Binary files /tmp/tmpehYfan/wluw9abOvJ/r-bioc-bsgenome-1.56.0/build/vignette.rds and /tmp/tmpehYfan/OPzkFgudhS/r-bioc-bsgenome-1.58.0/build/vignette.rds differ
diff -Nru r-bioc-bsgenome-1.56.0/debian/changelog r-bioc-bsgenome-1.58.0/debian/changelog
--- r-bioc-bsgenome-1.56.0/debian/changelog	2020-05-20 14:57:08.000000000 +0000
+++ r-bioc-bsgenome-1.58.0/debian/changelog	2020-11-03 12:55:17.000000000 +0000
@@ -1,3 +1,13 @@
+r-bioc-bsgenome (1.58.0-1) unstable; urgency=medium
+
+  * New upstream version
+  * debhelper-compat 13 (routine-update)
+  * No tab in license text (routine-update)
+  * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
+    Repository-Browse.
+
+ -- Andreas Tille <tille@debian.org>  Tue, 03 Nov 2020 13:55:17 +0100
+
 r-bioc-bsgenome (1.56.0-1) unstable; urgency=medium
 
   * Team upload.
diff -Nru r-bioc-bsgenome-1.56.0/debian/control r-bioc-bsgenome-1.58.0/debian/control
--- r-bioc-bsgenome-1.56.0/debian/control	2020-05-20 14:57:08.000000000 +0000
+++ r-bioc-bsgenome-1.58.0/debian/control	2020-11-03 12:55:17.000000000 +0000
@@ -4,18 +4,18 @@
 Section: gnu-r
 Testsuite: autopkgtest-pkg-r
 Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
                dh-r,
                r-base-dev,
                r-bioc-biocgenerics (>= 0.13.8),
                r-bioc-s4vectors (>= 0.17.28),
                r-bioc-iranges (>= 2.13.16),
-               r-bioc-genomeinfodb (>= 1.23.9),
+               r-bioc-genomeinfodb (>= 1.25.6),
                r-bioc-genomicranges (>= 1.31.10),
                r-bioc-biostrings (>= 2.47.6),
                r-bioc-rtracklayer (>= 1.39.7),
                r-cran-matrixstats,
-               r-bioc-xvector,
+               r-bioc-xvector (>= 0.29.3),
                r-bioc-rsamtools
 Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/r-pkg-team/r-bioc-bsgenome
diff -Nru r-bioc-bsgenome-1.56.0/debian/copyright r-bioc-bsgenome-1.58.0/debian/copyright
--- r-bioc-bsgenome-1.56.0/debian/copyright	2020-05-20 14:57:08.000000000 +0000
+++ r-bioc-bsgenome-1.58.0/debian/copyright	2020-11-03 12:55:17.000000000 +0000
@@ -13,9 +13,9 @@
 License: Artistic-2.0
 
 License: Artistic-2.0
-			 The "Artistic License"
+                         The "Artistic License"
  .
-				Preamble
+                                Preamble
  .
  1. You may make and give away verbatim copies of the source form of the
     Standard Version of this Package without restriction, provided that
diff -Nru r-bioc-bsgenome-1.56.0/debian/patches/remove_paragraphs_bound_to_fail_from_vignette.patch r-bioc-bsgenome-1.58.0/debian/patches/remove_paragraphs_bound_to_fail_from_vignette.patch
--- r-bioc-bsgenome-1.56.0/debian/patches/remove_paragraphs_bound_to_fail_from_vignette.patch	2020-05-20 14:57:08.000000000 +0000
+++ r-bioc-bsgenome-1.58.0/debian/patches/remove_paragraphs_bound_to_fail_from_vignette.patch	2020-11-03 12:55:17.000000000 +0000
@@ -11,7 +11,7 @@
 
 --- a/vignettes/GenomeSearching.Rnw
 +++ b/vignettes/GenomeSearching.Rnw
-@@ -107,135 +107,7 @@ The BSgenome data package for the ce2 ge
+@@ -107,132 +107,7 @@ The BSgenome data package for the ce2 ge
  available in Bioconductor but they could be added if there is demand for
  them.
  
@@ -31,17 +31,15 @@
 -@
 -
 -When displayed, some basic information about the origin of the
--genome is shown (organism, provider, provider version, etc...)
+-genome is shown (organism, genome, provider, etc...)
 -followed by the index of {\it single} sequences and eventually
 -an additional index of {\it multiple} sequences.
 -Methods (adequately called {\it accessor methods}) are defined
 -for individual access to this information:
 -<<b3>>=
--organism(genome)
--provider(genome)
--providerVersion(genome)
+-metadata(genome)
 -seqnames(genome)
--mseqnames(genome)
+-seqinfo(genome)
 -@
 -
 -See the man page for the \Rclass{BSgenome} class (\Rfunction{?BSgenome})
@@ -143,12 +141,11 @@
 -Note that the length of \Robject{m2[p2 == m2]} should be
 -equal to \Robject{countPattern(p2, chrI, max.mismatch=0)}.
 -
--
 +% DELETED
  
- % ---------------------------------------------------------------------------
  
-@@ -297,158 +169,7 @@ More precisely, here is the analysis we
+ % ---------------------------------------------------------------------------
+@@ -295,158 +170,7 @@ More precisely, here is the analysis we
  
  \end{itemize}
  
@@ -183,7 +180,7 @@
 -    genome <- BSgenome.Celegans.UCSC.ce2
 -    seqnames <- seqnames(genome)
 -    seqnames_in1string <- paste(seqnames, collapse=", ")
--    cat("Target:", providerVersion(genome),
+-    cat("Target:", metadata(genome)$genome,
 -        "chromosomes", seqnames_in1string, "\n")
 -    append <- FALSE
 -    for (seqname in seqnames) {
@@ -308,7 +305,7 @@
  
  
  % ---------------------------------------------------------------------------
-@@ -466,25 +187,8 @@ that actually implements the fast search
+@@ -464,25 +188,8 @@ that actually implements the fast search
  So if you need to reuse the same pattern a high number of times,
  it's a good idea to convert it {\it before} to pass it to the
  \Rmethod{matchPattern} or \Rmethod{countPattern} method.
@@ -336,7 +333,7 @@
  
  % The above example is Raphael's use case discussed on BioC on Feb 2006.
  % In Biostrings 1, the equivalent would be:
-@@ -528,14 +232,7 @@ repeats with period less than or equal t
+@@ -526,14 +233,7 @@ repeats with period less than or equal t
  For a given package, all the sequences will always have the same number of
  masks.
  
