-
Notifications
You must be signed in to change notification settings - Fork 0
/
index.html
232 lines (211 loc) · 42.2 KB
/
index.html
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
<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="pandoc" />
<meta name="author" content="L Collado-Torres" />
<meta name="date" content="2016-03-21" />
<title>derfinder counting paper Supplementary Website</title>
<style type="text/css">code{white-space: pre;}</style>
<link href="data:text/css,pre%20%2Eoperator%2C%0Apre%20%2Eparen%20%7B%0A%20color%3A%20rgb%28104%2C%20118%2C%20135%29%0A%7D%0A%0Apre%20%2Eliteral%20%7B%0A%20color%3A%20%23990073%0A%7D%0A%0Apre%20%2Enumber%20%7B%0A%20color%3A%20%23099%3B%0A%7D%0A%0Apre%20%2Ecomment%20%7B%0A%20color%3A%20%23998%3B%0A%20font%2Dstyle%3A%20italic%0A%7D%0A%0Apre%20%2Ekeyword%20%7B%0A%20color%3A%20%23900%3B%0A%20font%2Dweight%3A%20bold%0A%7D%0A%0Apre%20%2Eidentifier%20%7B%0A%20color%3A%20rgb%280%2C%200%2C%200%29%3B%0A%7D%0A%0Apre%20%2Estring%20%7B%0A%20color%3A%20%23d14%3B%0A%7D%0A" rel="stylesheet" type="text/css" />
<script src="data:application/x-javascript,%0Avar%20hljs%3Dnew%20function%28%29%7Bfunction%20m%28p%29%7Breturn%20p%2Ereplace%28%2F%26%2Fgm%2C%22%26amp%3B%22%29%2Ereplace%28%2F%3C%2Fgm%2C%22%26lt%3B%22%29%7Dfunction%20f%28r%2Cq%2Cp%29%7Breturn%20RegExp%28q%2C%22m%22%2B%28r%2EcI%3F%22i%22%3A%22%22%29%2B%28p%3F%22g%22%3A%22%22%29%29%7Dfunction%20b%28r%29%7Bfor%28var%20p%3D0%3Bp%3Cr%2EchildNodes%2Elength%3Bp%2B%2B%29%7Bvar%20q%3Dr%2EchildNodes%5Bp%5D%3Bif%28q%2EnodeName%3D%3D%22CODE%22%29%7Breturn%20q%7Dif%28%21%28q%2EnodeType%3D%3D3%26%26q%2EnodeValue%2Ematch%28%2F%5Cs%2B%2F%29%29%29%7Bbreak%7D%7D%7Dfunction%20h%28t%2Cs%29%7Bvar%20p%3D%22%22%3Bfor%28var%20r%3D0%3Br%3Ct%2EchildNodes%2Elength%3Br%2B%2B%29%7Bif%28t%2EchildNodes%5Br%5D%2EnodeType%3D%3D3%29%7Bvar%20q%3Dt%2EchildNodes%5Br%5D%2EnodeValue%3Bif%28s%29%7Bq%3Dq%2Ereplace%28%2F%5Cn%2Fg%2C%22%22%29%7Dp%2B%3Dq%7Delse%7Bif%28t%2EchildNodes%5Br%5D%2EnodeName%3D%3D%22BR%22%29%7Bp%2B%3D%22%5Cn%22%7Delse%7Bp%2B%3Dh%28t%2EchildNodes%5Br%5D%29%7D%7D%7Dif%28%2FMSIE%20%5B678%5D%2F%2Etest%28navigator%2EuserAgent%29%29%7Bp%3Dp%2Ereplace%28%2F%5Cr%2Fg%2C%22%5Cn%22%29%7Dreturn%20p%7Dfunction%20a%28s%29%7Bvar%20r%3Ds%2EclassName%2Esplit%28%2F%5Cs%2B%2F%29%3Br%3Dr%2Econcat%28s%2EparentNode%2EclassName%2Esplit%28%2F%5Cs%2B%2F%29%29%3Bfor%28var%20q%3D0%3Bq%3Cr%2Elength%3Bq%2B%2B%29%7Bvar%20p%3Dr%5Bq%5D%2Ereplace%28%2F%5Elanguage%2D%2F%2C%22%22%29%3Bif%28e%5Bp%5D%29%7Breturn%20p%7D%7D%7Dfunction%20c%28q%29%7Bvar%20p%3D%5B%5D%3B%28function%28s%2Ct%29%7Bfor%28var%20r%3D0%3Br%3Cs%2EchildNodes%2Elength%3Br%2B%2B%29%7Bif%28s%2EchildNodes%5Br%5D%2EnodeType%3D%3D3%29%7Bt%2B%3Ds%2EchildNodes%5Br%5D%2EnodeValue%2Elength%7Delse%7Bif%28s%2EchildNodes%5Br%5D%2EnodeName%3D%3D%22BR%22%29%7Bt%2B%3D1%7Delse%7Bif%28s%2EchildNodes%5Br%5D%2EnodeType%3D%3D1%29%7Bp%2Epush%28%7Bevent%3A%22start%22%2Coffset%3At%2Cnode%3As%2EchildNodes%5Br%5D%7D%29%3Bt%3Darguments%2Ecallee%28s%2EchildNodes%5Br%5D%2Ct%29%3Bp%2Epush%28%7Bevent%3A%22stop%22%2Coffset%3At%2Cnode%3As%2EchildNodes%5Br%5D%7D%29%7D%7D%7D%7Dreturn%20t%7D%29%28q%2C0%29%3Breturn%20p%7Dfunction%20k%28y%2Cw%2Cx%29%7Bvar%20q%3D0%3Bvar%20z%3D%22%22%3Bvar%20s%3D%5B%5D%3Bfunction%20u%28%29%7Bif%28y%2Elength%26%26w%2Elength%29%7Bif%28y%5B0%5D%2Eoffset%21%3Dw%5B0%5D%2Eoffset%29%7Breturn%28y%5B0%5D%2Eoffset%3Cw%5B0%5D%2Eoffset%29%3Fy%3Aw%7Delse%7Breturn%20w%5B0%5D%2Eevent%3D%3D%22start%22%3Fy%3Aw%7D%7Delse%7Breturn%20y%2Elength%3Fy%3Aw%7D%7Dfunction%20t%28D%29%7Bvar%20A%3D%22%3C%22%2BD%2EnodeName%2EtoLowerCase%28%29%3Bfor%28var%20B%3D0%3BB%3CD%2Eattributes%2Elength%3BB%2B%2B%29%7Bvar%20C%3DD%2Eattributes%5BB%5D%3BA%2B%3D%22%20%22%2BC%2EnodeName%2EtoLowerCase%28%29%3Bif%28C%2Evalue%21%3D%3Dundefined%26%26C%2Evalue%21%3D%3Dfalse%26%26C%2Evalue%21%3D%3Dnull%29%7BA%2B%3D%27%3D%22%27%2Bm%28C%2Evalue%29%2B%27%22%27%7D%7Dreturn%20A%2B%22%3E%22%7Dwhile%28y%2Elength%7C%7Cw%2Elength%29%7Bvar%20v%3Du%28%29%2Esplice%280%2C1%29%5B0%5D%3Bz%2B%3Dm%28x%2Esubstr%28q%2Cv%2Eoffset%2Dq%29%29%3Bq%3Dv%2Eoffset%3Bif%28v%2Eevent%3D%3D%22start%22%29%7Bz%2B%3Dt%28v%2Enode%29%3Bs%2Epush%28v%2Enode%29%7Delse%7Bif%28v%2Eevent%3D%3D%22stop%22%29%7Bvar%20p%2Cr%3Ds%2Elength%3Bdo%7Br%2D%2D%3Bp%3Ds%5Br%5D%3Bz%2B%3D%28%22%3C%2F%22%2Bp%2EnodeName%2EtoLowerCase%28%29%2B%22%3E%22%29%7Dwhile%28p%21%3Dv%2Enode%29%3Bs%2Esplice%28r%2C1%29%3Bwhile%28r%3Cs%2Elength%29%7Bz%2B%3Dt%28s%5Br%5D%29%3Br%2B%2B%7D%7D%7D%7Dreturn%20z%2Bm%28x%2Esubstr%28q%29%29%7Dfunction%20j%28%29%7Bfunction%20q%28x%2Cy%2Cv%29%7Bif%28x%2Ecompiled%29%7Breturn%7Dvar%20u%3Bvar%20s%3D%5B%5D%3Bif%28x%2Ek%29%7Bx%2ElR%3Df%28y%2Cx%2El%7C%7Chljs%2EIR%2Ctrue%29%3Bfor%28var%20w%20in%20x%2Ek%29%7Bif%28%21x%2Ek%2EhasOwnProperty%28w%29%29%7Bcontinue%7Dif%28x%2Ek%5Bw%5D%20instanceof%20Object%29%7Bu%3Dx%2Ek%5Bw%5D%7Delse%7Bu%3Dx%2Ek%3Bw%3D%22keyword%22%7Dfor%28var%20r%20in%20u%29%7Bif%28%21u%2EhasOwnProperty%28r%29%29%7Bcontinue%7Dx%2Ek%5Br%5D%3D%5Bw%2Cu%5Br%5D%5D%3Bs%2Epush%28r%29%7D%7D%7Dif%28%21v%29%7Bif%28x%2EbWK%29%7Bx%2Eb%3D%22%5C%5Cb%28%22%2Bs%2Ejoin%28%22%7C%22%29%2B%22%29%5C%5Cs%22%7Dx%2EbR%3Df%28y%2Cx%2Eb%3Fx%2Eb%3A%22%5C%5CB%7C%5C%5Cb%22%29%3Bif%28%21x%2Ee%26%26%21x%2EeW%29%7Bx%2Ee%3D%22%5C%5CB%7C%5C%5Cb%22%7Dif%28x%2Ee%29%7Bx%2EeR%3Df%28y%2Cx%2Ee%29%7D%7Dif%28x%2Ei%29%7Bx%2EiR%3Df%28y%2Cx%2Ei%29%7Dif%28x%2Er%3