Redefine generics from VariantAnnotation and SummarizedExperiment

To avoid long loading times from importing VariantAnnotation and
SummarizedExperiment, redefine generic methods from those packages.

DESCRIPTION

@@ -4,11 +4,10 @@ Title: Big Data Management of Whole-genome Sequence Variant Calls
 Version: 1.17.1
 Date: 2017-05-07
 Depends: R (>= 3.3.0), gdsfmt (>= 1.10.1)
-Imports: methods, parallel, IRanges, GenomicRanges, GenomeInfoDb
+Imports: methods, parallel, IRanges, GenomicRanges, GenomeInfoDb, Biostrings, S4Vectors
 LinkingTo: gdsfmt
 Suggests: digest, crayon, RUnit, knitr, Rcpp, SNPRelate, Biobase, BiocParallel,
-        BiocGenerics, Biostrings, S4Vectors, VariantAnnotation,
-        SummarizedExperiment
+        BiocGenerics, VariantAnnotation
 Authors@R: c(person("Xiuwen", "Zheng", role=c("aut", "cre"),
         email="[email protected]"),
         person("Stephanie", "Gogarten", role="aut",

NAMESPACE

@@ -28,18 +28,22 @@ importFrom(parallel, clusterApply, clusterApplyLB, clusterCall, detectCores,
     makeCluster, makeForkCluster, mclapply, stopCluster)
 importFrom(utils, read.table, flush.console)
 
+importFrom(S4Vectors, DataFrame, SimpleList)
 importClassesFrom(IRanges, IRanges)
-importFrom(IRanges, IRanges, IntegerList, NumericList, CharacterList)
+importFrom(IRanges, IRanges, IntegerList, NumericList, CharacterList, DataFrameList)
 importClassesFrom(GenomicRanges, GRanges, GRangesList)
 importFrom(GenomicRanges, GRanges)
 importMethodsFrom(GenomicRanges, granges)
-importMethodsFrom(GenomeInfoDb, seqnames)
+importMethodsFrom(GenomeInfoDb, seqnames, seqlevels)
+importFrom(GenomeInfoDb, renameSeqlevels)
+importFrom(Biostrings, DNAStringSet, DNAStringSetList)
 
 
 # Export all names
 exportPattern("^seq*")
 export(.onAttach, .Last.lib)
 
 exportClasses(SeqVarGDSClass)
-exportMethods(granges)
-exportMethods(seqClose, seqSetFilter)
+exportMethods(granges, ref, alt, qual, filt, header, fixed,
+              info, geno, colData, rowRanges)
+exportMethods(seqClose, seqSetFilter, seqAsVCF)

R/AllGenerics.R

@@ -6,3 +6,17 @@ setGeneric("seqSetFilter", function(object, variant.sel, ...)
     standardGeneric("seqSetFilter"))
 
 # setGeneric("seqAppend", function(object, ...) standardGeneric("seqAppend"))
+
+setGeneric("seqAsVCF", function(x, ...) standardGeneric("seqAsVCF"))
+
+# redefine generics from VariantAnnotation and SummarizedExperiment to reduce package load time
+setGeneric("ref", function(x, ...) standardGeneric("ref"))
+setGeneric("alt", function(x, ...) standardGeneric("alt"))
+setGeneric("qual", function(x, ...) standardGeneric("qual"))
+setGeneric("filt", function(x, ...) standardGeneric("filt"))
+setGeneric("fixed", function(x, ...) standardGeneric("fixed"))
+setGeneric("header", function(x, ...) standardGeneric("header"))
+setGeneric("info", function(x, ...) standardGeneric("info"))
+setGeneric("geno", function(x, ...) standardGeneric("geno"))
+setGeneric("rowRanges", function(x, ...) standardGeneric("rowRanges"))
+setGeneric("colData", function(x, ...) standardGeneric("colData"))

R/Internal.R

@@ -6,27 +6,6 @@
 #
 
 
-#######################################################################
-# Internal variable(s)
-#
-
-# package-wide variable
-.packageEnv <- new.env()
-
-# asVCF exported functions
-.asVCF_Export <- function()
-{
-    isTRUE(.packageEnv$vcf_export)
-}
-
-# set asVCF export flag
-.asVCF_SetTRUE <- function()
-{
-    .packageEnv$vcf_export <- TRUE
-}
-
-
-
 #######################################################################
 # Get the numbers of selected samples and variants
 #
@@ -727,3 +706,49 @@
 
     invisible()
 }
+
+#######################################################################
+# Convert to a VariantAnnotation object
+#
+
+.variableLengthToList <- function(x)
+{
+    xl <- list()
+    j <- 1L
+    for (i in 1:length(x$length))
+    {
+        len <- x$length[i]
+        if (len > 0L)
+        {
+            xl[[i]] <- x$data[j:(j+len-1)]
+            j <- j+len
+        } else {
+            xl[[i]] <- NA
+        }
+    }
+    xl
+}
+
+.toAtomicList <- function(x, type)
+{
+    switch(type,
+        Character=CharacterList(x),
+        String=CharacterList(x),
+        Integer=IntegerList(x),
+        Float=NumericList(x))
+}
+
+.variableLengthToMatrix <- function(x)
+{
+    xl <- list()
+    i <- 1L
+    for (j in seq_along(x))
+    {
+        for (k in seq_len(NROW(x[[j]])))
+        {
+            xl[[i]] <- x[[j]][k,]
+            i <- i + 1L
+        }
+    }
+    matrix(xl, nrow=NROW(x[[1L]]), ncol=length(x))
+}