@@ -352,7 +349,7 @@
  
  The built-in masks are named consistenly across all the BSgenome data packages
  available in Bioconductor:
-@@ -578,128 +275,7 @@ The {\it masked width} is the total numb
+@@ -576,128 +276,7 @@ The {\it masked width} is the total numb
  that are masked and the {\it masked ratio} is the {\it masked width}
  divided by the length of the sequence.
  
@@ -482,7 +479,7 @@
  
  
  % ---------------------------------------------------------------------------
-@@ -766,16 +342,13 @@ runAnalysis2 <- function(dict0, outfile=
+@@ -764,16 +343,13 @@ runAnalysis2 <- function(dict0, outfile=
  Remember that \Rfunction{matchPDict} only works if all the patterns in the
  input dictionary have the same length so for this 2nd analysis, we will truncate
  the patterns in \Robject{ce2dict0} to 15 nucleotides:
@@ -504,7 +501,7 @@
  
  
  % ---------------------------------------------------------------------------
-@@ -788,3 +361,4 @@ sessionInfo()
+@@ -786,3 +362,4 @@ sessionInfo()
  
  \end{document}
  
diff -Nru r-bioc-bsgenome-1.56.0/debian/upstream/metadata r-bioc-bsgenome-1.58.0/debian/upstream/metadata
--- r-bioc-bsgenome-1.56.0/debian/upstream/metadata	1970-01-01 00:00:00.000000000 +0000
+++ r-bioc-bsgenome-1.58.0/debian/upstream/metadata	2020-11-03 12:55:17.000000000 +0000
@@ -0,0 +1,5 @@
+---
+Bug-Database: https://github.com/Bioconductor/BSgenome/issues
+Bug-Submit: https://github.com/Bioconductor/BSgenome/issues/new
+Repository: https://github.com/Bioconductor/BSgenome.git
+Repository-Browse: https://github.com/Bioconductor/BSgenome
diff -Nru r-bioc-bsgenome-1.56.0/DESCRIPTION r-bioc-bsgenome-1.58.0/DESCRIPTION
--- r-bioc-bsgenome-1.56.0/DESCRIPTION	2020-04-27 23:50:24.000000000 +0000
+++ r-bioc-bsgenome-1.58.0/DESCRIPTION	2020-10-27 22:53:54.000000000 +0000
@@ -3,19 +3,22 @@
         genomes and their SNPs
 Description: Infrastructure shared by all the Biostrings-based genome data
 	packages.
-Version: 1.56.0
-Encoding: UTF-8
-Author: Hervé Pagès
-Maintainer: H. Pagès <hpages@fredhutch.org>
 biocViews: Genetics, Infrastructure, DataRepresentation,
         SequenceMatching, Annotation, SNP
+URL: https://bioconductor.org/packages/BSgenome
+BugReports: https://github.com/Bioconductor/BSgenome/issues
+Version: 1.58.0
+License: Artistic-2.0
+Encoding: UTF-8
+Author: Hervé Pagès
+Maintainer: H. Pagès <hpages.on.github@gmail.com>
 Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.13.8), S4Vectors (>=
-        0.17.28), IRanges (>= 2.13.16), GenomeInfoDb (>= 1.23.9),
+        0.17.28), IRanges (>= 2.13.16), GenomeInfoDb (>= 1.25.6),
         GenomicRanges (>= 1.31.10), Biostrings (>= 2.47.6), rtracklayer
         (>= 1.39.7)
 Imports: methods, utils, stats, matrixStats, BiocGenerics, S4Vectors,
-        IRanges, XVector, GenomeInfoDb, GenomicRanges, Biostrings,
-        Rsamtools, rtracklayer
+        IRanges, XVector (>= 0.29.3), GenomeInfoDb, GenomicRanges,
+        Biostrings, Rsamtools, rtracklayer
 Suggests: BiocManager, Biobase, BSgenome.Celegans.UCSC.ce2,
         BSgenome.Hsapiens.UCSC.hg38,
         BSgenome.Hsapiens.UCSC.hg38.masked,
@@ -26,7 +29,6 @@
         TxDb.Mmusculus.UCSC.mm10.knownGene,
         SNPlocs.Hsapiens.dbSNP144.GRCh38,
         XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, hgu95av2probe, RUnit
-License: Artistic-2.0
 LazyLoad: yes
 Collate: utils.R OnDiskLongTable_old-class.R OnDiskLongTable-class.R
         OnDiskNamedSequences-class.R SNPlocs-class.R
@@ -36,9 +38,9 @@
         extractAt-methods.R bsapply.R BSgenomeViews-class.R
         BSgenome-utils.R export-methods.R BSgenomeForge.R
 git_url: https://git.bioconductor.org/packages/BSgenome
-git_branch: RELEASE_3_11
-git_last_commit: 8364a0f
-git_last_commit_date: 2020-04-27
-Date/Publication: 2020-04-27
+git_branch: RELEASE_3_12
+git_last_commit: 3a4926e
+git_last_commit_date: 2020-10-27
+Date/Publication: 2020-10-27
 NeedsCompilation: no
-Packaged: 2020-04-27 23:50:24 UTC; biocbuild
+Packaged: 2020-10-27 22:53:54 UTC; biocbuild
Binary files /tmp/tmpehYfan/wluw9abOvJ/r-bioc-bsgenome-1.56.0/inst/doc/BSgenomeForge.pdf and /tmp/tmpehYfan/OPzkFgudhS/r-bioc-bsgenome-1.58.0/inst/doc/BSgenomeForge.pdf differ
diff -Nru r-bioc-bsgenome-1.56.0/inst/doc/BSgenomeForge.R r-bioc-bsgenome-1.58.0/inst/doc/BSgenomeForge.R
--- r-bioc-bsgenome-1.56.0/inst/doc/BSgenomeForge.R	2020-04-27 23:49:28.000000000 +0000
+++ r-bioc-bsgenome-1.58.0/inst/doc/BSgenomeForge.R	2020-10-27 22:52:59.000000000 +0000
@@ -1,7 +1,7 @@
 ### R code from vignette source 'BSgenomeForge.Rnw'
 