D%3D%3Dundefined%29%7Bx%2Er%3D1%7Dif%28%21x%2Ec%29%7Bx%2Ec%3D%5B%5D%7Dx%2Ecompiled%3Dtrue%3Bfor%28var%20t%3D0%3Bt%3Cx%2Ec%2Elength%3Bt%2B%2B%29%7Bif%28x%2Ec%5Bt%5D%3D%3D%22self%22%29%7Bx%2Ec%5Bt%5D%3Dx%7Dq%28x%2Ec%5Bt%5D%2Cy%2Cfalse%29%7Dif%28x%2Estarts%29%7Bq%28x%2Estarts%2Cy%2Cfalse%29%7D%7Dfor%28var%20p%20in%20e%29%7Bif%28%21e%2EhasOwnProperty%28p%29%29%7Bcontinue%7Dq%28e%5Bp%5D%2EdM%2Ce%5Bp%5D%2Ctrue%29%7D%7Dfunction%20d%28B%2CC%29%7Bif%28%21j%2Ecalled%29%7Bj%28%29%3Bj%2Ecalled%3Dtrue%7Dfunction%20q%28r%2CM%29%7Bfor%28var%20L%3D0%3BL%3CM%2Ec%2Elength%3BL%2B%2B%29%7Bif%28%28M%2Ec%5BL%5D%2EbR%2Eexec%28r%29%7C%7C%5Bnull%5D%29%5B0%5D%3D%3Dr%29%7Breturn%20M%2Ec%5BL%5D%7D%7D%7Dfunction%20v%28L%2Cr%29%7Bif%28D%5BL%5D%2Ee%26%26D%5BL%5D%2EeR%2Etest%28r%29%29%7Breturn%201%7Dif%28D%5BL%5D%2EeW%29%7Bvar%20M%3Dv%28L%2D1%2Cr%29%3Breturn%20M%3FM%2B1%3A0%7Dreturn%200%7Dfunction%20w%28r%2CL%29%7Breturn%20L%2Ei%26%26L%2EiR%2Etest%28r%29%7Dfunction%20K%28N%2CO%29%7Bvar%20M%3D%5B%5D%3Bfor%28var%20L%3D0%3BL%3CN%2Ec%2Elength%3BL%2B%2B%29%7BM%2Epush%28N%2Ec%5BL%5D%2Eb%29%7Dvar%20r%3DD%2Elength%2D1%3Bdo%7Bif%28D%5Br%5D%2Ee%29%7BM%2Epush%28D%5Br%5D%2Ee%29%7Dr%2D%2D%7Dwhile%28D%5Br%2B1%5D%2EeW%29%3Bif%28N%2Ei%29%7BM%2Epush%28N%2Ei%29%7Dreturn%20f%28O%2CM%2Ejoin%28%22%7C%22%29%2Ctrue%29%7Dfunction%20p%28M%2CL%29%7Bvar%20N%3DD%5BD%2Elength%2D1%5D%3Bif%28%21N%2Et%29%7BN%2Et%3DK%28N%2CE%29%7DN%2Et%2ElastIndex%3DL%3Bvar%20r%3DN%2Et%2Eexec%28M%29%3Breturn%20r%3F%5BM%2Esubstr%28L%2Cr%2Eindex%2DL%29%2Cr%5B0%5D%2Cfalse%5D%3A%5BM%2Esubstr%28L%29%2C%22%22%2Ctrue%5D%7Dfunction%20z%28N%2Cr%29%7Bvar%20L%3DE%2EcI%3Fr%5B0%5D%2EtoLowerCase%28%29%3Ar%5B0%5D%3Bvar%20M%3DN%2Ek%5BL%5D%3Bif%28M%26%26M%20instanceof%20Array%29%7Breturn%20M%7Dreturn%20false%7Dfunction%20F%28L%2CP%29%7BL%3Dm%28L%29%3Bif%28%21P%2Ek%29%7Breturn%20L%7Dvar%20r%3D%22%22%3Bvar%20O%3D0%3BP%2ElR%2ElastIndex%3D0%3Bvar%20M%3DP%2ElR%2Eexec%28L%29%3Bwhile%28M%29%7Br%2B%3DL%2Esubstr%28O%2CM%2Eindex%2DO%29%3Bvar%20N%3Dz%28P%2CM%29%3Bif%28N%29%7Bx%2B%3DN%5B1%5D%3Br%2B%3D%27%3Cspan%20class%3D%22%27%2BN%5B0%5D%2B%27%22%3E%27%2BM%5B0%5D%2B%22%3C%2Fspan%3E%22%7Delse%7Br%2B%3DM%5B0%5D%7DO%3DP%2ElR%2ElastIndex%3BM%3DP%2ElR%2Eexec%28L%29%7Dreturn%20r%2BL%2Esubstr%28O%2CL%2Elength%2DO%29%7Dfunction%20J%28L%2CM%29%7Bif%28M%2EsL%26%26e%5BM%2EsL%5D%29%7Bvar%20r%3Dd%28M%2EsL%2CL%29%3Bx%2B%3Dr%2Ekeyword%5Fcount%3Breturn%20r%2Evalue%7Delse%7Breturn%20F%28L%2CM%29%7D%7Dfunction%20I%28M%2Cr%29%7Bvar%20L%3DM%2EcN%3F%27%3Cspan%20class%3D%22%27%2BM%2EcN%2B%27%22%3E%27%3A%22%22%3Bif%28M%2ErB%29%7By%2B%3DL%3BM%2Ebuffer%3D%22%22%7Delse%7Bif%28M%2EeB%29%7By%2B%3Dm%28r%29%2BL%3BM%2Ebuffer%3D%22%22%7Delse%7By%2B%3DL%3BM%2Ebuffer%3Dr%7D%7DD%2Epush%28M%29%3BA%2B%3DM%2Er%7Dfunction%20G%28N%2CM%2CQ%29%7Bvar%20R%3DD%5BD%2Elength%2D1%5D%3Bif%28Q%29%7By%2B%3DJ%28R%2Ebuffer%2BN%2CR%29%3Breturn%20false%7Dvar%20P%3Dq%28M%2CR%29%3Bif%28P%29%7By%2B%3DJ%28R%2Ebuffer%2BN%2CR%29%3BI%28P%2CM%29%3Breturn%20P%2ErB%7Dvar%20L%3Dv%28D%2Elength%2D1%2CM%29%3Bif%28L%29%7Bvar%20O%3DR%2EcN%3F%22%3C%2Fspan%3E%22%3A%22%22%3Bif%28R%2ErE%29%7By%2B%3DJ%28R%2Ebuffer%2BN%2CR%29%2BO%7Delse%7Bif%28R%2EeE%29%7By%2B%3DJ%28R%2Ebuffer%2BN%2CR%29%2BO%2Bm%28M%29%7Delse%7By%2B%3DJ%28R%2Ebuffer%2BN%2BM%2CR%29%2BO%7D%7Dwhile%28L%3E1%29%7BO%3DD%5BD%2Elength%2D2%5D%2EcN%3F%22%3C%2Fspan%3E%22%3A%22%22%3By%2B%3DO%3BL%2D%2D%3BD%2Elength%2D%2D%7Dvar%20r%3DD%5BD%2Elength%2D1%5D%3BD%2Elength%2D%2D%3BD%5BD%2Elength%2D1%5D%2Ebuffer%3D%22%22%3Bif%28r%2Estarts%29%7BI%28r%2Estarts%2C%22%22%29%7Dreturn%20R%2ErE%7Dif%28w%28M%2CR%29%29%7Bthrow%22Illegal%22%7D%7Dvar%20E%3De%5BB%5D%3Bvar%20D%3D%5BE%2EdM%5D%3Bvar%20A%3D0%3Bvar%20x%3D0%3Bvar%20y%3D%22%22%3Btry%7Bvar%20s%2Cu%3D0%3BE%2EdM%2Ebuffer%3D%22%22%3Bdo%7Bs%3Dp%28C%2Cu%29%3Bvar%20t%3DG%28s%5B0%5D%2Cs%5B1%5D%2Cs%5B2%5D%29%3Bu%2B%3Ds%5B0%5D%2Elength%3Bif%28%21t%29%7Bu%2B%3Ds%5B1%5D%2Elength%7D%7Dwhile%28%21s%5B2%5D%29%3Bif%28D%2Elength%3E1%29%7Bthrow%22Illegal%22%7Dreturn%7Br%3AA%2Ckeyword%5Fcount%3Ax%2Cvalue%3Ay%7D%7Dcatch%28H%29%7Bif%28H%3D%3D%22Illegal%22%29%7Breturn%7Br%3A0%2Ckeyword%5Fcount%3A0%2Cvalue%3Am%28C%29%7D%7Delse%7Bthrow%20H%7D%7D%7Dfunction%20g%28t%29%7Bvar%20p%3D%7Bkeyword%5Fcount%3A0%2Cr%3A0%2Cvalue%3Am%28t%29%7D%3Bvar%20r%3Dp%3Bfor%28var%20q%20in%20e%29%7Bif%28%21e%2EhasOwnProperty%28q%29%29%7Bcontinue%7Dvar%20s%3Dd%28q%2Ct%29%3Bs%2Elanguage%3Dq%3Bif%28s%2Ekeyword%5Fcount%2Bs%2Er%3Er%2Ekeyword%5Fcount%2Br%2Er%29%7Br%3Ds%7Dif%28s%2Ekeyword%5Fcount%2Bs%2Er%3Ep%2Ekeyword%5Fcount%2Bp%2Er%29%7Br%3Dp%3Bp%3Ds%7D%7Dif%28r%2Elanguage%29%7Bp%2Esecond%5Fbest%3Dr%7Dreturn%20p%7Dfunction%20i%28r%2Cq%2Cp%29%7Bif%28q%29%7Br%3Dr%2Ereplace%28%2F%5E%28%28%3C%5B%5E%3E%5D%2B%3E%7C%5Ct%29%2B%29%2Fgm%2Cfunction%28t%2Cw%2Cv%2Cu%29%7Breturn%20w%2Ereplace%28%2F%5Ct%2Fg%2Cq%29%7D%29%7Dif%28p%29%7Br%3Dr%2Ereplace%28%2F%5Cn%2Fg%2C%22%3Cbr%3E%22%29%7Dreturn%20r%7Dfunction%20n%28t%2Cw%2Cr%29%7Bvar%20x%3Dh%28t%2Cr%29%3Bvar%20v%3Da%28t%29%3Bvar%20y%2Cs%3Bif%28v%29%7By%3Dd%28v%2Cx%29%7Delse%7Breturn%7Dvar%20q%3Dc%28t%29%3Bif%28q%2Elength%29%7Bs%3Ddocument%2EcreateElement%28%22pre%22%29%3Bs%2EinnerHTML%3Dy%2Evalue%3By%2Evalue%3Dk%28q%2Cc%28s%29%2Cx%29%7Dy%2Evalue%3Di%28y%2Evalue%2Cw%2Cr%29%3Bvar%20u%3Dt%2EclassName%3Bif%28%21u%2Ematch%28%22%28%5C%5Cs%7C%5E%29%28language%2D%29%3F%22%2Bv%2B%22%28%5C%5Cs%7C%24%29%22%29%29%7Bu%3Du%3F%28u%2B%22%20%22%2Bv%29%3Av%7Dif%28