Commit c686de4e authored by VladaMilch's avatar VladaMilch
Browse files

try separating outputDir and fastaDir

parent bbc03ac3
......@@ -54,7 +54,8 @@ makeNewAnnotationPackage <- function(alignment.dir,
level = level,
min_probe_number = min_probe_number,
quiet=quiet,
pkgNameSUFFIX = pkgNameSUFFIX)
pkgNameSUFFIX = pkgNameSUFFIX,
fastaDir=fastaDir)
# debugging msg start
cat(paste0(names(new_pd)))
# debugging msg end
......@@ -71,7 +72,8 @@ makeNewAnnotationPackage_inner <- function(alignment.dir,
level,
min_probe_number,
quiet=FALSE,
pkgNameSUFFIX
pkgNameSUFFIX,
fastaDir=fastaDir
)
{
stopifnot(class(pkgNameSUFFIX) == "character")
......@@ -80,14 +82,14 @@ makeNewAnnotationPackage_inner <- function(alignment.dir,
# checks for input parameters for alignments2parsedData inside the function
NEW_ParsedData <- alignments2parsedData(alignment.dir = alignment.dir,
Annotation = Annotation,
outputDir = outputDir,
outputDir = fastaDir,
level = level,
min_probe_number = min_probe_number,
package_seed = package_seed)
make_package_from_parsedData(parsedData = NEW_ParsedData,
object = package_seed[[1]], #seed
destDir = outputDir,
destDir = fastaDir,
quiet = quiet,
pkgNameSUFFIX = pkgNameSUFFIX,
annotation_type = package_seed[[3]])
......
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