bio-gngm 0.1.0
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- data/.document +5 -0
- data/Gemfile +20 -0
- data/Gemfile.lock +33 -0
- data/LICENSE.txt +20 -0
- data/README.rdoc +33 -0
- data/Rakefile +53 -0
- data/VERSION +1 -0
- data/bio-gngm.gemspec +173 -0
- data/doc/Bio.html +129 -0
- data/doc/Bio/DB.html +128 -0
- data/doc/Bio/DB/Pileup.html +316 -0
- data/doc/Bio/DB/Vcf.html +683 -0
- data/doc/Bio/Util.html +135 -0
- data/doc/Bio/Util/Gngm.html +1655 -0
- data/doc/LICENSE_txt.html +111 -0
- data/doc/_index.html +169 -0
- data/doc/class_list.html +47 -0
- data/doc/created.rid +4 -0
- data/doc/css/common.css +1 -0
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- data/doc/images/signal.png +0 -0
- data/doc/images/tag_blue.png +0 -0
- data/doc/images/tag_green.png +0 -0
- data/doc/images/threads.png +0 -0
- data/doc/images/transparent.png +0 -0
- data/doc/images/wrench.png +0 -0
- data/doc/images/wrench_orange.png +0 -0
- data/doc/images/zoom.png +0 -0
- data/doc/index.html +88 -0
- data/doc/js/app.js +205 -0
- data/doc/js/darkfish.js +153 -0
- data/doc/js/full_list.js +167 -0
- data/doc/js/jquery.js +18 -0
- data/doc/js/navigation.js +142 -0
- data/doc/js/search.js +94 -0
- data/doc/js/search_index.js +1 -0
- data/doc/js/searcher.js +228 -0
- data/doc/lib/bio-gngm_rb.html +103 -0
- data/doc/lib/bio/util/bio-gngm_rb.html +96 -0
- data/doc/method_list.html +382 -0
- data/doc/rdoc.css +543 -0
- data/doc/table_of_contents.html +161 -0
- data/examples/.DS_Store +0 -0
- data/examples/make_histograms.rb +40 -0
- data/examples/make_threads.rb +42 -0
- data/examples/make_threads_isize.rb +41 -0
- data/examples/use_indels.rb +36 -0
- data/lib/bio-gngm.rb +12 -0
- data/lib/bio/util/bio-gngm.rb +1029 -0
- data/scripts/get_subseq.rb +16 -0
- data/scripts/make_histograms_laerfyve.rb +83 -0
- data/scripts/make_histograms_laerfyve_stitched.rb +59 -0
- data/scripts/make_threads_isize_laerfyfe.rb +52 -0
- data/scripts/make_threads_unmapped_laerfyfe.rb +72 -0
- data/scripts/make_threads_unmapped_laerfyfe_pseudo.rb +56 -0
- data/scripts/make_threads_unmapped_simulation.rb +54 -0
- data/scripts/make_threads_unmapped_simulation_immediate_region.rb +59 -0
- data/scripts/optimise_freq_window_size.rb +82 -0
- data/stitched_contigs.zip +0 -0
- data/test/data/ids2.txt +1 -0
- data/test/data/sorted.bam +0 -0
- data/test/data/test +0 -0
- data/test/data/test.bam +0 -0
- data/test/data/test.fa +20 -0
- data/test/data/test.fai +0 -0
- data/test/data/test.sai +0 -0
- data/test/data/test.tam +10 -0
- data/test/data/test_chr.fasta +1000 -0
- data/test/data/test_chr.fasta.amb +2 -0
- data/test/data/test_chr.fasta.ann +3 -0
- data/test/data/test_chr.fasta.bwt +0 -0
- data/test/data/test_chr.fasta.fai +1 -0
- data/test/data/test_chr.fasta.pac +0 -0