%2FMSIE%20%5B678%5D%2F%2Etest%28navigator%2EuserAgent%29%26%26t%2EtagName%3D%3D%22CODE%22%26%26t%2EparentNode%2EtagName%3D%3D%22PRE%22%29%7Bs%3Dt%2EparentNode%3Bvar%20p%3Ddocument%2EcreateElement%28%22div%22%29%3Bp%2EinnerHTML%3D%22%3Cpre%3E%3Ccode%3E%22%2By%2Evalue%2B%22%3C%2Fcode%3E%3C%2Fpre%3E%22%3Bt%3Dp%2EfirstChild%2EfirstChild%3Bp%2EfirstChild%2EcN%3Ds%2EcN%3Bs%2EparentNode%2EreplaceChild%28p%2EfirstChild%2Cs%29%7Delse%7Bt%2EinnerHTML%3Dy%2Evalue%7Dt%2EclassName%3Du%3Bt%2Eresult%3D%7Blanguage%3Av%2Ckw%3Ay%2Ekeyword%5Fcount%2Cre%3Ay%2Er%7D%3Bif%28y%2Esecond%5Fbest%29%7Bt%2Esecond%5Fbest%3D%7Blanguage%3Ay%2Esecond%5Fbest%2Elanguage%2Ckw%3Ay%2Esecond%5Fbest%2Ekeyword%5Fcount%2Cre%3Ay%2Esecond%5Fbest%2Er%7D%7D%7Dfunction%20o%28%29%7Bif%28o%2Ecalled%29%7Breturn%7Do%2Ecalled%3Dtrue%3Bvar%20r%3Ddocument%2EgetElementsByTagName%28%22pre%22%29%3Bfor%28var%20p%3D0%3Bp%3Cr%2Elength%3Bp%2B%2B%29%7Bvar%20q%3Db%28r%5Bp%5D%29%3Bif%28q%29%7Bn%28q%2Chljs%2EtabReplace%29%7D%7D%7Dfunction%20l%28%29%7Bif%28window%2EaddEventListener%29%7Bwindow%2EaddEventListener%28%22DOMContentLoaded%22%2Co%2Cfalse%29%3Bwindow%2EaddEventListener%28%22load%22%2Co%2Cfalse%29%7Delse%7Bif%28window%2EattachEvent%29%7Bwindow%2EattachEvent%28%22onload%22%2Co%29%7Delse%7Bwindow%2Eonload%3Do%7D%7D%7Dvar%20e%3D%7B%7D%3Bthis%2ELANGUAGES%3De%3Bthis%2Ehighlight%3Dd%3Bthis%2EhighlightAuto%3Dg%3Bthis%2EfixMarkup%3Di%3Bthis%2EhighlightBlock%3Dn%3Bthis%2EinitHighlighting%3Do%3Bthis%2EinitHighlightingOnLoad%3Dl%3Bthis%2EIR%3D%22%5Ba%2DzA%2DZ%5D%5Ba%2DzA%2DZ0%2D9%5F%5D%2A%22%3Bthis%2EUIR%3D%22%5Ba%2DzA%2DZ%5F%5D%5Ba%2DzA%2DZ0%2D9%5F%5D%2A%22%3Bthis%2ENR%3D%22%5C%5Cb%5C%5Cd%2B%28%5C%5C%2E%5C%5Cd%2B%29%3F%22%3Bthis%2ECNR%3D%22%5C%5Cb%280%5BxX%5D%5Ba%2DfA%2DF0%2D9%5D%2B%7C%28%5C%5Cd%2B%28%5C%5C%2E%5C%5Cd%2A%29%3F%7C%5C%5C%2E%5C%5Cd%2B%29%28%5BeE%5D%5B%2D%2B%5D%3F%5C%5Cd%2B%29%3F%29%22%3Bthis%2EBNR%3D%22%5C%5Cb%280b%5B01%5D%2B%29%22%3Bthis%2ERSR%3D%22%21%7C%21%3D%7C%21%3D%3D%7C%25%7C%25%3D%7C%26%7C%26%26%7C%26%3D%7C%5C%5C%2A%7C%5C%5C%2A%3D%7C%5C%5C%2B%7C%5C%5C%2B%3D%7C%2C%7C%5C%5C%2E%7C%2D%7C%2D%3D%7C%2F%7C%2F%3D%7C%3A%7C%3B%7C%3C%7C%3C%3C%7C%3C%3C%3D%7C%3C%3D%7C%3D%7C%3D%3D%7C%3D%3D%3D%7C%3E%7C%3E%3D%7C%3E%3E%7C%3E%3E%3D%7C%3E%3E%3E%7C%3E%3E%3E%3D%7C%5C%5C%3F%7C%5C%5C%5B%7C%5C%5C%7B%7C%5C%5C%28%7C%5C%5C%5E%7C%5C%5C%5E%3D%7C%5C%5C%7C%7C%5C%5C%7C%3D%7C%5C%5C%7C%5C%5C%7C%7C%7E%22%3Bthis%2EER%3D%22%28%3F%21%5B%5C%5Cs%5C%5CS%5D%29%22%3Bthis%2EBE%3D%7Bb%3A%22%5C%5C%5C%5C%2E%22%2Cr%3A0%7D%3Bthis%2EASM%3D%7BcN%3A%22string%22%2Cb%3A%22%27%22%2Ce%3A%22%27%22%2Ci%3A%22%5C%5Cn%22%2Cc%3A%5Bthis%2EBE%5D%2Cr%3A0%7D%3Bthis%2EQSM%3D%7BcN%3A%22string%22%2Cb%3A%27%22%27%2Ce%3A%27%22%27%2Ci%3A%22%5C%5Cn%22%2Cc%3A%5Bthis%2EBE%5D%2Cr%3A0%7D%3Bthis%2ECLCM%3D%7BcN%3A%22comment%22%2Cb%3A%22%2F%2F%22%2Ce%3A%22%24%22%7D%3Bthis%2ECBLCLM%3D%7BcN%3A%22comment%22%2Cb%3A%22%2F%5C%5C%2A%22%2Ce%3A%22%5C%5C%2A%2F%22%7D%3Bthis%2EHCM%3D%7BcN%3A%22comment%22%2Cb%3A%22%23%22%2Ce%3A%22%24%22%7D%3Bthis%2ENM%3D%7BcN%3A%22number%22%2Cb%3Athis%2ENR%2Cr%3A0%7D%3Bthis%2ECNM%3D%7BcN%3A%22number%22%2Cb%3Athis%2ECNR%2Cr%3A0%7D%3Bthis%2EBNM%3D%7BcN%3A%22number%22%2Cb%3Athis%2EBNR%2Cr%3A0%7D%3Bthis%2Einherit%3Dfunction%28r%2Cs%29%7Bvar%20p%3D%7B%7D%3Bfor%28var%20q%20in%20r%29%7Bp%5Bq%5D%3Dr%5Bq%5D%7Dif%28s%29%7Bfor%28var%20q%20in%20s%29%7Bp%5Bq%5D%3Ds%5Bq%5D%7D%7Dreturn%20p%7D%7D%28%29%3Bhljs%2ELANGUAGES%2Ecpp%3Dfunction%28%29%7Bvar%20a%3D%7Bkeyword%3A%7B%22false%22%3A1%2C%22int%22%3A1%2C%22float%22%3A1%2C%22while%22%3A1%2C%22private%22%3A1%2C%22char%22%3A1%2C%22catch%22%3A1%2C%22export%22%3A1%2Cvirtual%3A1%2Coperator%3A2%2Csizeof%3A2%2Cdynamic%5Fcast%3A2%2Ctypedef%3A2%2Cconst%5Fcast%3A2%2C%22const%22%3A1%2Cstruct%3A1%2C%22for%22%3A1%2Cstatic%5Fcast%3A2%2Cunion%3A1%2Cnamespace%3A1%2Cunsigned%3A1%2C%22long%22%3A1%2C%22throw%22%3A1%2C%22volatile%22%3A2%2C%22static%22%3A1%2C%22protected%22%3A1%2Cbool%3A1%2Ctemplate%3A1%2Cmutable%3A1%2C%22if%22%3A1%2C%22public%22%3A1%2Cfriend%3A2%2C%22do%22%3A1%2C%22return%22%3A1%2C%22goto%22%3A1%2Cauto%3A1%2C%22void%22%3A2%2C%22enum%22%3A1%2C%22else%22%3A1%2C%22break%22%3A1%2C%22new%22%3A1%2Cextern%3A1%2Cusing%3A1%2C%22true%22%3A1%2C%22class%22%3A1%2Casm%3A1%2C%22case%22%3A1%2Ctypeid%3A1%2C%22short%22%3A1%2Creinterpret%5Fcast%3A2%2C%22default%22%3A1%2C%22double%22%3A1%2Cregister%3A1%2Cexplicit%3A1%2Csigned%3A1%2Ctypename%3A1%2C%22try%22%3A1%2C%22this%22%3A1%2C%22switch%22%3A1%2C%22continue%22%3A1%2Cwchar%5Ft%3A1%2Cinline%3A1%2C%22delete%22%3A1%2Calignof%3A1%2Cchar16%5Ft%3A1%2Cchar32%5Ft%3A1%2Cconstexpr%3A1%2Cdecltype%3A1%2Cnoexcept%3A1%2Cnullptr%3A1%2Cstatic%5Fassert%3A1%2Cthread%5Flocal%3A1%2Crestrict%3A1%2C%5FBool%3A1%2Ccomplex%3A1%7D%2Cbuilt%5Fin%3A%7Bstd%3A1%2Cstring%3A1%2Ccin%3A1%2Ccout%3A1%2Ccerr%3A1%2Cclog%3A1%2Cstringstream%3A1%2Cistringstream%3A1%2Costringstream%3A1%2Cauto%5Fptr%3A1%2Cdeque%3A1%2Clist%3A1%2Cqueue%3A1%2Cstack%3A1%2Cvector%3A1%2Cmap%3A1%2Cset%3A1%2Cbitset%3A1%2Cmultiset%3A1%2Cmultimap%3A1%2Cunordered%5Fset%3A1%2Cunordered%5Fmap%3A1%2Cunordered%5Fmultiset%3A1%2Cunordered%5Fmultimap%3A1%2Carray%3A1%2Cshared%5Fptr%3A1%7D%7D%3Breturn%7BdM%3A%7Bk%3Aa%2Ci%3A%22%3C%2F%22%2Cc%3A%5Bhljs%2ECLCM%2Chljs%2ECBLCLM%2Chljs%2EQSM%2C%7BcN%3A%22string%22%2Cb%3A%22%27%5C%5C%5C%5C%3F%2E%22%2Ce%3A%22%27%22%2Ci%3A%22%2E%22%7D%2C%7BcN%3A%22number%22%2Cb%3A%22%5C%5Cb%28%5C%5Cd%2B%28%5C%5C%2E%5C%5Cd%2A%29%3F%7C%