned-row">
|
|
52
|
-
<td><strong>Class</strong></td>
|
|
53
|
-
<td class="class-name-in-header">Bio::DB::SAM::Tools::SamfileT</td>
|
|
54
|
-
</tr>
|
|
55
|
-
<tr class="top-aligned-row">
|
|
56
|
-
<td><strong>In:</strong></td>
|
|
57
|
-
<td>
|
|
58
|
-
<a href="../../../../../files/lib/bio/db/sam/sam_rb.html">
|
|
59
|
-
lib/bio/db/sam/sam.rb
|
|
60
|
-
</a>
|
|
61
|
-
<br />
|
|
62
|
-
</td>
|
|
63
|
-
</tr>
|
|
64
|
-
|
|
65
|
-
<tr class="top-aligned-row">
|
|
66
|
-
<td><strong>Parent:</strong></td>
|
|
67
|
-
<td>
|
|
68
|
-
FFI::Struct
|
|
69
|
-
</td>
|
|
70
|
-
</tr>
|
|
71
|
-
</table>
|
|
72
|
-
</div>
|
|
73
|
-
<!-- banner header -->
|
|
74
|
-
|
|
75
|
-
<div id="bodyContent">
|
|
76
|
-
|
|
77
|
-
|
|
78
|
-
|
|
79
|
-
<div id="contextContent">
|
|
80
|
-
|
|
81
|
-
<div id="description">
|
|
82
|
-
<p>
|
|
83
|
-
typedef struct {
|
|
84
|
-
</p>
|
|
85
|
-
<pre>
|
|
86
|
-
int type;
|
|
87
|
-
union {
|
|
88
|
-
tamFile tamr;
|
|
89
|
-
bamFile bam;
|
|
90
|
-
FILE *tamw;
|
|
91
|
-
} x;
|
|
92
|
-
bam_header_t *header;
|
|
93
|
-
</pre>
|
|
94
|
-
<p>
|
|
95
|
-
} samfile_t;
|
|
96
|
-
</p>
|
|
97
|
-
|
|
98
|
-
</div>
|
|
99
|
-
|
|
100
|
-
|
|
101
|
-
</div>
|
|
102
|
-
|
|
103
|
-
|
|
104
|
-
</div>
|
|
105
|
-
|
|
106
|
-
|
|
107
|
-
<!-- if includes -->
|
|
108
|
-
|
|
109
|
-
<div id="section">
|
|
110
|
-
|
|
111
|
-
|
|
112
|
-
|
|
113
|
-
|
|
114
|
-
|
|
115
|
-
|
|
116
|
-
|
|
117
|
-
|
|
118
|
-
<!-- if method_list -->
|
|
119
|
-
|
|
120
|
-
|
|
121
|
-
</div>
|
|
122
|
-
|
|
123
|
-
|
|
124
|
-
<div id="validator-badges">
|
|
125
|
-
<p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
|
|
126
|
-
</div>
|
|
127
|
-
|
|
128
|
-
</body>
|
|
129
|
-
</html>
|
|
@@ -1,111 +0,0 @@
|
|
|
1
|
-
<?xml version="1.0" encoding="iso-8859-1"?>
|
|
2
|
-
<!DOCTYPE html
|
|
3
|
-
PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
|
|
4
|
-
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
5
|
-
|
|
6
|
-
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
|
|
7
|
-
<head>
|
|
8
|
-
<title>Class: Bio::DB::SAM::Tools::SamfileTX</title>
|
|
9
|
-
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
|
|
10
|
-
<meta http-equiv="Content-Script-Type" content="text/javascript" />
|
|
11
|
-
<link rel="stylesheet" href="../../../../.././rdoc-style.css" type="text/css" media="screen" />
|
|
12
|
-
<script type="text/javascript">
|
|
13
|
-
// <![CDATA[
|
|
14
|
-
|
|
15
|
-
function popupCode( url ) {
|
|
16
|
-
window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
|
|
17
|
-
}
|
|
18
|
-
|
|
19
|
-
function toggleCode( id ) {
|
|
20
|
-
if ( document.getElementById )
|
|
21
|
-
elem = document.getElementById( id );
|
|
22
|
-
else if ( document.all )
|
|
23
|
-
elem = eval( "document.all." + id );
|
|
24
|
-
else
|
|
25
|
-
return false;
|
|
26
|
-
|
|
27
|
-
elemStyle = elem.style;
|
|
28
|
-
|
|
29
|
-
if ( elemStyle.display != "block" ) {