- data/test/data/test_chr.fasta.rbwt +0 -0
- data/test/data/test_chr.fasta.rpac +0 -0
- data/test/data/test_chr.fasta.rsa +0 -0
- data/test/data/test_chr.fasta.sa +0 -0
- data/test/data/testu.bam +0 -0
- data/test/data/testu.bam.bai +0 -0
- data/test/helper.rb +18 -0
- data/test/test_bio-gngm.rb +126 -0
- metadata +276 -0
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}
|
|
77
|
+
|
|
78
|
+
function linkSummaries() {
|
|
79
|
+
$('.summary_signature').click(function() {
|
|
80
|
+
document.location = $(this).find('a').attr('href');
|
|
81
|
+
});
|
|
82
|
+
}
|
|
83
|
+
|
|
84
|
+
function framesInit() {
|
|
85
|
+
if (window.top.frames.main) {
|
|
86
|
+
document.body.className = 'frames';
|
|
87
|
+
$('#menu .noframes a').attr('href', document.location);
|
|
88
|
+
$('html head title', window.parent.document).text($('html head title').text());
|
|
89
|
+
}
|
|
90
|
+
}
|
|
91
|
+
|
|
92
|
+
function keyboardShortcuts() {
|
|
93
|
+
if (window.top.frames.main) return;
|
|
94
|
+
$(document).keypress(function(evt) {
|
|
95
|
+
if (evt.altKey || evt.ctrlKey || evt.metaKey || evt.shiftKey) return;
|
|
96
|
+
if (typeof evt.target !== "undefined" &&
|
|
97
|
+
(evt.target.nodeName == "INPUT" ||
|
|
98
|
+
evt.target.nodeName == "TEXTAREA")) return;
|
|
99
|
+
switch (evt.charCode) {
|
|
100
|
+
case 67: case 99: $('#class_list_link').click(); break; // 'c'
|
|
101
|
+
case 77: case 109: $('#method_list_link').click(); break; // 'm'
|
|
102
|
+
case 70: case 102: $('#file_list_link').click(); break; // 'f'
|
|
103
|
+
default: break;
|
|
104
|
+
}
|
|
105
|
+
});
|
|
106
|
+
}
|
|
107
|
+
|
|
108
|
+
function summaryToggle() {
|
|
109
|
+
$('.summary_toggle').click(function() {
|
|
110
|
+
localStorage.summaryCollapsed = $(this).text();
|
|
111
|
+
$(this).text($(this).text() == "collapse" ? "expand" : "collapse");
|
|
112
|
+
var next = $(this).parent().parent().next();
|
|
113
|
+
if (next.hasClass('compact')) {
|
|
114
|
+
next.toggle();
|
|
115
|
+
next.next().toggle();
|
|
116
|
+
}
|
|
117
|
+
else if (next.hasClass('summary')) {
|
|
118
|
+
var list = $('<ul class="summary compact" />');
|
|
119
|
+
list.html(next.html());
|
|
120
|
+
list.find('.summary_desc, .note').remove();
|
|
121
|
+
list.find('a').each(function() {
|
|
122
|
+
$(this).html($(this).find('strong').html());
|
|
123
|
+
$(this).parent().html($(this)[0].outerHTML);
|
|
124
|
+
});
|
|
125
|
+
next.before(list);
|
|
126
|
+
next.toggle();
|
|
127
|
+
}
|
|
128
|
+
return false;
|
|
129
|
+
});
|
|
130
|
+
if (localStorage) {
|
|
131
|
+
if (localStorage.summaryCollapsed == "collapse") $('.summary_toggle').click();
|
|
132
|
+
else localStorage.summaryCollapsed = "expand";
|
|
133
|
+
}
|
|
134
|
+
}
|
|
135
|
+
|
|
136
|
+
function fixOutsideWorldLinks() {
|
|
137
|
+
