1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
|
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<!-- NewPage -->
<html lang="en">
<head>
<!-- Generated by javadoc (version 1.7.0_51) on Wed Oct 01 16:41:56 BST 2014 -->
<title>QualityScoreAndErrorGenerator</title>
<meta name="date" content="2014-10-01">
<link rel="stylesheet" type="text/css" href="../stylesheet.css" title="Style">
</head>
<body>
<script type="text/javascript"><!--
if (location.href.indexOf('is-external=true') == -1) {
parent.document.title="QualityScoreAndErrorGenerator";
}
//-->
</script>
<noscript>
<div>JavaScript is disabled on your browser.</div>
</noscript>
<!-- ========= START OF TOP NAVBAR ======= -->
<div class="topNav"><a name="navbar_top">
<!-- -->
</a><a href="#skip-navbar_top" title="Skip navigation links"></a><a name="navbar_top_firstrow">
<!-- -->
</a>
<ul class="navList" title="Navigation">
<li><a href="../artificialFastqGenerator/package-summary.html">Package</a></li>
<li class="navBarCell1Rev">Class</li>
<li><a href="class-use/QualityScoreAndErrorGenerator.html">Use</a></li>
<li><a href="package-tree.html">Tree</a></li>
<li><a href="../deprecated-list.html">Deprecated</a></li>
<li><a href="../index-files/index-1.html">Index</a></li>
<li><a href="../help-doc.html">Help</a></li>
</ul>
</div>
<div class="subNav">
<ul class="navList">
<li><a href="../artificialFastqGenerator/NucleobaseAndReadFactory.html" title="class in artificialFastqGenerator"><span class="strong">Prev Class</span></a></li>
<li><a href="../artificialFastqGenerator/Read.html" title="class in artificialFastqGenerator"><span class="strong">Next Class</span></a></li>
</ul>
<ul class="navList">
<li><a href="../index.html?artificialFastqGenerator/QualityScoreAndErrorGenerator.html" target="_top">Frames</a></li>
<li><a href="QualityScoreAndErrorGenerator.html" target="_top">No Frames</a></li>
</ul>
<ul class="navList" id="allclasses_navbar_top">
<li><a href="../allclasses-noframe.html">All Classes</a></li>
</ul>
<div>
<script type="text/javascript"><!--
allClassesLink = document.getElementById("allclasses_navbar_top");
if(window==top) {
allClassesLink.style.display = "block";
}
else {
allClassesLink.style.display = "none";
}
//-->
</script>
</div>
<div>
<ul class="subNavList">
<li>Summary: </li>
<li>Nested | </li>
<li><a href="#field_summary">Field</a> | </li>
<li><a href="#constructor_summary">Constr</a> | </li>
<li><a href="#method_summary">Method</a></li>
</ul>
<ul class="subNavList">
<li>Detail: </li>
<li><a href="#field_detail">Field</a> | </li>
<li><a href="#constructor_detail">Constr</a> | </li>
<li><a href="#method_detail">Method</a></li>
</ul>
</div>
<a name="skip-navbar_top">
<!-- -->
</a></div>
<!-- ========= END OF TOP NAVBAR ========= -->
<!-- ======== START OF CLASS DATA ======== -->
<div class="header">
<div class="subTitle">artificialFastqGenerator</div>
<h2 title="Class QualityScoreAndErrorGenerator" class="title">Class QualityScoreAndErrorGenerator</h2>
</div>
<div class="contentContainer">
<ul class="inheritance">
<li>java.lang.Object</li>
<li>
<ul class="inheritance">
<li>artificialFastqGenerator.QualityScoreAndErrorGenerator</li>
</ul>
</li>
</ul>
<div class="description">
<ul class="blockList">
<li class="blockList">
<hr>
<br>
<pre>public class <span class="strong">QualityScoreAndErrorGenerator</span>
extends java.lang.Object</pre>
<div class="block">An instance of this class can be used to generate (1) ASCII encodings of Phred quality scores for bases in reads; (2)
base-call errors. (1) is done by taking quality scores from a pre-existing FASTQ file, and (2) by generating an error with
a probability that depends on the base's phred score.
