update seqExport()

zhengxwen · Mar 27, 2024 · ae90aa3 · ae90aa3
1 parent b29f95f
commit ae90aa3
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Showing 4 changed files with 15 additions and 7 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: SeqArray
 Type: Package
 Title: Data Management of Large-Scale Whole-Genome Sequence Variant Calls
-Version: 1.42.3
-Date: 2024-03-22
+Version: 1.43.4
+Date: 2024-03-27
 Depends: R (>= 3.5.0), gdsfmt (>= 1.31.1)
 Imports: methods, parallel, IRanges, GenomicRanges, GenomeInfoDb, Biostrings,
         S4Vectors

diff --git a/NEWS b/NEWS
@@ -12,6 +12,9 @@ UTILITIES
       sex chromosomes, when the alleles are partially missing (e.g., genotypes
       on chromosome X for males)
 
+    o new 'verbose.clean' in `seqExport()` to control the level of information
+      display
+
 
 CHANGES IN VERSION 1.42.3
 -------------------------

diff --git a/R/UtilsExport.R b/R/UtilsExport.R
@@ -11,7 +11,7 @@
 # Export to a GDS file
 #
 seqExport <- function(gdsfile, out.fn, info.var=NULL, fmt.var=NULL,
-    samp.var=NULL, optimize=TRUE, digest=TRUE, verbose=TRUE)
+    samp.var=NULL, optimize=TRUE, digest=TRUE, verbose=TRUE, verbose.clean=NA)
 {
     stopifnot(inherits(gdsfile, "SeqVarGDSClass"))
     stopifnot(is.character(out.fn), length(out.fn)==1L)
@@ -23,6 +23,8 @@ seqExport <- function(gdsfile, out.fn, info.var=NULL, fmt.var=NULL,
     stopifnot(is.logical(optimize), length(optimize)==1L)
     stopifnot(is.logical(digest) | is.character(digest), length(digest)==1L)
     stopifnot(is.logical(verbose), length(verbose)==1L)
+    stopifnot(is.logical(verbose.clean), length(verbose.clean)==1L)
+    if (is.na(verbose.clean)) verbose.clean <- verbose
 
     #######################################################################
 
@@ -331,9 +333,9 @@ seqExport <- function(gdsfile, out.fn, info.var=NULL, fmt.var=NULL,
     # optimize access efficiency
     if (optimize)
     {
-        if (verbose)
+        if (verbose.clean)
             cat("Optimize the access efficiency ...\n")
-        cleanup.gds(out.fn, verbose=verbose)
+        cleanup.gds(out.fn, verbose=verbose.clean)
     }
 
     # output

diff --git a/man/seqExport.Rd b/man/seqExport.Rd
@@ -7,7 +7,7 @@ by \code{seqSetFilter()}.
 }
 \usage{
 seqExport(gdsfile, out.fn, info.var=NULL, fmt.var=NULL, samp.var=NULL,
-    optimize=TRUE, digest=TRUE, verbose=TRUE)
+    optimize=TRUE, digest=TRUE, verbose=TRUE, verbose.clean=NA)
 }
 \arguments{
     \item{gdsfile}{a \code{\link{SeqVarGDSClass}} object}
@@ -24,14 +24,17 @@ seqExport(gdsfile, out.fn, info.var=NULL, fmt.var=NULL, samp.var=NULL,
         "sha256", "sha384" or "sha512"); add md5 hash codes to the GDS file
         if TRUE or a digest algorithm is specified}
     \item{verbose}{if \code{TRUE}, show information}
+    \item{verbose.clean}{when \code{verbose.clean=NA}, set it to \code{verbose};
+        whether display information when calling \code{cleanup.gds} or not;
+        only applicable when \code{optimize=TRUE}}
 }
 \value{
     Return the file name of GDS format with an absolute path.
 }
 
 \author{Xiuwen Zheng}
 \seealso{
-    \code{\link{seqVCF2GDS}}
+    \code{\link{seqVCF2GDS}}, \code{\link{cleanup.gds}}
 }
 
 \examples{