 ###################################################
-### code chunk number 1: BSgenomeForge.Rnw:193-196
+### code chunk number 1: BSgenomeForge.Rnw:189-192
 ###################################################
 library(Biostrings)
 file <- system.file("extdata", "ce2chrM.fa.gz", package="BSgenome")
@@ -9,7 +9,7 @@
 
 
 ###################################################
-### code chunk number 2: BSgenomeForge.Rnw:429-440
+### code chunk number 2: BSgenomeForge.Rnw:422-433
 ###################################################
 library(BSgenome)
 seed_files <- system.file("extdata", "GentlemanLab", package="BSgenome")
@@ -25,14 +25,14 @@
 
 
 ###################################################
-### code chunk number 3: BSgenomeForge.Rnw:453-455 (eval = FALSE)
+### code chunk number 3: BSgenomeForge.Rnw:446-448 (eval = FALSE)
 ###################################################
 ## library(BSgenome)
 ## forgeBSgenomeDataPkg("path/to/my/seed")
 
 
 ###################################################
-### code chunk number 4: BSgenomeForge.Rnw:678-683
+### code chunk number 4: BSgenomeForge.Rnw:671-676
 ###################################################
 library(BSgenome)
 seed_files <- system.file("extdata", "GentlemanLab", package="BSgenome")
@@ -42,14 +42,14 @@
 
 
 ###################################################
-### code chunk number 5: BSgenomeForge.Rnw:698-700 (eval = FALSE)
+### code chunk number 5: BSgenomeForge.Rnw:691-693 (eval = FALSE)
 ###################################################
 ## library(BSgenome)
 ## forgeMaskedBSgenomeDataPkg("path/to/my/seed")
 
 
 ###################################################
-### code chunk number 6: BSgenomeForge.Rnw:742-743
+### code chunk number 6: BSgenomeForge.Rnw:735-736
 ###################################################
 sessionInfo()
 
diff -Nru r-bioc-bsgenome-1.56.0/inst/doc/BSgenomeForge.Rnw r-bioc-bsgenome-1.58.0/inst/doc/BSgenomeForge.Rnw
--- r-bioc-bsgenome-1.56.0/inst/doc/BSgenomeForge.Rnw	2020-04-27 20:20:26.000000000 +0000
+++ r-bioc-bsgenome-1.58.0/inst/doc/BSgenomeForge.Rnw	2020-10-27 17:17:33.000000000 +0000
@@ -75,13 +75,6 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 
-IMPORTANT NOTE: Starting with Bioconductor 2.14, the
-\Rfunction{forgeBSgenomeDataPkg} function doesn't handle masks anymore
-i.e. now it produces a \term{BSgenome data package} that contains only
-the bare sequences. A new function \Rfunction{forgeMaskedBSgenomeDataPkg}
-has been added to forge a \term{BSgenome data package} with masked
-sequences. This vignette has been updated to reflect these changes.
-
 This vignette describes the process of forging a \term{BSgenome data package}.
 It is intended for Bioconductor users who want to make a new \term{BSgenome
 data package}, not for regular users of these packages.
@@ -128,9 +121,12 @@
 \Rpackage{Biostrings} or \Rpackage{BSgenome} packages.
 
 Questions, comments or bug reports about this vignette or about the
-BSgenomeForge functions are welcome. Please address them to the author
-(\code{hpages@fredhutch.org}) or post them on the Bioconductor support
-site \footnote{\url{https://support.bioconductor.org/}}.
+BSgenomeForge functions are welcome. Please use the Bioconductor support
+site \footnote{\url{https://support.bioconductor.org/}} if you have
+questions or need help about forging a \term{BSgenome data package},
+or about anything related to the \Rpackage{BSgenome} package. For bug
+reports or feature requests, please open an issue on GitHub at
+\url{https://github.com/Bioconductor/BSgenome/issues}.
 
 In the next section (``How to forge a BSgenome data package with bare
 sequences''), we describe how to forge a \term{BSgenome data package}
@@ -318,27 +314,24 @@
       the \textit{List of UCSC genome releases} table
       \footnote{\url{http://genome.ucsc.edu/FAQ/FAQreleases\#release1}}.
 