Copyright (C) 2012 The Institute of Cancer Research (ICR).
This file is part of ArtificialFastqGenerator v1.0.0.
ArtificialFastqGenerator is free software: you can redistribute it and/or modify it under the terms of the GNU General
Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any
later version.
This program is distributed in the hope that it will be useful but WITHOUT ANY WARRANTY; without even the implied warranty
of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU Public License along with this program. If not, see
<http://www.gnu.org/licenses/>
Authour's contact email: Matthew.Frampton@icr.ac.uk</div>
</li>
</ul>
</div>
<div class="summary">
<ul class="blockList">
<li class="blockList">
<!-- =========== FIELD SUMMARY =========== -->
<ul class="blockList">
<li class="blockList"><a name="field_summary">
<!-- -->
</a>
<h3>Field Summary</h3>
<table class="overviewSummary" border="0" cellpadding="3" cellspacing="0" summary="Field Summary table, listing fields, and an explanation">
<caption><span>Fields</span><span class="tabEnd"> </span></caption>
<tr>
<th class="colFirst" scope="col">Modifier and Type</th>
<th class="colLast" scope="col">Field and Description</th>
</tr>
<tr class="altColor">
<td class="colFirst"><code>static char[]</code></td>
<td class="colLast"><code><strong><a href="../artificialFastqGenerator/QualityScoreAndErrorGenerator.html#encodedSangerQualityScores">encodedSangerQualityScores</a></strong></code> </td>
</tr>
</table>
</li>
</ul>
<!-- ======== CONSTRUCTOR SUMMARY ======== -->
<ul class="blockList">
<li class="blockList"><a name="constructor_summary">
<!-- -->
</a>
<h3>Constructor Summary</h3>
<table class="overviewSummary" border="0" cellpadding="3" cellspacing="0" summary="Constructor Summary table, listing constructors, and an explanation">
<caption><span>Constructors</span><span class="tabEnd"> </span></caption>
<tr>
<th class="colOne" scope="col">Constructor and Description</th>
</tr>
<tr class="altColor">
<td class="colOne"><code><strong><a href="../artificialFastqGenerator/QualityScoreAndErrorGenerator.html#QualityScoreAndErrorGenerator(int, boolean, boolean, java.lang.String, java.lang.String)">QualityScoreAndErrorGenerator</a></strong>(int readLength,
boolean useRealQualityScores,
boolean simulateErrorInRead,
java.lang.String fastq1ForQualityScoresPath,
java.lang.String fastq2ForQualityScoresPath)</code>
<div class="block">Initialise a new QualityScoreAndErrorGenerator object.</div>
</td>
</tr>
</table>
</li>
</ul>
<!-- ========== METHOD SUMMARY =========== -->
<ul class="blockList">
<li class="blockList"><a name="method_summary">
<!-- -->
</a>
<h3>Method Summary</h3>
<table class="overviewSummary" border="0" cellpadding="3" cellspacing="0" summary="Method Summary table, listing methods, and an explanation">
<caption><span>Methods</span><span class="tabEnd"> </span></caption>
<tr>
<th class="colFirst" scope="col">Modifier and Type</th>
<th class="colLast" scope="col">Method and Description</th>
</tr>
<tr class="altColor">
<td class="colFirst"><code>long</code></td>
<td class="colLast"><code><strong><a href="../artificialFastqGenerator/QualityScoreAndErrorGenerator.html#getNumACGTBasesCalled()">getNumACGTBasesCalled</a></strong>()</code>
<div class="block">Get the number of ACGT bases.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><code>long</code></td>
<td class="colLast"><code><strong><a href="../artificialFastqGenerator/QualityScoreAndErrorGenerator.html#getNumBaseCallErrors()">getNumBaseCallErrors</a></strong>()</code>
<div class="block">Get the number of base call errors that have been simulated.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><code>java.util.ArrayList<char[]></code></td>