5C%5C%2E%5C%5Cd%2B%29%28u%7CU%7Cl%7CL%7Cul%7CUL%7Cf%7CF%29%22%7D%2Chljs%2ECNM%2C%7BcN%3A%22preprocessor%22%2Cb%3A%22%23%22%2Ce%3A%22%24%22%7D%2C%7BcN%3A%22stl%5Fcontainer%22%2Cb%3A%22%5C%5Cb%28deque%7Clist%7Cqueue%7Cstack%7Cvector%7Cmap%7Cset%7Cbitset%7Cmultiset%7Cmultimap%7Cunordered%5Fmap%7Cunordered%5Fset%7Cunordered%5Fmultiset%7Cunordered%5Fmultimap%7Carray%29%5C%5Cs%2A%3C%22%2Ce%3A%22%3E%22%2Ck%3Aa%2Cr%3A10%2Cc%3A%5B%22self%22%5D%7D%5D%7D%7D%7D%28%29%3Bhljs%2ELANGUAGES%2Er%3D%7BdM%3A%7Bc%3A%5Bhljs%2EHCM%2C%7BcN%3A%22number%22%2Cb%3A%22%5C%5Cb0%5BxX%5D%5B0%2D9a%2DfA%2DF%5D%2B%5BLi%5D%3F%5C%5Cb%22%2Ce%3Ahljs%2EIMMEDIATE%5FRE%2Cr%3A0%7D%2C%7BcN%3A%22number%22%2Cb%3A%22%5C%5Cb%5C%5Cd%2B%28%3F%3A%5BeE%5D%5B%2B%5C%5C%2D%5D%3F%5C%5Cd%2A%29%3FL%5C%5Cb%22%2Ce%3Ahljs%2EIMMEDIATE%5FRE%2Cr%3A0%7D%2C%7BcN%3A%22number%22%2Cb%3A%22%5C%5Cb%5C%5Cd%2B%5C%5C%2E%28%3F%21%5C%5Cd%29%28%3F%3Ai%5C%5Cb%29%3F%22%2Ce%3Ahljs%2EIMMEDIATE%5FRE%2Cr%3A1%7D%2C%7BcN%3A%22number%22%2Cb%3A%22%5C%5Cb%5C%5Cd%2B%28%3F%3A%5C%5C%2E%5C%5Cd%2A%29%3F%28%3F%3A%5BeE%5D%5B%2B%5C%5C%2D%5D%3F%5C%5Cd%2A%29%3Fi%3F%5C%5Cb%22%2Ce%3Ahljs%2EIMMEDIATE%5FRE%2Cr%3A0%7D%2C%7BcN%3A%22number%22%2Cb%3A%22%5C%5C%2E%5C%5Cd%2B%28%3F%3A%5BeE%5D%5B%2B%5C%5C%2D%5D%3F%5C%5Cd%2A%29%3Fi%3F%5C%5Cb%22%2Ce%3Ahljs%2EIMMEDIATE%5FRE%2Cr%3A1%7D%2C%7BcN%3A%22keyword%22%2Cb%3A%22%28%3F%3AtryCatch%7Clibrary%7CsetGeneric%7CsetGroupGeneric%29%5C%5Cb%22%2Ce%3Ahljs%2EIMMEDIATE%5FRE%2Cr%3A10%7D%2C%7BcN%3A%22keyword%22%2Cb%3A%22%5C%5C%2E%5C%5C%2E%5C%5C%2E%22%2Ce%3Ahljs%2EIMMEDIATE%5FRE%2Cr%3A10%7D%2C%7BcN%3A%22keyword%22%2Cb%3A%22%5C%5C%2E%5C%5C%2E%5C%5Cd%2B%28%3F%21%5B%5C%5Cw%2E%5D%29%22%2Ce%3Ahljs%2EIMMEDIATE%5FRE%2Cr%3A10%7D%2C%7BcN%3A%22keyword%22%2Cb%3A%22%5C%5Cb%28%3F%3Afunction%29%22%2Ce%3Ahljs%2EIMMEDIATE%5FRE%2Cr%3A2%7D%2C%7BcN%3A%22keyword%22%2Cb%3A%22%28%3F%3Aif%7Cin%7Cbreak%7Cnext%7Crepeat%7Celse%7Cfor%7Creturn%7Cswitch%7Cwhile%7Ctry%7Cstop%7Cwarning%7Crequire%7Cattach%7Cdetach%7Csource%7CsetMethod%7CsetClass%29%5C%5Cb%22%2Ce%3Ahljs%2EIMMEDIATE%5FRE%2Cr%3A1%7D%2C%7BcN%3A%22literal%22%2Cb%3A%22%28%3F%3ANA%7CNA%5Finteger%5F%7CNA%5Freal%5F%7CNA%5Fcharacter%5F%7CNA%5Fcomplex%5F%29%5C%5Cb%22%2Ce%3Ahljs%2EIMMEDIATE%5FRE%2Cr%3A10%7D%2C%7BcN%3A%22literal%22%2Cb%3A%22%28%3F%3ANULL%7CTRUE%7CFALSE%7CT%7CF%7CInf%7CNaN%29%5C%5Cb%22%2Ce%3Ahljs%2EIMMEDIATE%5FRE%2Cr%3A1%7D%2C%7BcN%3A%22identifier%22%2Cb%3A%22%5Ba%2DzA%2DZ%2E%5D%5Ba%2DzA%2DZ0%2D9%2E%5F%5D%2A%5C%5Cb%22%2Ce%3Ahljs%2EIMMEDIATE%5FRE%2Cr%3A0%7D%2C%7BcN%3A%22operator%22%2Cb%3A%22%3C%5C%5C%2D%28%3F%21%5C%5Cs%2A%5C%5Cd%29%22%2Ce%3Ahljs%2EIMMEDIATE%5FRE%2Cr%3A2%7D%2C%7BcN%3A%22operator%22%2Cb%3A%22%5C%5C%2D%3E%7C%3C%5C%5C%2D%22%2Ce%3Ahljs%2EIMMEDIATE%5FRE%2Cr%3A1%7D%2C%7BcN%3A%22operator%22%2Cb%3A%22%25%25%7C%7E%22%2Ce%3Ahljs%2EIMMEDIATE%5FRE%7D%2C%7BcN%3A%22operator%22%2Cb%3A%22%3E%3D%7C%3C%3D%7C%3D%3D%7C%21%3D%7C%5C%5C%7C%5C%5C%7C%7C%26%26%7C%3D%7C%5C%5C%2B%7C%5C%5C%2D%7C%5C%5C%2A%7C%2F%7C%5C%5C%5E%7C%3E%7C%3C%7C%21%7C%26%7C%5C%5C%7C%7C%5C%5C%24%7C%3A%22%2Ce%3Ahljs%2EIMMEDIATE%5FRE%2Cr%3A0%7D%2C%7BcN%3A%22operator%22%2Cb%3A%22%25%22%2Ce%3A%22%25%22%2Ci%3A%22%5C%5Cn%22%2Cr%3A1%7D%2C%7BcN%3A%22identifier%22%2Cb%3A%22%60%22%2Ce%3A%22%60%22%2Cr%3A0%7D%2C%7BcN%3A%22string%22%2Cb%3A%27%22%27%2Ce%3A%27%22%27%2Cc%3A%5Bhljs%2EBE%5D%2Cr%3A0%7D%2C%7BcN%3A%22string%22%2Cb%3A%22%27%22%2Ce%3A%22%27%22%2Cc%3A%5Bhljs%2EBE%5D%2Cr%3A0%7D%2C%7BcN%3A%22paren%22%2Cb%3A%22%5B%5B%28%7B%5C%5C%5D%29%7D%5D%22%2Ce%3Ahljs%2EIMMEDIATE%5FRE%2Cr%3A0%7D%5D%7D%7D%3B%0Ahljs%2EinitHighlightingOnLoad%28%29%3B%0A%0A"></script>
<style type="text/css">
pre:not([class]) {
background-color: white;
}
</style>
<script type="text/javascript">
if (window.hljs && document.readyState && document.readyState === "complete") {
window.setTimeout(function() {
hljs.initHighlighting();
}, 0);
}
</script>
<link href="data:text/css,body%2C%20td%20%7B%0A%20%20%20font%2Dfamily%3A%20sans%2Dserif%3B%0A%20%20%20background%2Dcolor%3A%20white%3B%0A%20%20%20font%2Dsize%3A%2013px%3B%0A%7D%0A%0Abody%20%7B%0A%20%20max%2Dwidth%3A%20800px%3B%0A%20%20margin%3A%200%20auto%3B%0A%20%20padding%3A%201em%201em%202em%3B%0A%20%20line%2Dheight%3A%2020px%3B%0A%7D%0A%0A%2F%2A%20Table%20of%20contents%20style%20%2A%2F%0A%0Adiv%23TOC%20li%20%7B%0A%20%20%20%20list%2Dstyle%3Anone%3B%0A%20%20%20%20background%2Dimage%3Anone%3B%0A%20%20%20%20background%2Drepeat%3Anone%3B%0A%20%20%20%20background%2Dposition%3A0%3B%0A%7D%0A%0A%2F%2A%20element%20spacing%20%2A%2F%0A%0Ap%2C%20pre%20%7B%20%0A%20%20margin%3A%200em%200em%201em%3B%0A%7D%0A%0A%2F%2A%20center%20images%20and%20tables%20%2A%2F%0Aimg%2C%20table%20%7B%0A%20%20margin%3A%200em%20auto%201em%3B%0A%7D%0A%0Ap%20%7B%0A%20%20text%2Dalign%3A%20justify%3B%0A%7D%0A%0Att%2C%20code%2C%20pre%20%7B%0A%20%20%20font%2Dfamily%3A%20%27DejaVu%20Sans%20Mono%27%2C%20%27Droid%20Sans%20Mono%27%2C%20%27Lucida%20Console%27%2C%20Consolas%2C%20Monaco%2C%20monospace%3B%0A%7D%0A%0Ah1%2C%20h2%2C%20h3%2C%20h4%2C%20h5%2C%20h6%20%7B%20%0A%20%20font%2Dfamily%3A%20Helvetica%2C%20Arial%2C%20sans%2Dserif%3B%0A%20%20margin%3A%201%2E2em%200em%200%2E6em%200em%3B%0A%20%20font%2Dweight%3A%20bold%3B%0A%7D%0A%0Ah1%2Etitle%20%7B%0A%20%20font%2Dsize%3A%20250%25%3B%0A%20%20font%2Dweight%3A%20normal%3B%0A%20%20color%3A%20%2387b13f%3B%0A%20%20line%2Dheight%3A%201%2E1em%3B%0A%20%20margin%2Dtop%3A%200px%3B%0A%20%20border%2Dbottom%3A%200px%3B%0A%7D%