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
|
setGeneric("ScanBamParam",
function(flag=scanBamFlag(), simpleCigar=FALSE,
reverseComplement=FALSE, tag=character(0),
tagFilter=list(), what=character(0), which,
mapqFilter=NA_integer_)
standardGeneric("ScanBamParam"),
signature="which")
setGeneric("scanBam",
function(file, index=file, ...,
param=ScanBamParam(what=scanBamWhat()))
standardGeneric("scanBam"),
signature="file")
setGeneric("scanBamHeader",
function(files, ...) standardGeneric("scanBamHeader"))
setGeneric("countBam",
function(file, index=file, ..., param=ScanBamParam())
standardGeneric("countBam"),
signature="file")
setGeneric("idxstatsBam",
function(file, index=file, ...) standardGeneric("idxstatsBam"),
signature="file")
setGeneric("asBam",
function(file, destination = sub("\\.sam(\\.gz)?", "", file), ...)
standardGeneric("asBam"))
setGeneric("asSam",
function(file, destination = sub("\\.bam", "", file), ...)
standardGeneric("asSam"))
setGeneric("sortBam",
function(file, destination, ...)
standardGeneric("sortBam"))
setGeneric("mergeBam",
function(files, destination, ...)
standardGeneric("mergeBam"),
signature="files")
setGeneric("indexBam",
function(files, ...) standardGeneric("indexBam"))
setGeneric("filterBam",
function(file, destination, index=file, ...)
standardGeneric("filterBam"))
setGeneric("quickBamFlagSummary",
function(file, ..., param=ScanBamParam(), main.groups.only=FALSE)
standardGeneric("quickBamFlagSummary"),
signature="file")
setGeneric("indexFa",
function(file, ...) standardGeneric("indexFa"))
setGeneric("scanFaIndex",
function(file, ...) standardGeneric("scanFaIndex"))
setGeneric("countFa",
function(file, ...) standardGeneric("countFa"))
setGeneric("scanFa",
function(file, param, ...,
as=c("DNAStringSet", "RNAStringSet", "AAStringSet"))
standardGeneric("scanFa"),
signature=c("file", "param"))
setGeneric("readPileup",
function(file, ...) standardGeneric("readPileup"))
## bcf
setGeneric("ScanBcfParam",
function(fixed=character(), info=character(), geno=character(),
samples=character(), trimEmpty=TRUE, which, ...)
standardGeneric("ScanBcfParam"),
signature="which")
setGeneric("isOpen")
setGeneric("isIncomplete")
setGeneric("scanBcfHeader",
function(file, ...) standardGeneric("scanBcfHeader"))
setGeneric("scanBcf",
function(file, ...) standardGeneric("scanBcf"))
setGeneric("asBcf",
function(file, dictionary, destination, ...,
overwrite=FALSE, indexDestination=TRUE)
standardGeneric("asBcf"),
signature="file")
setGeneric("indexBcf",
function(file, ...) standardGeneric("indexBcf"))
## other
setGeneric("BamViews",
function(bamPaths=character(0),
bamIndicies=bamPaths,
bamSamples=DataFrame(row.names=
make.unique(basename(bamPaths))),
bamRanges,
bamExperiment=list(), ...)
standardGeneric("BamViews"),
signature="bamRanges")
## tabix
setGeneric("seqnamesTabix", function(file, ...)
standardGeneric("seqnamesTabix"))
setGeneric("headerTabix", function(file, ...)
standardGeneric("headerTabix"))
setGeneric("scanTabix", function(file, ..., param)
standardGeneric("scanTabix"))
setGeneric("yieldTabix", function(file, ..., yieldSize=1000000L)
standardGeneric("yieldTabix"),
signature="file")
## pileup
setGeneric("pileup",
function(file, index=file, ..., scanBamParam=ScanBamParam(),
pileupParam=PileupParam())
standardGeneric("pileup"),
signature=signature("file"))
setGeneric(".asRegions", function(x) standardGeneric(".asRegions"))
setGeneric("applyPileups",
function(files, FUN, ..., param)
{
.Deprecated("pileup")
standardGeneric("applyPileups")
},
signature=c("files", "param"))
## RsamtoolsFile(s)
setGeneric("index",
function(object, ..., asNA=TRUE)
standardGeneric("index"),
signature="object")
setGeneric("index<-",
function(object, ..., value) standardGeneric("index<-"))
setGeneric("gzindex",
function(object, asNA=TRUE)
standardGeneric("gzindex"),
signature="object")
setGeneric("gzindex<-",
function(object, value) standardGeneric("gzindex<-"))
setGeneric("yieldSize",
function(object, ...) standardGeneric("yieldSize"))
setGeneric("yieldSize<-",
function(object, ..., value) standardGeneric("yieldSize<-"))
setGeneric("obeyQname",
function(object, ...) standardGeneric("obeyQname"))
setGeneric("obeyQname<-",
function(object, ..., value) standardGeneric("obeyQname<-"))
setGeneric("asMates",
function(object, ...) standardGeneric("asMates"))
setGeneric("asMates<-",
function(object, ..., value) standardGeneric("asMates<-"))
setGeneric("qnamePrefixEnd",
function(object, ...) standardGeneric("qnamePrefixEnd"))
setGeneric("qnamePrefixEnd<-",
function(object, ..., value) standardGeneric("qnamePrefixEnd<-"))
setGeneric("qnameSuffixStart",
function(object, ...) standardGeneric("qnameSuffixStart"))
setGeneric("qnameSuffixStart<-",
function(object, ..., value) standardGeneric("qnameSuffixStart<-"))
setGeneric("isOpen")
setGeneric("testPairedEndBam", function(file, index=file, ...)
standardGeneric("testPairedEndBam"),
signature="file")
|