-\item \code{provider}: The provider of the \term{sequence data files} e.g.
-      \code{UCSC}, \code{NCBI}, \code{BDGP}, \code{FlyBase}, etc...
-      Should preferably match part 3 of the package name (field \code{Package}).
-
-\item \code{provider\_version}: The provider-side version of the genome.
+\item \code{genome}: The name of the genome. Typically the name of an NCBI
+      assembly (e.g. \code{GRCh38.p12}, \code{WBcel235}, \code{TAIR10.1},
+      \code{ARS-UCD1.2}, etc...) or UCSC genome (e.g. \code{hg38},
+      \code{bosTau9}, \code{galGal6}, \code{ce11}, etc...).
       Should preferably match part 4 of the package name (field \code{Package}).
       For the packages built by the Bioconductor project from a UCSC genome,
       this field corresponds to the \code{UCSC VERSION} field of the
       \textit{List of UCSC genome releases} table.
 
+\item \code{provider}: The provider of the \term{sequence data files} e.g.
+      \code{UCSC}, \code{NCBI}, \code{BDGP}, \code{FlyBase}, etc...
+      Should preferably match part 3 of the package name (field \code{Package}).
+
 \item \code{release\_date}: When this assembly of the genome was released.
       For the packages built by the Bioconductor project from a UCSC genome,
       this field corresponds to the \code{RELEASE DATE} field of the
       \textit{List of UCSC genome releases} table.
 
-\item \code{release\_name}: The release name or build number of this assembly
-      of the genome.
-      For the packages built by the Bioconductor project from a UCSC genome,
-      this field corresponds to the \code{RELEASE NAME} field of the
-      \textit{List of UCSC genome releases} table.
-
 \item \code{source\_url}: The permanent URL where the \term{sequence data
       files} used to forge the \term{target package} can be found.
 
Binary files /tmp/tmpehYfan/wluw9abOvJ/r-bioc-bsgenome-1.56.0/inst/doc/GenomeSearching.pdf and /tmp/tmpehYfan/OPzkFgudhS/r-bioc-bsgenome-1.58.0/inst/doc/GenomeSearching.pdf differ
diff -Nru r-bioc-bsgenome-1.56.0/inst/doc/GenomeSearching.R r-bioc-bsgenome-1.58.0/inst/doc/GenomeSearching.R
--- r-bioc-bsgenome-1.56.0/inst/doc/GenomeSearching.R	2020-04-27 23:50:23.000000000 +0000
+++ r-bioc-bsgenome-1.58.0/inst/doc/GenomeSearching.R	2020-10-27 22:53:54.000000000 +0000
@@ -18,11 +18,9 @@
 ###################################################
 ### code chunk number 3: b3
 ###################################################
-organism(genome)
-provider(genome)
-providerVersion(genome)
+metadata(genome)
 seqnames(genome)
-mseqnames(genome)
+seqinfo(genome)
 
 
 ###################################################
@@ -123,7 +121,7 @@
     genome <- BSgenome.Celegans.UCSC.ce2
     seqnames <- seqnames(genome)
     seqnames_in1string <- paste(seqnames, collapse=", ")
-    cat("Target:", providerVersion(genome),
+    cat("Target:", metadata(genome)$genome,
         "chromosomes", seqnames_in1string, "\n")
     append <- FALSE
     for (seqname in seqnames) {
@@ -351,7 +349,7 @@
 runOneStrandAnalysis <- function(dict0, bsgenome, seqnames, strand,
                                  outfile="", append=FALSE)
 {
-    cat("\nTarget: strand", strand, "of", providerVersion(bsgenome),
+    cat("\nTarget: strand", strand, "of", metadata(bsgenome)$genome,
         "chromosomes", paste(seqnames, collapse=", "), "\n")
     if (strand == "-")
         dict0 <- reverseComplement(dict0)
diff -Nru r-bioc-bsgenome-1.56.0/inst/doc/GenomeSearching.Rnw r-bioc-bsgenome-1.58.0/inst/doc/GenomeSearching.Rnw
--- r-bioc-bsgenome-1.56.0/inst/doc/GenomeSearching.Rnw	2020-04-27 20:20:26.000000000 +0000
+++ r-bioc-bsgenome-1.58.0/inst/doc/GenomeSearching.Rnw	2020-10-27 17:17:33.000000000 +0000
@@ -123,17 +123,15 @@
 @
 
 When displayed, some basic information about the origin of the
-genome is shown (organism, provider, provider version, etc...)
+genome is shown (organism, genome, provider, etc...)
 followed by the index of {\it single} sequences and eventually
 an additional index of {\it multiple} sequences.
 Methods (adequately called {\it accessor methods}) are defined
 for individual access to this information:
 <<b3>>=
-organism(genome)
-provider(genome)
-providerVersion(genome)
+metadata(genome)
 seqnames(genome)
-mseqnames(genome)
+seqinfo(genome)
 @
 
