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
|
setMethod("filterVcf", "character",
function(file, genome, destination, ..., verbose=TRUE,
index=FALSE, prefilters=FilterRules(),
filters=FilterRules(), param=ScanVcfParam())
{
if (file.exists(destination))
stop(sprintf("file '%s' exists and will not be over-written",
destination))
tbx <- open(TabixFile(file, yieldSize=100000))
on.exit(close(tbx))
filterVcf(tbx, genome=genome, destination=destination, ...,
verbose=verbose, index=index, prefilters=prefilters,
filters=filters, param=param)
})
.unlistScan <- function(...)
unlist(scanTabix(...), use.names=FALSE)
.prefilter <-
function(tbxFile, verbose, prefilters, param, ...)
{
if (verbose)
message("starting prefilter")
if (length(vcfWhich(param))) {
warning("vcfWhich(param) ignored when using prefilter")
vcfWhich(param) <- GRanges()
}
if (!isOpen(tbxFile)) {
open(tbxFile)
on.exit(close(tbxFile), add=TRUE)
}
prefilteredFilename <- tempfile()
prefiltered <- file(prefilteredFilename, "w")
needsClosing <- TRUE
on.exit(if (needsClosing) close(prefiltered), add=TRUE)
## copy header
writeLines(headerTabix(tbxFile)$header, prefiltered)
## prefilter
param <- vcfWhich(param)
nTotal <- 0L
while (length(tbxChunk <- .unlistScan(tbxFile, ..., param=param))) {
if (verbose)
message("prefiltering ", nTotal <- nTotal + length(tbxChunk),
" records")
tbxChunk <- subsetByFilter(tbxChunk, prefilters)
writeLines(tbxChunk, prefiltered)
}
close(prefiltered)
needsClosing <- FALSE
prefilteredFilename
}
.filter <-
function(tbxFile, genome, destination, verbose, filters, param, ...)
{
if (verbose)
message("starting filter")
if (length(vcfWhich(param))) {
yieldSize(tbxFile) <- NA_integer_
vcfChunk <- readVcf(tbxFile, genome, ..., param=param)
if (verbose)
message("filtering ", nrow(vcfChunk), " records")
vcfChunk <- subsetByFilter(vcfChunk, filters)
writeVcf(vcfChunk, filtered)
} else {
if (!isOpen(tbxFile)) {
open(tbxFile)
on.exit(close(tbxFile), add=TRUE)
}
filtered <- file(destination, open="w")
needsClosing <- TRUE
on.exit(if (needsClosing) close(filtered), add=TRUE)
nTotal <- 0L
while (nrow(vcfChunk <- readVcf(tbxFile, genome, ..., param=param))) {
if (verbose)
message("filtering ", nTotal <- nTotal + nrow(vcfChunk),
" records")
vcfChunk <- subsetByFilter(vcfChunk, filters)
writeVcf(vcfChunk, filtered)
}
close(filtered)
needsClosing <- FALSE
}
if (verbose)
message("completed filtering")
destination
}
setMethod("filterVcf", "TabixFile",
function(file, genome, destination, ..., verbose = TRUE,
index = FALSE,
prefilters = FilterRules(), filters = FilterRules(),
param = ScanVcfParam())
{
if (!isSingleString(destination))
stop("'destination' must be character(1)")
if (!isTRUEorFALSE(verbose))
stop("'verbose' must be TRUE or FALSE")
if (!isTRUEorFALSE(index))
stop("'index' must be TRUE or FALSE")
if (!length(prefilters) && !length(filters))
stop("no 'prefilters' or 'filters' specified")
if (length(prefilters)) {
yieldSize <- yieldSize(file)
file <- .prefilter(file, verbose, prefilters, param, ...)
if(verbose){
message(sprintf("prefiltered to %s", file))
}
if (length(filters)) {
## TabixFile needs to be bgzipped and indexed
## FIXME: all records are read at next stage, so no need to index?
if (verbose)
message("prefilter compressing and indexing ", sQuote(file))
gzFilename <- bgzip(file, overwrite = TRUE)
indexTabix(gzFilename, format = "vcf4")
file <- TabixFile(gzFilename, yieldSize=yieldSize)
} else {
## file.rename does not work across file systems, so be expensive
file.copy(file, destination)
unlink(file)
}
}
if (length(filters)) {
file <- .filter(file, genome, destination, verbose, filters,
param, ...)
} # if filters
if (index) {
if (verbose)
message("compressing and indexing ", sQuote(file))
gzFilename <- sprintf("%s.gz", destination)
gzFilename <- bgzip(file, gzFilename, overwrite = TRUE)
destination <- indexTabix(gzFilename, format = "vcf")
unlink(file)
}
invisible(destination)
})
|