|
|
30
|
-
elemStyle.display = "block"
|
|
31
|
-
} else {
|
|
32
|
-
elemStyle.display = "none"
|
|
33
|
-
}
|
|
34
|
-
|
|
35
|
-
return true;
|
|
36
|
-
}
|
|
37
|
-
|
|
38
|
-
// Make codeblocks hidden by default
|
|
39
|
-
document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
|
|
40
|
-
|
|
41
|
-
// ]]>
|
|
42
|
-
</script>
|
|
43
|
-
|
|
44
|
-
</head>
|
|
45
|
-
<body>
|
|
46
|
-
|
|
47
|
-
|
|
48
|
-
|
|
49
|
-
<div id="classHeader">
|
|
50
|
-
<table class="header-table">
|
|
51
|
-
<tr class="top-aligned-row">
|
|
52
|
-
<td><strong>Class</strong></td>
|
|
53
|
-
<td class="class-name-in-header">Bio::DB::SAM::Tools::SamfileTX</td>
|
|
54
|
-
</tr>
|
|
55
|
-
<tr class="top-aligned-row">
|
|
56
|
-
<td><strong>In:</strong></td>
|
|
57
|
-
<td>
|
|
58
|
-
<a href="../../../../../files/lib/bio/db/sam/sam_rb.html">
|
|
59
|
-
lib/bio/db/sam/sam.rb
|
|
60
|
-
</a>
|
|
61
|
-
<br />
|
|
62
|
-
</td>
|
|
63
|
-
</tr>
|
|
64
|
-
|
|
65
|
-
<tr class="top-aligned-row">
|
|
66
|
-
<td><strong>Parent:</strong></td>
|
|
67
|
-
<td>
|
|
68
|
-
FFI::Union
|
|
69
|
-
</td>
|
|
70
|
-
</tr>
|
|
71
|
-
</table>
|
|
72
|
-
</div>
|
|
73
|
-
<!-- banner header -->
|
|
74
|
-
|
|
75
|
-
<div id="bodyContent">
|
|
76
|
-
|
|
77
|
-
|
|
78
|
-
|
|
79
|
-
<div id="contextContent">
|
|
80
|
-
|
|
81
|
-
|
|
82
|
-
|
|
83
|
-
</div>
|
|
84
|
-
|
|
85
|
-
|
|
86
|
-
</div>
|
|
87
|
-
|
|
88
|
-
|
|
89
|
-
<!-- if includes -->
|
|
90
|
-
|
|
91
|
-
<div id="section">
|
|
92
|
-
|
|
93
|
-
|
|
94
|
-
|
|
95
|
-
|
|
96
|
-
|
|
97
|
-
|
|
98
|
-
|
|
99
|
-
|
|
100
|
-
<!-- if method_list -->
|
|
101
|
-
|
|
102
|
-
|
|
103
|
-
</div>
|
|
104
|
-
|
|
105
|
-
|
|
106
|
-
<div id="validator-badges">
|
|
107
|
-
<p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
|
|
108
|
-
</div>
|
|
109
|
-
|
|
110
|
-
</body>
|
|
111
|
-
</html>
|
|
@@ -1,140 +0,0 @@
|
|
|
1
|
-
<?xml version="1.0" encoding="iso-8859-1"?>
|
|
2
|
-
<!DOCTYPE html
|
|
3
|
-
PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
|
|
4
|
-
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
5
|
-
|
|
6
|
-
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
|
|
7
|
-
<head>
|
|
8
|
-
<title>Class: Bio::DB::SAMException</title>
|
|
9
|
-
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
|
|
10
|
-
<meta http-equiv="Content-Script-Type" content="text/javascript" />
|
|
11
|
-
<link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
|
|
12
|
-
<script type="text/javascript">
|
|
13
|
-
// <![CDATA[
|
|
14
|
-
|
|
15
|
-
function popupCode( url ) {
|
|
16
|
-
window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
|
|
17
|
-
}
|
|
18
|
-
|
|
19
|
-
function toggleCode( id ) {
|
|
20
|
-
if ( document.getElementById )
|
|
21
|
-
elem = document.getElementById( id );
|
|
22
|
-
else if ( document.all )
|
|
23
|
-
elem = eval( "document.all." + id );
|
|
24
|
-
else
|
|
25
|
-
return false;
|
|
26
|
-
|
|
27