 See the man page for the \Rclass{BSgenome} class (\Rfunction{?BSgenome})
@@ -328,7 +326,7 @@
     genome <- BSgenome.Celegans.UCSC.ce2
     seqnames <- seqnames(genome)
     seqnames_in1string <- paste(seqnames, collapse=", ")
-    cat("Target:", providerVersion(genome),
+    cat("Target:", metadata(genome)$genome,
         "chromosomes", seqnames_in1string, "\n")
     append <- FALSE
     for (seqname in seqnames) {
@@ -737,7 +735,7 @@
 runOneStrandAnalysis <- function(dict0, bsgenome, seqnames, strand,
                                  outfile="", append=FALSE)
 {
-    cat("\nTarget: strand", strand, "of", providerVersion(bsgenome),
+    cat("\nTarget: strand", strand, "of", metadata(bsgenome)$genome,
         "chromosomes", paste(seqnames, collapse=", "), "\n")
     if (strand == "-")
         dict0 <- reverseComplement(dict0)
diff -Nru r-bioc-bsgenome-1.56.0/inst/extdata/GentlemanLab/BSgenome.Athaliana.TAIR.TAIR10.1-seed r-bioc-bsgenome-1.58.0/inst/extdata/GentlemanLab/BSgenome.Athaliana.TAIR.TAIR10.1-seed
--- r-bioc-bsgenome-1.56.0/inst/extdata/GentlemanLab/BSgenome.Athaliana.TAIR.TAIR10.1-seed	1970-01-01 00:00:00.000000000 +0000
+++ r-bioc-bsgenome-1.58.0/inst/extdata/GentlemanLab/BSgenome.Athaliana.TAIR.TAIR10.1-seed	2020-10-27 17:17:33.000000000 +0000
@@ -0,0 +1,16 @@
+Package: BSgenome.Athaliana.TAIR.TAIR10.1
+Title: Full genome sequences for Arabidopsis thaliana (TAIR10.1)
+Description: Full genome sequences for Arabidopsis thaliana as provided by TAIR (TAIR10.1, RefSeq assembly accession: GCF_000001735.4) and stored in Biostrings objects.
+Version: 1.5.0
+organism: Arabidopsis thaliana
+common_name: Thale cress
+genome: TAIR10.1
+provider: TAIR
+release_date: 2018/03/15
+source_url: https://www.ncbi.nlm.nih.gov/assembly/GCF_000001735.4
+organism_biocview: Arabidopsis_thaliana
+BSgenomeObjname: Athaliana
+SrcDataFiles: GCF_000001735.4_TAIR10.1_genomic.fna.gz from https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/735/GCF_000001735.4_TAIR10.1/
+PkgExamples: genome[["1"]]
+seqs_srcdir: /home/hpages/BSgenomeForge/srcdata/BSgenome.Athaliana.TAIR.TAIR10.1/seqs
+ondisk_seq_format: rds
diff -Nru r-bioc-bsgenome-1.56.0/inst/extdata/GentlemanLab/BSgenome.Athaliana.TAIR.TAIR10.1-tools/splitbigfasta.R r-bioc-bsgenome-1.58.0/inst/extdata/GentlemanLab/BSgenome.Athaliana.TAIR.TAIR10.1-tools/splitbigfasta.R
--- r-bioc-bsgenome-1.56.0/inst/extdata/GentlemanLab/BSgenome.Athaliana.TAIR.TAIR10.1-tools/splitbigfasta.R	1970-01-01 00:00:00.000000000 +0000
+++ r-bioc-bsgenome-1.58.0/inst/extdata/GentlemanLab/BSgenome.Athaliana.TAIR.TAIR10.1-tools/splitbigfasta.R	2020-10-27 17:17:33.000000000 +0000
@@ -0,0 +1,19 @@
+###
+library(Biostrings)
+library(GenomeInfoDb)
+
+### Download GCF_000001735.4_TAIR10.1_genomic.fna.gz from
+### https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/735/GCF_000001735.4_TAIR10.1/
+TAIR10.1 <- readDNAStringSet("GCF_000001735.4_TAIR10.1_genomic.fna.gz")
+current_RefSeqAccn <- unlist(heads(strsplit(names(TAIR10.1), " ", fixed=TRUE), n=1L))
+chrominfo <- getChromInfoFromNCBI("TAIR10.1")
+expected_RefSeqAccn <- chrominfo[ , "RefSeqAccn"]
+stopifnot(identical(expected_RefSeqAccn, current_RefSeqAccn))
+names(TAIR10.1) <- chrominfo[ , "SequenceName"]
+
+for (i in seq_along(TAIR10.1)) {
+    filename <- paste0(names(TAIR10.1)[[i]], ".fa")
+    cat("writing ", filename, "\n", sep="")
+    writeXStringSet(TAIR10.1[i], file=filename, width=50L)
+}
+
diff -Nru r-bioc-bsgenome-1.56.0/inst/extdata/GentlemanLab/BSgenome.Gmellonella.NCBI.ASM364042v2-seed r-bioc-bsgenome-1.58.0/inst/extdata/GentlemanLab/BSgenome.Gmellonella.NCBI.ASM364042v2-seed
--- r-bioc-bsgenome-1.56.0/inst/extdata/GentlemanLab/BSgenome.Gmellonella.NCBI.ASM364042v2-seed	1970-01-01 00:00:00.000000000 +0000
+++ r-bioc-bsgenome-1.58.0/inst/extdata/GentlemanLab/BSgenome.Gmellonella.NCBI.ASM364042v2-seed	2020-10-27 17:17:33.000000000 +0000
@@ -0,0 +1,17 @@
+Package: BSgenome.Gmellonella.NCBI.ASM364042v2
+Title: Full genome sequences for Galleria mellonella (ASM364042v2)
+Description: Full genome sequences for Galleria mellonella as provided by NCBI (assembly ASM364042v2, assembly accession GCF_003640425.2) and stored in Biostrings objects.
+Version: 1.5.0
+organism: Galleria mellonella
+common_name: Greater wax moth
+genome: ASM364042v2
+provider: NCBI
+release_date: 2019/11/06
+source_url: https://www.ncbi.nlm.nih.gov/assembly/GCF_003640425.2
+organism_biocview: Galleria_mellonella
+BSgenomeObjname: Gmellonella
+circ_seqs: "NC_028532.1"
+SrcDataFiles: GCF_003640425.2_ASM364042v2_genomic.fna.gz from https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/640/425/GCF_003640425.2_ASM364042v2/
+PkgExamples: genome[["NC_028532.1"]]
+seqs_srcdir: /home/hpages/BSgenomeForge/srcdata/BSgenome.Gmellonella.NCBI.ASM364042v2/seqs
+seqfile_name: ASM364042v2.sorted.2bit
diff -Nru r-bioc-bsgenome-1.56.0/inst/extdata/GentlemanLab/BSgenome.Gmellonella.NCBI.ASM364042v2-tools/fasta_to_sorted_2bit.R r-bioc-bsgenome-1.58.0/inst/extdata/GentlemanLab/BSgenome.Gmellonella.NCBI.ASM364042v2-tools/fasta_to_sorted_2bit.R
--- r-bioc-bsgenome-1.56.0/inst/extdata/GentlemanLab/BSgenome.Gmellonella.NCBI.ASM364042v2-tools/fasta_to_sorted_2bit.R	1970-01-01 00:00:00.000000000 +0000
+++ r-bioc-bsgenome-1.58.0/inst/extdata/GentlemanLab/BSgenome.Gmellonella.NCBI.ASM364042v2-tools/fasta_to_sorted_2bit.R	2020-10-27 17:17:33.000000000 +0000
@@ -0,0 +1,26 @@
+###
+library(Biostrings)
+
+### Download GCF_003640425.2_ASM364042v2_genomic.fna.gz from
+### https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/640/425/GCF_003640425.2_ASM364042v2/
+dna <- readDNAStringSet("GCF_003640425.2_ASM364042v2_genomic.fna.gz")
+
+### Check seqnames.