0A%0Ah1%20%7B%0A%20%20font%2Dsize%3A%20160%25%3B%0A%20%20font%2Dweight%3A%20normal%3B%0A%20%20line%2Dheight%3A%201%2E4em%3B%0A%20%20border%2Dbottom%3A%201px%20%231a81c2%20solid%3B%0A%7D%0A%0Ah2%20%7B%0A%20%20font%2Dsize%3A%20130%25%3B%20%20%0A%7D%0A%0Ah1%2C%20h2%2C%20h3%20%7B%0A%20%20color%3A%20%231a81c2%3B%0A%7D%0A%0Ah3%2C%20h4%2C%20h5%2C%20h6%20%7B%0A%20%20font%2Dsize%3A115%25%3B%0A%7D%20%2F%2A%20not%20expecting%20to%20dive%20deeper%20than%20four%20levels%20on%20a%20single%20page%20%2A%2F%0A%0A%2F%2A%20links%20are%20simply%20blue%2C%20hovering%20slightly%20less%20blue%20%2A%2F%0Aa%20%7B%20color%3A%20%231a81c2%3B%20%7D%0Aa%3Aactive%20%7B%20outline%3A%20none%3B%20%7D%0Aa%3Avisited%20%7B%20color%3A%20%231a81c2%3B%20%7D%0Aa%3Ahover%20%7B%20color%3A%20%234c94c2%3B%20%7D%0A%0Apre%2C%20img%20%7B%0A%20%20max%2Dwidth%3A%20100%25%3B%0A%20%20display%3A%20block%3B%0A%7D%0A%0Apre%20%7B%0A%20%20border%3A%200px%20none%3B%0A%20%20background%2Dcolor%3A%20%23F8F8F8%3B%0A%20%20white%2Dspace%3A%20pre%3B%0A%20%20overflow%2Dx%3A%20auto%3B%0A%7D%0A%0Apre%20code%20%7B%0A%20%20border%3A%201px%20%23aaa%20dashed%3B%0A%20%20background%2Dcolor%3A%20white%3B%0A%20%20display%3A%20block%3B%0A%20%20padding%3A%201em%3B%20%20%0A%20%20color%3A%20%23111%3B%0A%20%20overflow%2Dx%3A%20inherit%3B%0A%7D%0A%0A%2F%2A%20markdown%20v1%20%2A%2F%0Apre%20code%5Bclass%5D%20%7B%0A%20%20background%2Dcolor%3A%20inherit%3B%0A%7D%0A%0A%2F%2A%20markdown%20v2%20%2A%2F%0Apre%5Bclass%5D%20code%20%7B%0A%20%20background%2Dcolor%3A%20inherit%3B%0A%7D%0A%0A%2F%2A%20formatting%20of%20inline%20code%20%2A%2F%0Acode%20%7B%20%0A%20%20background%2Dcolor%3A%20transparent%3B%0A%20%20color%3A%20%2387b13f%3B%0A%20%20font%2Dsize%3A%2092%25%3B%0A%7D%0A%0A%2F%2A%20formatting%20of%20tables%20%2A%2F%0A%0Atable%2C%20td%2C%20th%20%7B%0A%20%20border%3A%20none%3B%0A%20%20padding%3A%200%200%2E5em%3B%0A%7D%0A%0A%2F%2A%20alternating%20row%20colors%20%2A%2F%0Atbody%20tr%3Anth%2Dchild%28odd%29%20td%20%7B%0A%20%20background%2Dcolor%3A%20%23F8F8F8%3B%0A%7D%0A%0Ablockquote%20%7B%0A%20%20%20color%3A%23666666%3B%0A%20%20%20margin%3A0%3B%0A%20%20%20padding%2Dleft%3A%201em%3B%0A%20%20%20border%2Dleft%3A%200%2E5em%20%23EEE%20solid%3B%0A%7D%0A%0Ahr%20%7B%0A%20%20%20height%3A%200px%3B%0A%20%20%20border%2Dbottom%3A%20none%3B%0A%20%20%20border%2Dtop%2Dwidth%3A%20thin%3B%0A%20%20%20border%2Dtop%2Dstyle%3A%20dotted%3B%0A%20%20%20border%2Dtop%2Dcolor%3A%20%23999999%3B%0A%7D%0A%0Aspan%2Eheader%2Dsection%2Dnumber%20%7B%0A%20%20padding%2Dright%3A%201em%3B%0A%7D%0A%0Aspan%2Etoc%2Dsection%2Dnumber%3A%3Aafter%20%7B%0A%20%20%20%20content%3A%20%22%20%20%22%3B%0A%20%20%20%20white%2Dspace%3A%20pre%3B%0A%7D%0A%0A%40media%20print%20%7B%0A%20%20%20%2A%20%7B%0A%20%20%20%20%20%20background%3A%20transparent%20%21important%3B%0A%20%20%20%20%20%20color%3A%20black%20%21important%3B%0A%20%20%20%20%20%20filter%3Anone%20%21important%3B%0A%20%20%20%20%20%20%2Dms%2Dfilter%3A%20none%20%21important%3B%0A%20%20%20%7D%0A%0A%20%20%20body%20%7B%0A%20%20%20%20%20%20font%2Dsize%3A12pt%3B%0A%20%20%20%20%20%20max%2Dwidth%3A100%25%3B%0A%20%20%20%7D%0A%0A%20%20%20a%2C%20a%3Avisited%20%7B%0A%20%20%20%20%20%20text%2Ddecoration%3A%20underline%3B%0A%20%20%20%7D%0A%0A%20%20%20hr%20%7B%0A%20%20%20%20%20%20visibility%3A%20hidden%3B%0A%20%20%20%20%20%20page%2Dbreak%2Dbefore%3A%20always%3B%0A%20%20%20%7D%0A%0A%20%20%20pre%2C%20blockquote%20%7B%0A%20%20%20%20%20%20padding%2Dright%3A%201em%3B%0A%20%20%20%20%20%20page%2Dbreak%2Dinside%3A%20avoid%3B%0A%20%20%20%7D%0A%0A%20%20%20tr%2C%20img%20%7B%0A%20%20%20%20%20%20page%2Dbreak%2Dinside%3A%20avoid%3B%0A%20%20%20%7D%0A%0A%20%20%20img%20%7B%0A%20%20%20%20%20%20max%2Dwidth%3A%20100%25%20%21important%3B%0A%20%20%20%7D%0A%0A%20%20%20%40page%20%3Aleft%20%7B%0A%20%20%20%20%20%20margin%3A%2015mm%2020mm%2015mm%2010mm%3B%0A%20%20%20%7D%0A%0A%20%20%20%40page%20%3Aright%20%7B%0A%20%20%20%20%20%20margin%3A%2015mm%2010mm%2015mm%2020mm%3B%0A%20%20%20%7D%0A%0A%20%20%20p%2C%20h2%2C%20h3%20%7B%0A%20%20%20%20%20%20orphans%3A%203%3B%20widows%3A%203%3B%0A%20%20%20%7D%0A%0A%20%20%20h2%2C%20h3%20%7B%0A%20%20%20%20%20%20page%2Dbreak%2Dafter%3A%20avoid%3B%0A%20%20%20%7D%0A%7D%0A" rel="stylesheet" type="text/css" />
<script type="text/javascript">
document.addEventListener("DOMContentLoaded", function() {
var links = document.links;
for (var i = 0, linksLength = links.length; i < linksLength; i++)
if(links[i].hostname != window.location.hostname)
links[i].target = '_blank';
});
</script>
</head>
<body>
<div id="header">
<h1 class="title">derfinder counting paper Supplementary Website</h1>
<h4 class="author"><em>L Collado-Torres</em></h4>
<h4 class="date"><em>21 March 2016</em></h4>
</div>
<h1>Contents</h1>
<div id="TOC">
<ul>
<li><a href="#hippocampus-and-time-course-data-sets"><span class="toc-section-number">1</span> Hippocampus and time-course data sets</a><ul>
<li><a href="#code-to-reproduce-analyses"><span class="toc-section-number">1.1</span> Code to reproduce analyses</a></li>
<li><a href="#single-base-level"><span class="toc-section-number">1.2</span> Single base-level</a><ul>
<li><a href="#quick-overview-html-report"><span class="toc-section-number">1.2.1</span> Quick overview HTML report</a></li>
<li><a href="#csv-files-and-annotation-comparison"><span class="toc-section-number">1.2.2</span> CSV files and annotation comparison</a></li>
</ul></li>