$('a').each(function() {
|
|
138
|
+
if (window.location.host != this.host) this.target = '_parent';
|
|
139
|
+
});
|
|
140
|
+
}
|
|
141
|
+
|
|
142
|
+
function generateTOC() {
|
|
143
|
+
if ($('#filecontents').length === 0) return;
|
|
144
|
+
var _toc = $('<ol class="top"></ol>');
|
|
145
|
+
var show = false;
|
|
146
|
+
var toc = _toc;
|
|
147
|
+
var counter = 0;
|
|
148
|
+
var tags = ['h2', 'h3', 'h4', 'h5', 'h6'];
|
|
149
|
+
var i;
|
|
150
|
+
if ($('#filecontents h1').length > 1) tags.unshift('h1');
|
|
151
|
+
for (i = 0; i < tags.length; i++) { tags[i] = '#filecontents ' + tags[i]; }
|
|
152
|
+
var lastTag = parseInt(tags[0][1], 10);
|
|
153
|
+
$(tags.join(', ')).each(function() {
|
|
154
|
+
if (this.id == "filecontents") return;
|
|
155
|
+
show = true;
|
|
156
|
+
var thisTag = parseInt(this.tagName[1], 10);
|
|
157
|
+
if (this.id.length === 0) {
|
|
158
|
+
var proposedId = $(this).text().replace(/[^a-z0-9-]/ig, '_');
|
|
159
|
+
if ($('#' + proposedId).length > 0) { proposedId += counter; counter++; }
|
|
160
|
+
this.id = proposedId;
|
|
161
|
+
}
|
|
162
|
+
if (thisTag > lastTag) {
|
|
163
|
+
for (i = 0; i < thisTag - lastTag; i++) {
|
|
164
|
+
var tmp = $('<ol/>'); toc.append(tmp); toc = tmp;
|
|
165
|
+
}
|
|
166
|
+
}
|
|
167
|
+
if (thisTag < lastTag) {
|
|
168
|
+
for (i = 0; i < lastTag - thisTag; i++) toc = toc.parent();
|
|
169
|
+
}
|
|
170
|
+
toc.append('<li><a href="#' + this.id + '">' + $(this).text() + '</a></li>');
|
|
171
|
+
lastTag = thisTag;
|
|
172
|
+
});
|
|
173
|
+
if (!show) return;
|
|
174
|
+
html = '<div id="toc"><p class="title"><a class="hide_toc" href="#"><strong>Table of Contents</strong></a> <small>(<a href="#" class="float_toc">left</a>)</small></p></div>';
|
|
175
|
+
$('#content').prepend(html);
|
|
176
|
+
$('#toc').append(_toc);
|
|
177
|
+
$('#toc .hide_toc').toggle(function() {
|
|
178
|
+
$('#toc .top').slideUp('fast');
|
|
179
|
+
$('#toc').toggleClass('hidden');
|
|
180
|
+
$('#toc .title small').toggle();
|
|
181
|
+
}, function() {
|
|
182
|
+
$('#toc .top').slideDown('fast');
|
|
183
|
+
$('#toc').toggleClass('hidden');
|
|
184
|
+
$('#toc .title small').toggle();
|
|
185
|
+
});
|
|
186
|
+
$('#toc .float_toc').toggle(function() {
|
|
187
|
+
$(this).text('float');
|
|
188
|
+
$('#toc').toggleClass('nofloat');
|
|
189
|
+
}, function() {
|
|
190
|
+
$(this).text('left');
|
|
191
|
+
$('#toc').toggleClass('nofloat');
|
|
192
|
+
});
|
|
193
|
+
}
|
|
194
|
+
|
|
195
|
+
$(framesInit);
|
|
196
|
+
$(createSourceLinks);
|
|
197
|
+
$(createDefineLinks);
|
|
198
|
+
$(createFullTreeLinks);
|
|
199
|
+
$(fixBoxInfoHeights);
|
|
200
|
+
$(searchFrameLinks);
|
|
201
|
+
$(linkSummaries);
|
|
202
|
+
$(keyboardShortcuts);
|
|
203
|
+
$(summaryToggle);
|
|
204
|
+
$(fixOutsideWorldLinks);