+current_RefSeqAccn <- unlist(heads(strsplit(names(dna), " ", fixed=TRUE), n=1L))
+library(GenomeInfoDb)
+chrominfo <- getChromInfoFromNCBI("GCF_003640425.2")
+expected_RefSeqAccn <- chrominfo[ , "RefSeqAccn"]
+stopifnot(setequal(expected_RefSeqAccn, current_RefSeqAccn))
+
+### Reorder sequences.
+dna <- dna[match(expected_RefSeqAccn, current_RefSeqAccn)]
+
+### Rename sequences. An alternative would be to rename them to
+### chrominfo[ , "SequenceName"] but these names are VERY ugly (e.g.
+### "ScRZk8e_1;HRSCAF=1").
+names(dna) <- expected_RefSeqAccn
+
+### Export as 2bit.
+library(rtracklayer)
+export(dna, "ASM364042v2.sorted.2bit")
+
diff -Nru r-bioc-bsgenome-1.56.0/inst/extdata/GentlemanLab/BSgenome.Ppaniscus.UCSC.panPan1-seed r-bioc-bsgenome-1.58.0/inst/extdata/GentlemanLab/BSgenome.Ppaniscus.UCSC.panPan1-seed
--- r-bioc-bsgenome-1.56.0/inst/extdata/GentlemanLab/BSgenome.Ppaniscus.UCSC.panPan1-seed	1970-01-01 00:00:00.000000000 +0000
+++ r-bioc-bsgenome-1.58.0/inst/extdata/GentlemanLab/BSgenome.Ppaniscus.UCSC.panPan1-seed	2020-10-27 17:17:33.000000000 +0000
@@ -0,0 +1,17 @@
+Package: BSgenome.Ppaniscus.UCSC.panPan1
+Title: Full genome sequences for Pan paniscus (UCSC version panPan1)
+Description: Full genome sequences for Pan paniscus (Bonobo) as provided by UCSC (panPan1, May 2012) and stored in Biostrings objects.
+Version: 1.4.3
+organism: Pan paniscus
+common_name: Bonobo
+provider: UCSC
+provider_version: panPan1
+release_date: May 2012
+release_name: Max-Planck Institute panpan1
+source_url: https://hgdownload.cse.ucsc.edu/goldenPath/panPan1/bigZips/
+organism_biocview: Pan_paniscus
+BSgenomeObjname: Ppaniscus
+SrcDataFiles: panPan1.2bit from https://hgdownload.cse.ucsc.edu/goldenPath/panPan1/bigZips/
+PkgExamples: genome$AJFE01000001  # same as genome[["AJFE01000001"]]
+seqs_srcdir: /home/hpages/BSgenomeForge/srcdata/BSgenome.Ppaniscus.UCSC.panPan1/seqs
+seqfile_name: panPan1.2bit
diff -Nru r-bioc-bsgenome-1.56.0/inst/extdata/GentlemanLab/BSgenome.Ppaniscus.UCSC.panPan2-seed r-bioc-bsgenome-1.58.0/inst/extdata/GentlemanLab/BSgenome.Ppaniscus.UCSC.panPan2-seed
--- r-bioc-bsgenome-1.56.0/inst/extdata/GentlemanLab/BSgenome.Ppaniscus.UCSC.panPan2-seed	1970-01-01 00:00:00.000000000 +0000
+++ r-bioc-bsgenome-1.58.0/inst/extdata/GentlemanLab/BSgenome.Ppaniscus.UCSC.panPan2-seed	2020-10-27 17:17:33.000000000 +0000
@@ -0,0 +1,17 @@
+Package: BSgenome.Ppaniscus.UCSC.panPan2
+Title: Full genome sequences for Pan paniscus (UCSC version panPan2)
+Description: Full genome sequences for Pan paniscus (Bonobo) as provided by UCSC (panPan2, Dec. 2015) and stored in Biostrings objects.
+Version: 1.4.3
+organism: Pan paniscus
+common_name: Bonobo
+provider: UCSC
+provider_version: panPan2
+release_date: Dec. 2015
+release_name: Max-Planck Institute for Evolutionary Anthropology panpan1.1
+source_url: https://hgdownload.cse.ucsc.edu/goldenPath/panPan2/bigZips/
+organism_biocview: Pan_paniscus
+BSgenomeObjname: Ppaniscus
+SrcDataFiles: panPan2.2bit from https://hgdownload.cse.ucsc.edu/goldenPath/panPan2/bigZips/
+PkgExamples: genome$chr1  # same as genome[["chr1"]]
+seqs_srcdir: /home/hpages/BSgenomeForge/srcdata/BSgenome.Ppaniscus.UCSC.panPan2/seqs
+seqfile_name: panPan2.2bit
diff -Nru r-bioc-bsgenome-1.56.0/inst/extdata/GentlemanLab/ForgeAll.R r-bioc-bsgenome-1.58.0/inst/extdata/GentlemanLab/ForgeAll.R
--- r-bioc-bsgenome-1.56.0/inst/extdata/GentlemanLab/ForgeAll.R	2020-04-27 20:20:26.000000000 +0000
+++ r-bioc-bsgenome-1.58.0/inst/extdata/GentlemanLab/ForgeAll.R	2020-10-27 17:17:33.000000000 +0000
@@ -12,6 +12,7 @@
   "BSgenome.Amellifera.UCSC.apiMel2",
   "BSgenome.Athaliana.TAIR.04232008",
   "BSgenome.Athaliana.TAIR.TAIR9",
+  "BSgenome.Athaliana.TAIR.TAIR10.1",
   "BSgenome.Btaurus.UCSC.bosTau3",
   "BSgenome.Btaurus.UCSC.bosTau4",
   "BSgenome.Btaurus.UCSC.bosTau6",
@@ -35,6 +36,7 @@
   "BSgenome.Dvirilis.Ensembl.dvircaf1",
   "BSgenome.Ecoli.NCBI.20080805",
   "BSgenome.Gaculeatus.UCSC.gasAcu1",
+  "BSgenome.Gmellonella.NCBI.ASM364042v2",
   "BSgenome.Ggallus.UCSC.galGal3",
   "BSgenome.Ggallus.UCSC.galGal4",
   "BSgenome.Ggallus.UCSC.galGal5",
@@ -54,6 +56,8 @@
   "BSgenome.Mmusculus.UCSC.mm8",
   "BSgenome.Mmusculus.UCSC.mm9",
   "BSgenome.Mmusculus.UCSC.mm10",
+  "BSgenome.Ppaniscus.UCSC.panPan1",
+  "BSgenome.Ppaniscus.UCSC.panPan2",
   "BSgenome.Ptroglodytes.UCSC.panTro2",
   "BSgenome.Ptroglodytes.UCSC.panTro3",
   "BSgenome.Ptroglodytes.UCSC.panTro5",
diff -Nru r-bioc-bsgenome-1.56.0/inst/pkgtemplates/BSgenome_datapkg/DESCRIPTION r-bioc-bsgenome-1.58.0/inst/pkgtemplates/BSgenome_datapkg/DESCRIPTION
--- r-bioc-bsgenome-1.56.0/inst/pkgtemplates/BSgenome_datapkg/DESCRIPTION	2020-04-27 20:20:26.000000000 +0000
+++ r-bioc-bsgenome-1.58.0/inst/pkgtemplates/BSgenome_datapkg/DESCRIPTION	2020-10-27 17:17:33.000000000 +0000
@@ -4,15 +4,14 @@
 Version: @PKGVERSION@
 Author: @AUTHOR@
 Maintainer: @MAINTAINER@
-Depends: BSgenome (>= @BSGENOMEVERSION@)
+Depends: R (>= 3.5.0), BSgenome (>= @BSGENOMEVERSION@)
 Imports: BSgenome
 Suggests: @SUGGESTS@
 License: @LICENSE@
 organism: @ORGANISM@
 common_name: @COMMONNAME@
+genome: @GENOME@
 provider: @PROVIDER@
-provider_version: @PROVIDERVERSION@
 release_date: @RELEASEDATE@
-release_name: @RELEASENAME@
 source_url: @SOURCEURL@
 biocViews: AnnotationData, Genetics, BSgenome, @ORGANISMBIOCVIEW@
diff -Nru r-bioc-bsgenome-1.56.0/inst/pkgtemplates/BSgenome_datapkg/NAMESPACE r-bioc-bsgenome-1.58.0/inst/pkgtemplates/BSgenome_datapkg/NAMESPACE
--- r-bioc-bsgenome-1.56.0/inst/pkgtemplates/BSgenome_datapkg/NAMESPACE	2020-04-27 20:20:26.000000000 +0000
+++ r-bioc-bsgenome-1.58.0/inst/pkgtemplates/BSgenome_datapkg/NAMESPACE	2020-10-27 17:17:33.000000000 +0000
@@ -1,9 +1,9 @@
 import(BSgenome)
 