<li><a href="#timing-and-memory-information"><span class="toc-section-number">1.3</span> Timing and memory information</a></li>
</ul></li>
<li><a href="#hippo-vs-previous-results"><span class="toc-section-number">2</span> Hippo vs previous results</a></li>
<li><a href="#additional-analyses"><span class="toc-section-number">3</span> Additional analyses</a></li>
<li><a href="#reproducibility"><span class="toc-section-number">4</span> Reproducibility</a></li>
<li><a href="#bibliography"><span class="toc-section-number">5</span> Bibliography</a></li>
</ul>
</div>
<p>This page describes the supplementary material for the <code>derfinder</code> counting paper. All the <code>bash</code>, <code>R</code> and <code>R Markdown</code> source files used to analyze the data for this project as well as generate the HTML reports are available in this website. However, it is easier to view them at <a href="https://github.com/leekgroup/derCountSupp">github.com/leekgroup/derCountSupp</a>.</p>
<div id="hippocampus-and-time-course-data-sets" class="section level1">
<h1><span class="header-section-number">1</span> Hippocampus and time-course data sets</h1>
<p>This section of the website describes the code and reports associated with the hippocampus and time-course data sets that are referred to in the paper.</p>
<div id="code-to-reproduce-analyses" class="section level2">
<h2><span class="header-section-number">1.1</span> Code to reproduce analyses</h2>
<p>There are 9 main <code>bash</code> scripts named _step1-*_ through _step9-*_.</p>
<ol style="list-style-type: decimal">
<li><em>fullCoverage</em> loads the data from the raw files. See <a href="step1-fullCoverage.sh" class="uri">step1-fullCoverage.sh</a> and <a href="step1-fullCoverage.R" class="uri">step1-fullCoverage.R</a>.</li>
<li><em>makeModels</em> creates the models used for the single base-level analysis. See <a href="step2-makeModels.sh" class="uri">step2-makeModels.sh</a> and <a href="step2-makeModels.R" class="uri">step2-makeModels.R</a>.</li>
<li><em>analyzeChr</em> runs the single base-level analysis by chromosome. See <a href="step3-analyzeChr.sh" class="uri">step3-analyzeChr.sh</a> and <a href="step3-analyzeChr.R" class="uri">step3-analyzeChr.R</a>.</li>
<li><em>mergeResults</em> merges the single base-level analysis results for all the chromosomes. See <a href="step4-mergeResults.sh" class="uri">step4-mergeResults.sh</a>.</li>
<li><em>derfinderReport</em> generates a HTML report for the single base-level DERs. See <a href="step5-derfinderReport.sh" class="uri">step5-derfinderReport.sh</a>.</li>
<li><em>regionMatrix</em> identifies the expressed regions for the expressed regions-level approach. See <a href="step6-regionMatrix.sh" class="uri">step6-regionMatrix.sh</a>.</li>
<li><em>regMatVsDERs</em> creates a simple HTML report comparing the single-base and expressed-regions approaches. See <a href="step7-regMatVsDERs.sh" class="uri">step7-regMatVsDERs.sh</a> and <a href="step7-regMatVsDERs.Rmd" class="uri">step7-regMatVsDERs.Rmd</a>.</li>
<li><em>coverageToExon</em> creates an exon count table using known annotation information. See <a href="step8-coverageToExon.sh" class="uri">step8-coverageToExon.sh</a> and <a href="step8-coverageToExon.R" class="uri">step8-coverageToExon.R</a>.</li>
<li><em>summaryInfo</em> creates a HTML report with brief summary information for the given experiment. See <a href="step9-summaryInfo.sh" class="uri">step9-summaryInfo.sh</a>, <a href="step9-summaryInfo.R" class="uri">step9-summaryInfo.R</a>, and <a href="step9-summaryInfo.Rmd" class="uri">step9-summaryInfo.Rmd</a>.</li>
</ol>
<p>There are also 3 optional <code>bash</code> scripts used when BAM files are available.</p>
<ol style="list-style-type: decimal">
<li><em>sortSam</em> creates sorted by sequence name SAM files. See <a href="optional1-sortSam.sh" class="uri">optional1-sortSam.sh</a>.</li>
<li><em>HTSeq</em> creates the exon count tables using <code>HTSeq</code>. See <a href="optional2-HTSeq.sh" class="uri">optional2-HTSeq.sh</a>.</li>
<li><em>summOv</em> uses <code>GenomicRanges</code> to create the exon count tables. See <a href="optional3-summOv.sh" class="uri">optional3-summOv.sh</a> and <a href="optional3-summOv.R" class="uri">optional3-summOv.R</a>.</li>
<li><em>featureCounts</em></li>
</ol>
<p>A final <code>bash</code> script, <a href="run-all.sh" class="uri">run-all.sh</a>, can be used to run the main 9 steps (or a subset of them).</p>
<p>All scripts show at the beginning the way they were used. Some of them generate intermediate small <code>bash</code> scripts, for example one script per chromosome for the <em>analyzeChr</em> step. For some steps, there is a companion <code>R</code> or <code>R Markdown</code> code file when the code is more involved or an HTML file is generated in the particular step.</p>
<p>The <a href="check-analysis-time.R" class="uri">check-analysis-time.R</a> script was useful for checking the progress of the <em>step3-analyzeChr</em> jobs and detect whenever a node in the cluster was presenting problems.</p>
<p>We expect that these scripts will be useful to <code>derfinder</code> users who want to automate the single base-level and/or expressed regions-level analyses for several data sets and/or have the jobs run automatically without having to check if each step has finished running.</p>