|
|
205
|
+
$(generateTOC);
|
data/doc/js/darkfish.js
ADDED
|
@@ -0,0 +1,153 @@
|
|
|
1
|
+
/**
|
|
2
|
+
*
|
|
3
|
+
* Darkfish Page Functions
|
|
4
|
+
* $Id: darkfish.js 53 2009-01-07 02:52:03Z deveiant $
|
|
5
|
+
*
|
|
6
|
+
* Author: Michael Granger <mgranger@laika.com>
|
|
7
|
+
*
|
|
8
|
+
*/
|
|
9
|
+
|
|
10
|
+
/* Provide console simulation for firebug-less environments */
|
|
11
|
+
if (!("console" in window) || !("firebug" in console)) {
|
|
12
|
+
var names = ["log", "debug", "info", "warn", "error", "assert", "dir", "dirxml",
|
|
13
|
+
"group", "groupEnd", "time", "timeEnd", "count", "trace", "profile", "profileEnd"];
|
|
14
|
+
|
|
15
|
+
window.console = {};
|
|
16
|
+
for (var i = 0; i < names.length; ++i)
|
|
17
|
+
window.console[names[i]] = function() {};
|
|
18
|
+
};
|
|
19
|
+
|
|
20
|
+
|
|
21
|
+
/**
|
|
22
|
+
* Unwrap the first element that matches the given @expr@ from the targets and return them.
|
|
23
|
+
*/
|
|
24
|
+
$.fn.unwrap = function( expr ) {
|
|
25
|
+
return this.each( function() {
|
|
26
|
+
$(this).parents( expr ).eq( 0 ).after( this ).remove();
|
|
27
|
+
});
|
|
28
|
+
};
|
|
29
|
+
|
|
30
|
+
|
|
31
|
+
function showSource( e ) {
|
|
32
|
+
var target = e.target;
|
|
33
|
+
var codeSections = $(target).
|
|
34
|
+
parents('.method-detail').
|
|
35
|
+
find('.method-source-code');
|
|
36
|
+
|
|
37
|
+
$(target).
|
|
38
|
+
parents('.method-detail').
|
|
39
|
+
find('.method-source-code').
|
|
40
|
+
slideToggle();
|
|
41
|
+
};
|
|
42
|
+
|
|
43
|
+
function hookSourceViews() {
|
|
44
|
+
$('.method-heading').click( showSource );
|
|
45
|
+
};
|
|
46
|
+
|
|
47
|
+
function toggleDebuggingSection() {
|
|
48
|
+
$('.debugging-section').slideToggle();
|
|
49
|
+
};
|
|
50
|
+
|
|
51
|
+
function hookDebuggingToggle() {
|
|
52
|
+
$('#debugging-toggle img').click( toggleDebuggingSection );
|
|
53
|
+
};
|
|
54
|
+
|
|
55
|
+
function hookTableOfContentsToggle() {
|
|
56
|
+
$('.indexpage li .toc-toggle').each( function() {
|
|
57
|
+
$(this).click( function() {
|
|
58
|
+
$(this).toggleClass('open');
|
|
59
|
+
});
|
|
60
|
+
|
|
61
|
+
var section = $(this).next();
|
|
62
|
+
|
|
63
|
+
$(this).click( function() {
|
|
64
|
+
section.slideToggle();
|
|
65
|
+
});
|
|
66
|
+
});
|
|
67
|
+
}
|
|
68
|
+
|
|
69
|
+
function hookSearch() {
|
|
70
|
+
var input = $('#search-field').eq(0);
|
|
71
|
+
var result = $('#search-results').eq(0);
|
|
72
|
+
$(result).show();
|
|
73
|
+
|
|
74
|
+
var search_section = $('#search-section').get(0);
|
|
75
|
+
$(search_section).show();
|
|
76
|
+
|
|
77
|
+
var search = new Search(search_data, input, result);
|
|
78
|
+
|
|
79
|
+
search.renderItem = function(result) {
|
|
80
|
+
var li = document.createElement('li');
|
|
81
|
+
var html = '';
|
|
82
|
+
