git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@85505 bc3139a8-67e5-0310-9ffc-ced21a209358
Michael Lawrence authored on 14/01/2014 19:12:06
| ... | ... |
@@ -11,12 +11,15 @@ setGeneric("gsnap", function(input_a, input_b = NULL, params, ...)
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| 11 | 11 |
|
| 12 | 12 |
setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),
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| 13 | 13 |
function(input_a, input_b, params, |
| 14 |
- output = file_path_sans_ext(input_a, TRUE), |
|
| 14 |
+ output = file.path(getwd(), |
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| 15 |
+ file_path_sans_ext(basename(input_a), TRUE)), |
|
| 15 | 16 |
consolidate = TRUE, ...) |
| 16 | 17 |
{
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| 17 | 18 |
if (!is.null(input_b) && length(input_a) != length(input_b)) |
| 18 | 19 |
stop("If 'input_b' is non-NULL, it must have the same length",
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| 19 | 20 |
" as 'input_a'") |
| 21 |
+ if (any(is.na(input_a)) || any(is.na(input_b))) |
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| 22 |
+ stop("'input_a' and 'input_b' must not contain NA's")
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|
| 20 | 23 |
if (length(input_a) > 1L) {
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| 21 | 24 |
return(GsnapOutputList(mapply(gsnap, input_a, input_b, |
| 22 | 25 |
MoreArgs = list(params, output, |
| ... | ... |
@@ -30,7 +33,7 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),
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| 30 | 33 |
params <- initialize(params, ...) |
| 31 | 34 |
params_list <- as.list(params) |
| 32 | 35 |
if (gsnap_split_output(params)) {
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| 33 |
- params_list$split_output <- basename(output) |
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| 36 |
+ params_list$split_output <- output |
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| 34 | 37 |
output_path <- output_dir |
| 35 | 38 |
} else {
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| 36 | 39 |
output_path <- paste0(output, ".sam") |