<p>Note that all <code>bash</code> scripts are tailored for the cluster we have access to which administer job queues with Sun Grid Engine (SGE).</p>
</div>
<div id="single-base-level" class="section level2">
<h2><span class="header-section-number">1.2</span> Single base-level</h2>
<div id="quick-overview-html-report" class="section level3">
<h3><span class="header-section-number">1.2.1</span> Quick overview HTML report</h3>
<p>This HTML report contains basic information on the <code>derfinder</code> <a id="cite-derfinder"></a>(<a href="http://www.biorxiv.org/content/early/2015/02/19/015370.abstract">Collado-Torres, Frazee, Love, Irizarry, et al., 2015</a>) results from the <em>Hippo</em> data set. The report answers basic questions such as:</p>
<ul>
<li>What is the number of filtered bases?</li>
<li>What is the number of candidate regions?</li>
<li>How many candidate regions are significant?</li>
</ul>
<p>It also illustrates three clusters of candidate differentially expressed regions (DERs) from the single base-level analysis. You can view the report by following this link:</p>
<ul>
<li><a href="hippo/summaryInfo/run3-v1.0.10/summaryInfo.html">Hippo</a></li>
</ul>
</div>
<div id="csv-files-and-annotation-comparison" class="section level3">
<h3><span class="header-section-number">1.2.2</span> CSV files and annotation comparison</h3>
<p>This HTML report has the code for loading the R data files and generating the CSV files. The report also has Venn diagrams showing the number of candidate DERs from the single base-level analysis that overlap known exons, introns and intergenic regions using the UCSC hg19 annotation. It also includes a detailed description of the columns in the CSV files.</p>
<p>View the <a href="venn/venn.html">venn</a> report or its <code>R Markdown</code> source file <a href="venn/venn.Rmd">venn.Rmd</a>.</p>
</div>
</div>
<div id="timing-and-memory-information" class="section level2">
<h2><span class="header-section-number">1.3</span> Timing and memory information</h2>
<p>This HTML report has code for reading and processing the time and memory information for each job extracted with <a href="https://github.com/alyssafrazee/efficiency_analytics">efficiency_analytics</a> <a id="cite-eff"></a>(<a href="http://dx.doi.org/10.6084/m9.figshare.878000">Frazee, 2014</a>). The report contains a detailed description of the analysis steps and tables summarizing the maximum memory and time for each analysis step if all the jobs for that particular step were running simultaneously. Finally, there is an interactive table with the timing results.</p>
<p>View the <a href="timing/timing.html">timing</a> report or check the <code>R Markdown</code> file <a href="timing/timing.Rmd">timing.Rmd</a>.</p>
</div>
</div>
<div id="hippo-vs-previous-results" class="section level1">
<h1><span class="header-section-number">2</span> Hippo vs previous results</h1>
<p><a href="hippo/pnas/compareVsPNAS.html">compareVsPNAS</a> is an HTML report comparing 29 regions that were previously found to be differentially expressed <a id="cite-zhou2011"></a>(<a href="#bib-zhou2011">Zhou, Zhifeng, Yuan, Qiaoping, et al., 2011</a>) versus the <code>derfinder</code> single base-level results. It also has code for identified differentially expressed disjoint exons. The additional script <a href="hippo/counts-gene/counts-gene.R">counts-gene.R</a> has the code for gene counting with <code>summarizeOverlaps()</code>. <a href="hippo/pnas/compareVsPNAS-gene.html">compareVsPNAS-gene</a> compares the results between <code>DESeq2</code> and <code>edgeR</code>-robust against <code>derfinder</code> at the gene level with 40 total plots: 10 for each case of agreement/disagreement.</p>
<p>View the <a href="hippo/pnas/compareVsPNAS.html">compareVsPNAS</a> report or check the <code>R Markdown</code> file <a href="hippo/pnas/compareVsPNAS.Rmd">compareVsPNAS.Rmd</a> run by the <a href="hippo/pnas/runComparison.sh">runComparison.sh</a> script. Also view the <a href="hippo/pnas/compareVsPNAS-gene.html">compareVsPNAS-gene</a> report and its linked <code>R Markdown</code> file <a href="hippo/pnas/compareVsPNAS-gene.Rmd">compareVsPNAS-gene.Rmd</a>.</p>
</div>
<div id="additional-analyses" class="section level1">
<h1><span class="header-section-number">3</span> Additional analyses</h1>
<p>The following <code>R</code> source files have the code for reproducing additional analyses described in the paper</p>
<ul>
<li><a href="additional-analyses/feature_counts.R">feature_counts.R</a> Feature counts analysis of Hippo and Snyder data sets.</li>
<li><a href="gff/createGFF.R">createGFF.R</a> and <a href="gff/runGFF.sh">runGFF.sh</a> create the GFF file used the script <a href="optional2-HTSeq.sh" class="uri">optional2-HTSeq.sh</a>.</li>
</ul>
<p>This scripts also include other exploratory code.</p>
</div>
<div id="reproducibility" class="section level1">
<h1><span class="header-section-number">4</span> Reproducibility</h1>
<p>Date this page was generated.</p>
<pre><code>## [1] "2016-03-21 10:16:26 EDT"</code></pre>
<p>Wallclock time spent generating the report.</p>
<pre><code>## Time difference of 1.172 secs</code></pre>
<p><code>R</code> session information.</p>
<pre><code>## Session info -----------------------------------------------------------------------------------------------------------</code></pre>