|
|
83
|
+
// TODO add relative path to <script> per-page
|
|
84
|
+
html += '<p class="search-match"><a href="' + rdoc_rel_prefix + result.path + '">' + this.hlt(result.title);
|
|
85
|
+
if (result.params)
|
|
86
|
+
html += '<span class="params">' + result.params + '</span>';
|
|
87
|
+
html += '</a>';
|
|
88
|
+
|
|
89
|
+
|
|
90
|
+
if (result.namespace)
|
|
91
|
+
html += '<p class="search-namespace">' + this.hlt(result.namespace);
|
|
92
|
+
|
|
93
|
+
if (result.snippet)
|
|
94
|
+
html += '<div class="search-snippet">' + result.snippet + '</div>';
|
|
95
|
+
|
|
96
|
+
li.innerHTML = html;
|
|
97
|
+
|
|
98
|
+
return li;
|
|
99
|
+
}
|
|
100
|
+
|
|
101
|
+
search.select = function(result) {
|
|
102
|
+
var result_element = result.get(0);
|
|
103
|
+
window.location.href = result_element.firstChild.firstChild.href;
|
|
104
|
+
}
|
|
105
|
+
|
|
106
|
+
search.scrollIntoView = search.scrollInWindow;
|
|
107
|
+
};
|
|
108
|
+
|
|
109
|
+
function highlightTarget( anchor ) {
|
|
110
|
+
console.debug( "Highlighting target '%s'.", anchor );
|
|
111
|
+
|
|
112
|
+
$("a[name=" + anchor + "]").each( function() {
|
|
113
|
+
if ( !$(this).parent().parent().hasClass('target-section') ) {
|
|
114
|
+
console.debug( "Wrapping the target-section" );
|
|
115
|
+
$('div.method-detail').unwrap( 'div.target-section' );
|
|
116
|
+
$(this).parent().wrap( '<div class="target-section"></div>' );
|
|
117
|
+
} else {
|
|
118
|
+
console.debug( "Already wrapped." );
|
|
119
|
+
}
|
|
120
|
+
});
|
|
121
|
+
};
|
|
122
|
+
|
|
123
|
+
function highlightLocationTarget() {
|
|
124
|
+
console.debug( "Location hash: %s", window.location.hash );
|
|
125
|
+
if ( ! window.location.hash || window.location.hash.length == 0 ) return;
|
|
126
|
+
|
|
127
|
+
var anchor = window.location.hash.substring(1);
|
|
128
|
+
console.debug( "Found anchor: %s; matching %s", anchor, "a[name=" + anchor + "]" );
|
|
129
|
+
|
|
130
|
+
highlightTarget( anchor );
|
|
131
|
+
};
|
|
132
|
+
|
|
133
|
+
function highlightClickTarget( event ) {
|
|
134
|
+
console.debug( "Highlighting click target for event %o", event.target );
|
|
135
|
+
try {
|
|
136
|
+
var anchor = $(event.target).attr( 'href' ).substring(1);
|
|
137
|
+
console.debug( "Found target anchor: %s", anchor );
|
|
138
|
+
highlightTarget( anchor );
|
|
139
|
+
} catch ( err ) {
|
|
140
|
+
console.error( "Exception while highlighting: %o", err );
|
|
141
|
+
};
|
|
142
|
+
};
|
|
143
|
+
|
|
144
|
+
|
|
145
|
+
$(document).ready( function() {
|
|
146
|
+
hookSourceViews();
|
|
147
|
+
hookDebuggingToggle();
|
|
148
|
+
hookSearch();
|
|
149
|
+
highlightLocationTarget();
|
|
150
|
+
hookTableOfContentsToggle();
|
|
151
|
+
|
|
152
|
+
$('ul.link-list a').bind( "click", highlightClickTarget );
|
|
153
|
+
});
|