<td class="colLast"><code><strong><a href="../artificialFastqGenerator/QualityScoreAndErrorGenerator.html#getQualityScoresAndGenotypesRead(boolean, java.util.ArrayList)">getQualityScoresAndGenotypesRead</a></strong>(boolean isLeft,
java.util.ArrayList<<a href="../artificialFastqGenerator/Nucleobase.html" title="class in artificialFastqGenerator">Nucleobase</a>> nucleobases)</code>
<div class="block">Get the encoded phred quality scores and the genotypes read.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><code>void</code></td>
<td class="colLast"><code><strong><a href="../artificialFastqGenerator/QualityScoreAndErrorGenerator.html#resetNumBaseCallErrors()">resetNumBaseCallErrors</a></strong>()</code>
<div class="block">Reset the number of simulated base call errors to 0.</div>
</td>
</tr>
</table>
<ul class="blockList">
<li class="blockList"><a name="methods_inherited_from_class_java.lang.Object">
<!-- -->
</a>
<h3>Methods inherited from class java.lang.Object</h3>
<code>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</code></li>
</ul>
</li>
</ul>
</li>
</ul>
</div>
<div class="details">
<ul class="blockList">
<li class="blockList">
<!-- ============ FIELD DETAIL =========== -->
<ul class="blockList">
<li class="blockList"><a name="field_detail">
<!-- -->
</a>
<h3>Field Detail</h3>
<a name="encodedSangerQualityScores">
<!-- -->
</a>
<ul class="blockListLast">
<li class="blockList">
<h4>encodedSangerQualityScores</h4>
<pre>public static final char[] encodedSangerQualityScores</pre>
</li>
</ul>
</li>
</ul>
<!-- ========= CONSTRUCTOR DETAIL ======== -->
<ul class="blockList">
<li class="blockList"><a name="constructor_detail">
<!-- -->
</a>
<h3>Constructor Detail</h3>
<a name="QualityScoreAndErrorGenerator(int, boolean, boolean, java.lang.String, java.lang.String)">
<!-- -->
</a>
<ul class="blockListLast">
<li class="blockList">
<h4>QualityScoreAndErrorGenerator</h4>
<pre>public QualityScoreAndErrorGenerator(int readLength,
boolean useRealQualityScores,
boolean simulateErrorInRead,
java.lang.String fastq1ForQualityScoresPath,
java.lang.String fastq2ForQualityScoresPath)</pre>
<div class="block">Initialise a new QualityScoreAndErrorGenerator object.</div>
<dl><dt><span class="strong">Parameters:</span></dt><dd><code>readLength</code> - - the length of each read.</dd><dd><code>useRealQualityScores</code> - - true if using quality scores from an existing fastq file, else false.</dd><dd><code>simulateErrorInRead</code> - - true if simulating error in reads, else false.</dd><dd><code>fastq1ForQualityScoresPath</code> - - the 1st fastq file whose quality scores are used.</dd><dd><code>fastq2ForQualityScoresPath</code> - - the 2nd fastq file whose quality scores are used.</dd></dl>
</li>
</ul>
</li>
</ul>
<!-- ============ METHOD DETAIL ========== -->
<ul class="blockList">
<li class="blockList"><a name="method_detail">
<!-- -->
</a>
<h3>Method Detail</h3>
<a name="getQualityScoresAndGenotypesRead(boolean, java.util.ArrayList)">
<!-- -->
</a>
<ul class="blockList">
<li class="blockList">
<h4>getQualityScoresAndGenotypesRead</h4>
<pre>public java.util.ArrayList<char[]> getQualityScoresAndGenotypesRead(boolean isLeft,
java.util.ArrayList<<a href="../artificialFastqGenerator/Nucleobase.html" title="class in artificialFastqGenerator">Nucleobase</a>> nucleobases)</pre>
<div class="block">Get the encoded phred quality scores and the genotypes read. If the read is right-end, then it should align to the
-ive strand, so reverse nucleobases, and read their complements.</div>