-### Don't export @PKGNAME@ or @BSGENOMEOBJNAME@ (the new and old names of the
-### BSgenome object defined in this package): the object is created and its 2
-### names are dynamically exported at load time (refer to R/zzz.R for the
-### details).
+### Don't export @PKGNAME@ or @BSGENOMEOBJNAME@ (the new and
+### old names of the BSgenome object defined in this package): the object
+### is created and its 2 names are dynamically exported at load time (refer
+### to R/zzz.R for the details).
 #export(@PKGNAME@)
 #export(@BSGENOMEOBJNAME@)
 
diff -Nru r-bioc-bsgenome-1.56.0/inst/pkgtemplates/BSgenome_datapkg/R/zzz.R r-bioc-bsgenome-1.58.0/inst/pkgtemplates/BSgenome_datapkg/R/zzz.R
--- r-bioc-bsgenome-1.56.0/inst/pkgtemplates/BSgenome_datapkg/R/zzz.R	2020-04-27 20:20:26.000000000 +0000
+++ r-bioc-bsgenome-1.58.0/inst/pkgtemplates/BSgenome_datapkg/R/zzz.R	2020-10-27 17:17:33.000000000 +0000
@@ -21,10 +21,9 @@
     bsgenome <- BSgenome(
         organism="@ORGANISM@",
         common_name="@COMMONNAME@",
+        genome="@GENOME@",
         provider="@PROVIDER@",
-        provider_version="@PROVIDERVERSION@",
         release_date="@RELEASEDATE@",
-        release_name="@RELEASENAME@",
         source_url="@SOURCEURL@",
         seqnames=.seqnames,
         circ_seqs=.circ_seqs,
diff -Nru r-bioc-bsgenome-1.56.0/inst/pkgtemplates/MaskedBSgenome_datapkg/DESCRIPTION r-bioc-bsgenome-1.58.0/inst/pkgtemplates/MaskedBSgenome_datapkg/DESCRIPTION
--- r-bioc-bsgenome-1.56.0/inst/pkgtemplates/MaskedBSgenome_datapkg/DESCRIPTION	2020-04-27 20:20:26.000000000 +0000
+++ r-bioc-bsgenome-1.58.0/inst/pkgtemplates/MaskedBSgenome_datapkg/DESCRIPTION	2020-10-27 17:17:33.000000000 +0000
@@ -10,9 +10,8 @@
 License: @LICENSE@
 organism: @ORGANISM@
 common_name: @COMMONNAME@
+genome: @GENOME@
 provider: @PROVIDER@
-provider_version: @PROVIDERVERSION@
 release_date: @RELEASEDATE@
-release_name: @RELEASENAME@
 source_url: @SOURCEURL@
 biocViews: AnnotationData, Genetics, BSgenome, @ORGANISMBIOCVIEW@
diff -Nru r-bioc-bsgenome-1.56.0/man/available.genomes.Rd r-bioc-bsgenome-1.58.0/man/available.genomes.Rd
--- r-bioc-bsgenome-1.56.0/man/available.genomes.Rd	2020-04-27 20:20:26.000000000 +0000
+++ r-bioc-bsgenome-1.58.0/man/available.genomes.Rd	2020-10-27 17:17:33.000000000 +0000
@@ -38,9 +38,11 @@
   }
   \item{genome}{
     A \link{BSgenome} object, or the full name of an installed BSgenome
-    data package, or a short string specifying a genome assembly (a.k.a.
-    provider version) that refers unambiguously to an installed BSgenome
-    data package.
+    data package, or a short string specifying the name of an NCBI assembly
+    (e.g. \code{"GRCh38"}, \code{"TAIR10.1"}, etc...) or UCSC genome (e.g.
+    \code{"hg38"}, \code{"bosTau9"}, \code{"galGal6"}, \code{"ce11"}, etc...).
+    The supplied short string must refer unambiguously to an installed
+    BSgenome data package.
   }
   \item{masked}{
     \code{TRUE} or \code{FALSE}. Whether to search for the \emph{masked}
@@ -75,11 +77,10 @@
           genome sequences. We formally refer to it as the \emph{provider}
           of the genome. E.g. \code{UCSC}, \code{NCBI}, \code{TAIR}, etc...
 