<pre><code>## setting value
## version R version 3.2.2 (2015-08-14)
## system x86_64, darwin13.4.0
## ui X11
## language (EN)
## collate en_US.UTF-8
## tz America/New_York
## date 2016-03-21</code></pre>
<pre><code>## Packages ---------------------------------------------------------------------------------------------------------------</code></pre>
<pre><code>## package * version date source
## bibtex 0.4.0 2014-12-31 CRAN (R 3.2.0)
## BiocStyle * 1.8.0 2015-10-14 Bioconductor
## bitops 1.0-6 2013-08-17 CRAN (R 3.2.0)
## devtools 1.10.0 2016-01-23 CRAN (R 3.2.3)
## digest 0.6.9 2016-01-08 CRAN (R 3.2.3)
## evaluate 0.8 2015-09-18 CRAN (R 3.2.0)
## formatR 1.2.1 2015-09-18 CRAN (R 3.2.0)
## htmltools 0.3 2015-12-29 CRAN (R 3.2.3)
## httr 1.1.0 2016-01-28 CRAN (R 3.2.3)
## knitcitations * 1.0.7 2015-10-28 CRAN (R 3.2.0)
## knitr 1.12.3 2016-01-22 CRAN (R 3.2.3)
## lubridate 1.5.0 2015-12-03 CRAN (R 3.2.3)
## magrittr 1.5 2014-11-22 CRAN (R 3.2.0)
## memoise 1.0.0 2016-01-29 CRAN (R 3.2.3)
## plyr 1.8.3 2015-06-12 CRAN (R 3.2.1)
## R6 2.1.2 2016-01-26 CRAN (R 3.2.3)
## Rcpp 0.12.3 2016-01-10 CRAN (R 3.2.3)
## RCurl 1.95-4.7 2015-06-30 CRAN (R 3.2.1)
## RefManageR 0.10.6 2016-02-15 CRAN (R 3.2.3)
## RJSONIO 1.3-0 2014-07-28 CRAN (R 3.2.0)
## rmarkdown * 0.9.2 2016-01-01 CRAN (R 3.2.3)
## stringi 1.0-1 2015-10-22 CRAN (R 3.2.0)
## stringr 1.0.0 2015-04-30 CRAN (R 3.2.0)
## XML 3.98-1.3 2015-06-30 CRAN (R 3.2.0)
## yaml 2.1.13 2014-06-12 CRAN (R 3.2.0)</code></pre>
<p>You can view the source <code>R Markdown</code> file for this page at <a href="index.Rmd" class="uri">index.Rmd</a>.</p>
</div>
<div id="bibliography" class="section level1">
<h1><span class="header-section-number">5</span> Bibliography</h1>
<p>This report was generated using <code>BiocStyle</code> <a id="cite-BiocStyle"></a>(<a href="https://github.com/Bioconductor/BiocStyle">Morgan, Oleś, and Huber, 2016</a>) with <code>knitr</code> <a id="cite-knitr"></a>(<a href="http://www.crcpress.com/product/isbn/9781466561595">Xie, 2014</a>) and <code>rmarkdown</code> <a id="cite-rmarkdown"></a>(<a href="http://CRAN.R-project.org/package=rmarkdown">Allaire, Cheng, Xie, McPherson, et al., 2016</a>) running behind the scenes.</p>
<p>Citations were made with <code>knitcitations</code> <a id="cite-knitcitations"></a>(<a href="http://CRAN.R-project.org/package=knitcitations">Boettiger, 2015</a>). Citation file: <a href="index.bib" class="uri">index.bib</a>.</p>
<p>
<a id="bib-rmarkdown"></a><a href="#cite-rmarkdown">[1]</a><cite> J. Allaire, J. Cheng, Y. Xie, J. McPherson, et al. <em>rmarkdown: Dynamic Documents for R</em>. R package version 0.9.2. 2016. URL: <a href="http://CRAN.R-project.org/package=rmarkdown">http://CRAN.R-project.org/package=rmarkdown</a>.</cite>
</p>
<p>
<a id="bib-knitcitations"></a><a href="#cite-knitcitations">[2]</a><cite> C. Boettiger. <em>knitcitations: Citations for ‘Knitr’ Markdown Files</em>. R package version 1.0.7. 2015. URL: <a href="http://CRAN.R-project.org/package=knitcitations">http://CRAN.R-project.org/package=knitcitations</a>.</cite>
</p>
<p>
<a id="bib-derfinder"></a><a href="#cite-derfinder">[3]</a><cite> L. Collado-Torres, A. C. Frazee, M. I. Love, R. A. Irizarry, et al. “derfinder: Software for annotation-agnostic RNA-seq differential expression analysis”. In: <em>bioRxiv</em> (2015). DOI: <a href="http://dx.doi.org/10.1101/015370">10.1101/015370</a>. URL: <a href="http://www.biorxiv.org/content/early/2015/02/19/015370.abstract">http://www.biorxiv.org/content/early/2015/02/19/015370.abstract</a>.</cite>
</p>
<p>
<a id="bib-eff"></a><a href="#cite-eff">[4]</a><cite> A. Frazee. <em>Efficiency analysis of Sun Grid Engine batch jobs</em>. 2014. URL: <a href="http://dx.doi.org/10.6084/m9.figshare.878000">http://dx.doi.org/10.6084/m9.figshare.878000</a>.</cite>
</p>
<p>
<a id="bib-BiocStyle"></a><a href="#cite-BiocStyle">[5]</a><cite> M. Morgan, A. Oleś and W. Huber. <em>BiocStyle: Standard styles for vignettes and other Bioconductor documents</em>. R package version 1.8.0. 2016. URL: <a href="https://github.com/Bioconductor/BiocStyle">https://github.com/Bioconductor/BiocStyle</a>.</cite>
</p>
<p>
<a id="bib-knitr"></a><a href="#cite-knitr">[6]</a><cite> Y. Xie. “knitr: A Comprehensive Tool for Reproducible Research in R”. In: <em>Implementing Reproducible Computational Research</em>. Ed. by V. Stodden, F. Leisch and R. D. Peng. ISBN 978-1466561595. Chapman and Hall/CRC, 2014. URL: <a href="http://www.crcpress.com/product/isbn/9781466561595">http://www.crcpress.com/product/isbn/9781466561595</a>.</cite>
</p>
<p>
<a id="bib-zhou2011"></a><a href="#cite-zhou2011">[7]</a><cite> Zhou, Zhifeng, Yuan, Qiaoping, et al. “Substance-specific and shared transcription and epigenetic changes in the human hippocampus chronically exposed to cocaine and alcohol”. In: <em>Proceedings of the National Academy of Sciences of the United States of America</em> 108.16 (2011), pp. 6626-6631.</cite>
</p>
</div>
<!-- dynamically load mathjax for compatibility with self-contained -->
<script>
(function () {
var script = document.createElement("script");
script.type = "text/javascript";
script.src = "https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";
document.getElementsByTagName("head")[0].appendChild(script);
})();
</script>
</body>
</html>