<dl><dt><span class="strong">Parameters:</span></dt><dd><code>isLeft</code> - - true if the read is a left read, else false.</dd><dd><code>nucleobases</code> - - human reference sequence nucleobases which the read is a read of.</dd>
<dt><span class="strong">Returns:</span></dt><dd>finalQualityScoresAndGenotypesRead - an ArrayList of char arrays containing the final quality scores and the
genotypes that get read.</dd></dl>
</li>
</ul>
<a name="getNumBaseCallErrors()">
<!-- -->
</a>
<ul class="blockList">
<li class="blockList">
<h4>getNumBaseCallErrors</h4>
<pre>public long getNumBaseCallErrors()</pre>
<div class="block">Get the number of base call errors that have been simulated.</div>
<dl><dt><span class="strong">Returns:</span></dt><dd>numBaseCallErrors - the number of bases for which base calls have been simulated.</dd></dl>
</li>
</ul>
<a name="resetNumBaseCallErrors()">
<!-- -->
</a>
<ul class="blockList">
<li class="blockList">
<h4>resetNumBaseCallErrors</h4>
<pre>public void resetNumBaseCallErrors()</pre>
<div class="block">Reset the number of simulated base call errors to 0.</div>
</li>
</ul>
<a name="getNumACGTBasesCalled()">
<!-- -->
</a>
<ul class="blockListLast">
<li class="blockList">
<h4>getNumACGTBasesCalled</h4>
<pre>public long getNumACGTBasesCalled()</pre>
<div class="block">Get the number of ACGT bases.</div>
<dl><dt><span class="strong">Returns:</span></dt><dd>numACGTBaseCalls - the number of ACGT bases that have been called.</dd></dl>
</li>
</ul>
</li>
</ul>
</li>
</ul>
</div>
</div>
<!-- ========= END OF CLASS DATA ========= -->
<!-- ======= START OF BOTTOM NAVBAR ====== -->
<div class="bottomNav"><a name="navbar_bottom">
<!-- -->
</a><a href="#skip-navbar_bottom" title="Skip navigation links"></a><a name="navbar_bottom_firstrow">
<!-- -->
</a>
<ul class="navList" title="Navigation">
<li><a href="../artificialFastqGenerator/package-summary.html">Package</a></li>
<li class="navBarCell1Rev">Class</li>
<li><a href="class-use/QualityScoreAndErrorGenerator.html">Use</a></li>
<li><a href="package-tree.html">Tree</a></li>
<li><a href="../deprecated-list.html">Deprecated</a></li>
<li><a href="../index-files/index-1.html">Index</a></li>
<li><a href="../help-doc.html">Help</a></li>
</ul>
</div>
<div class="subNav">
<ul class="navList">
<li><a href="../artificialFastqGenerator/NucleobaseAndReadFactory.html" title="class in artificialFastqGenerator"><span class="strong">Prev Class</span></a></li>
<li><a href="../artificialFastqGenerator/Read.html" title="class in artificialFastqGenerator"><span class="strong">Next Class</span></a></li>
</ul>
<ul class="navList">
<li><a href="../index.html?artificialFastqGenerator/QualityScoreAndErrorGenerator.html" target="_top">Frames</a></li>
<li><a href="QualityScoreAndErrorGenerator.html" target="_top">No Frames</a></li>
</ul>
<ul class="navList" id="allclasses_navbar_bottom">
<li><a href="../allclasses-noframe.html">All Classes</a></li>
</ul>
<div>
<script type="text/javascript"><!--
allClassesLink = document.getElementById("allclasses_navbar_bottom");
if(window==top) {
allClassesLink.style.display = "block";
}
else {
allClassesLink.style.display = "none";
}
//-->
</script>
</div>
<div>
<ul class="subNavList">
<li>Summary: </li>
<li>Nested | </li>
<li><a href="#field_summary">Field</a> | </li>
<li><a href="#constructor_summary">Constr</a> | </li>
<li><a href="#method_summary">Method</a></li>
</ul>
<ul class="subNavList">
<li>Detail: </li>
<li><a href="#field_detail">Field</a> | </li>
<li><a href="#constructor_detail">Constr</a> | </li>
<li><a href="#method_detail">Method</a></li>
</ul>
</div>
<a name="skip-navbar_bottom">
<!-- -->
</a></div>
<!-- ======== END OF BOTTOM NAVBAR ======= -->
</body>
</html>
|