|
-
elemStyle = elem.style;
|
|
28
|
-
|
|
29
|
-
if ( elemStyle.display != "block" ) {
|
|
30
|
-
elemStyle.display = "block"
|
|
31
|
-
} else {
|
|
32
|
-
elemStyle.display = "none"
|
|
33
|
-
}
|
|
34
|
-
|
|
35
|
-
return true;
|
|
36
|
-
}
|
|
37
|
-
|
|
38
|
-
// Make codeblocks hidden by default
|
|
39
|
-
document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
|
|
40
|
-
|
|
41
|
-
// ]]>
|
|
42
|
-
</script>
|
|
43
|
-
|
|
44
|
-
</head>
|
|
45
|
-
<body>
|
|
46
|
-
|
|
47
|
-
|
|
48
|
-
|
|
49
|
-
<div id="classHeader">
|
|
50
|
-
<table class="header-table">
|
|
51
|
-
<tr class="top-aligned-row">
|
|
52
|
-
<td><strong>Class</strong></td>
|
|
53
|
-
<td class="class-name-in-header">Bio::DB::SAMException</td>
|
|
54
|
-
</tr>
|
|
55
|
-
<tr class="top-aligned-row">
|
|
56
|
-
<td><strong>In:</strong></td>
|
|
57
|
-
<td>
|
|
58
|
-
<a href="../../../files/lib/bio/db/sam_rb.html">
|
|
59
|
-
lib/bio/db/sam.rb
|
|
60
|
-
</a>
|
|
61
|
-
<br />
|
|
62
|
-
</td>
|
|
63
|
-
</tr>
|
|
64
|
-
|
|
65
|
-
<tr class="top-aligned-row">
|
|
66
|
-
<td><strong>Parent:</strong></td>
|
|
67
|
-
<td>
|
|
68
|
-
RuntimeError
|
|
69
|
-
</td>
|
|
70
|
-
</tr>
|
|
71
|
-
</table>
|
|
72
|
-
</div>
|
|
73
|
-
<!-- banner header -->
|
|
74
|
-
|
|
75
|
-
<div id="bodyContent">
|
|
76
|
-
|
|
77
|
-
|
|
78
|
-
|
|
79
|
-
<div id="contextContent">
|
|
80
|
-
|
|
81
|
-
|
|
82
|
-
|
|
83
|
-
</div>
|
|
84
|
-
|
|
85
|
-
<div id="method-list">
|
|
86
|
-
<h3 class="section-bar">Methods</h3>
|
|
87
|
-
|
|
88
|
-
<div class="name-list">
|
|
89
|
-
<a href="#M000016">new</a>
|
|
90
|
-
</div>
|
|
91
|
-
</div>
|
|
92
|
-
|
|
93
|
-
</div>
|
|
94
|
-
|
|
95
|
-
|
|
96
|
-
<!-- if includes -->
|
|
97
|
-
|
|
98
|
-
<div id="section">
|
|
99
|
-
|
|
100
|
-
|
|
101
|
-
|
|
102
|
-
|
|
103
|
-
|
|
104
|
-
|
|
105
|
-
|
|
106
|
-
|
|
107
|
-
<!-- if method_list -->
|
|
108
|
-
<div id="methods">
|
|
109
|
-
<h3 class="section-bar">Public Class methods</h3>
|
|
110
|
-
|
|
111
|
-
<div id="method-M000016" class="method-detail">
|
|
112
|
-
<a name="M000016"></a>
|
|
113
|
-
|
|
114
|
-
<div class="method-heading">
|
|
115
|
-
<a href="SAMException.src/M000016.html" target="Code" class="method-signature"
|
|
116
|
-
onclick="popupCode('SAMException.src/M000016.html');return false;">
|
|
117
|
-
<span class="method-name">new</span><span class="method-args">()</span>
|
|
118
|
-
</a>
|
|
119
|
-
</div>
|
|
120
|
-
|
|
121
|
-
<div class="method-description">
|
|
122
|
-
<p>
|
|
123
|
-
we can add further variables to give information of the excpetion
|
|
124
|
-
</p>
|
|
125
|
-
</div>
|
|
126
|
-
</div>
|
|
127
|
-
|
|
128
|
-
|
|
129
|
-
</div>
|
|
130
|
-
|
|
131
|
-
|
|
132
|
-
</div>
|
|
133
|
-
|
|
134
|
-
|
|
135
|
-
<div id="validator-badges">
|
|
136
|
-
<p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
|
|
137
|
-
</div>
|
|
138
|
-
|
|
139
|
-
</body>
|
|
140
|
-
</html>
|