variant_count in seqVCF2GDS()

Author: zhengxwen

NEWS

@@ -8,6 +8,10 @@ UTILITIES
       `seqVCF2GDS()` is faster when obtaining the number of variants for
       splitting files.
 
+    o new 'variant_count' in `seqVCF2GDS()` to specify the number of variants
+      in the VCF file when it is known; it is only applicable when multiple
+      cores are used.
+
 
 CHANGES IN VERSION 1.46.0
 -------------------------

R/ConvVCF2GDS.R

@@ -545,7 +545,8 @@ seqVCF2GDS <- function(vcf.fn, out.fn, header=NULL,
     storage.option="LZMA_RA", info.import=NULL, fmt.import=NULL,
     genotype.var.name="GT", ignore.chr.prefix="chr",
     scenario=c("general", "imputation"), reference=NULL, start=1L, count=-1L,
-    optimize=TRUE, raise.error=TRUE, digest=TRUE, parallel=FALSE, verbose=TRUE)
+    variant_count=NA_integer_, optimize=TRUE, raise.error=TRUE, digest=TRUE,
+    parallel=FALSE, verbose=TRUE)
 {
     # check
     if (!inherits(vcf.fn, "connection"))
@@ -592,20 +593,15 @@ seqVCF2GDS <- function(vcf.fn, out.fn, header=NULL,
     {
         if (pnum > 1L)
             stop("No parallel support when the input is a connection object.")
-    }
-
-    if (is.character(vcf.fn))
-        variant_count <- attr(vcf.fn, "variant_count")
-    else
-        variant_count <- NULL
-    if (!is.null(variant_count))
+        if (length(variant_count)!=1L || !is.na(variant_count))
+            warning("'variant_count' is not used in seqVCF2GDS() when 'vcf.fn' is a connection object.")
+    } else if (!identical(variant_count, NA_integer_))
     {
         if (!is.numeric(variant_count))
-            stop("the attribute 'variant_count' of 'vcf.fn' should be a numeric vector.")
+            stop("'variant_count' should be a numeric vector.")
         if (length(variant_count) != length(vcf.fn))
-            stop("the attribute 'variant_count' of 'vcf.fn' should be as the same length as 'vcf.fn'.")
+            stop("'variant_count' and 'vcf.fn' should have the same length.")
     }
-
     if (verbose) cat(date(), "\n", sep="")
 
     genotype.storage <- "bit2"
@@ -785,12 +781,18 @@ seqVCF2GDS <- function(vcf.fn, out.fn, header=NULL,
         }
 
         # get the number of variants in each VCF file
-        num_array <- vapply(vcf.fn, function(fn)
+        for (i in seq_along(vcf.fn))
         {
-            v <- seqVCF_Header(fn, getnum=TRUE, parallel=parallel, verbose=FALSE)
-            v$num.variant
-        }, 0L)
-        num_var <- sum(num_array)
+            v <- variant_count[i]
+            if (is.na(v) || (v < 0L))
+            {
+                fn <- vcf.fn[i]
+                variant_count[i] <- seqVCF_Header(fn, getnum=TRUE,
+                    parallel=parallel, verbose=FALSE)$num.variant
+            }
+        }
+        num_var <- sum(variant_count)
+        if (anyNA(num_var)) stop("Getting invalid # of variants.")
 
         if (start < 1L)
             stop("'start' should be a positive integer if conversion in parallel.")
@@ -822,31 +824,25 @@ seqVCF2GDS <- function(vcf.fn, out.fn, header=NULL,
             seqParallel(parallel, NULL, FUN = function(
                 vcf.fn, header, storage.option, info.import, fmt.import,
                 genotype.var.name, ignore.chr.prefix, scenario, optim,
-                raise.err, ptmpfn, psplit, num_array)
+                raise.err, ptmpfn, psplit, variant_count)
             {
-                # load package
-                library(SeqArray, quietly=TRUE, verbose=FALSE)
-
-                attr(vcf.fn, "variant_count") <- num_array
                 i <- process_index  # the process id, starting from one
-
-                seqVCF2GDS(vcf.fn, ptmpfn[i], header=oldheader,
+                SeqArray::seqVCF2GDS(vcf.fn, ptmpfn[i], header=oldheader,
                     storage.option=storage.option, info.import=info.import,
                     fmt.import=fmt.import, genotype.var.name=genotype.var.name,
                     ignore.chr.prefix=ignore.chr.prefix,
                     start = psplit[[1L]][i], count = psplit[[2L]][i],
+                    variant_count=variant_count,
                     optimize=optim, scenario=scenario, raise.error=raise.err,
                     digest=FALSE, parallel=FALSE, verbose=FALSE)
-
-                invisible()
-
+                invisible()  # return
             }, split="none",
                 vcf.fn=vcf.fn, header=header, storage.option=storage.option,
                 info.import=info.import, fmt.import=fmt.import,
                 genotype.var.name=genotype.var.name,
                 ignore.chr.prefix=ignore.chr.prefix, scenario=scenario,
                 optim=optimize, raise.err=raise.error,
-                ptmpfn=ptmpfn, psplit=psplit, num_array=num_array)
+                ptmpfn=ptmpfn, psplit=psplit, variant_count=variant_count)
 
             if (verbose)
                 cat("    >>> Done (", date(), ") <<<\n", sep="")

man/seqVCF2GDS.Rd

@@ -9,8 +9,9 @@
 seqVCF2GDS(vcf.fn, out.fn, header=NULL, storage.option="LZMA_RA",
     info.import=NULL, fmt.import=NULL, genotype.var.name="GT",
     ignore.chr.prefix="chr", scenario=c("general", "imputation"),
-    reference=NULL, start=1L, count=-1L, optimize=TRUE, raise.error=TRUE,
-    digest=TRUE, parallel=FALSE, verbose=TRUE)
+    reference=NULL, start=1L, count=-1L, variant_count=NA_integer_,
+    optimize=TRUE, raise.error=TRUE, digest=TRUE, parallel=FALSE,
+    verbose=TRUE)
 seqBCF2GDS(bcf.fn, out.fn, header=NULL, storage.option="LZMA_RA",
     info.import=NULL, fmt.import=NULL, genotype.var.name="GT",
     ignore.chr.prefix="chr", scenario=c("general", "imputation"),
@@ -50,6 +51,11 @@ seqBCF2GDS(bcf.fn, out.fn, header=NULL, storage.option="LZMA_RA",
     \item{start}{the starting variant if importing part of VCF files}
     \item{count}{the maximum count of variant if importing part of VCF files,
         -1 indicates importing to the end}
+    \item{variant_count}{\code{NA_integer_} (default) or a numeric vector
+        specifying the numbers of variants in the VCF file(s) in \code{vcf.fn};
+        only applicable when multiple cores are used; if the number of variants
+        is known, the conversion can skip counting the variants before
+        splitting the file(s); \code{variant_count} could be an approximate}
     \item{optimize}{if \code{TRUE}, optimize the access efficiency by calling
         \code{\link{cleanup.gds}}}
     \item{raise.error}{\code{TRUE}: throw an error if numeric conversion fails;