-    \item The 4th part is the release string or number used by this
-          organisation for this particular genome assembly. We formally
-          refer to it as the \emph{provider version} of the genome.
-          E.g. \code{hg38}, \code{GRCh38}, \code{hg19}, \code{mm10},
-          \code{susScr11}, etc...
+    \item The 4th part is a short string specifying the name of an NCBI
+          assembly (e.g. \code{GRCh38}, \code{TAIR10.1}, etc...) or UCSC
+          genome (e.g. \code{hg38}, \code{mm10}, \code{susScr11},
+          \code{bosTau9}, \code{galGal6}, \code{ce11}, etc...).
 
     \item If the package contains masked sequences, its name has the
           \code{.masked} suffix added to it, which is typically the 5th part.
@@ -98,7 +99,7 @@
   \code{installed.genomes}). If \code{splitNameParts=TRUE}, the list of
   packages is returned in a data frame with one row per package and the
   following columns: \code{pkgname} (character), \code{organism} (factor),
-  \code{provider} (factor), \code{provider_version} (character), and
+  \code{provider} (factor), \code{genome} (character), and
   \code{masked} (logical).
 
   For \code{getBSgenome}: the \link{BSgenome} object containing the sequences
@@ -153,15 +154,15 @@
 genome <- getBSgenome("BSgenome.Celegans.UCSC.ce2")
 genome
 
-## Specify a genome assembly (a.k.a. provider version):
+## Specify a UCSC genome:
 genome <- getBSgenome("hg38")
 class(genome)  # BSgenome object
-providerVersion(genome)
+seqinfo(genome)
 genome$chrM
 
 genome <- getBSgenome("hg38", masked=TRUE)
 class(genome)  # MaskedBSgenome object
-providerVersion(genome)
+seqinfo(genome)
 genome$chr22
 }
 
diff -Nru r-bioc-bsgenome-1.56.0/man/BSgenome-class.Rd r-bioc-bsgenome-1.58.0/man/BSgenome-class.Rd
--- r-bioc-bsgenome-1.56.0/man/BSgenome-class.Rd	2020-04-27 20:20:26.000000000 +0000
+++ r-bioc-bsgenome-1.58.0/man/BSgenome-class.Rd	2020-10-27 17:17:33.000000000 +0000
@@ -7,14 +7,22 @@
 \alias{BSgenome}
 
 % Accessors:
-\alias{length,BSgenome-method}
+\alias{organism,BSgenome-method}
+\alias{commonName,BSgenome-method}
+\alias{provider,BSgenome-method}
+\alias{providerVersion,BSgenome-method}
+\alias{releaseDate,BSgenome-method}
+\alias{releaseName,BSgenome-method}
 \alias{sourceUrl}
 \alias{sourceUrl,BSgenome-method}
+\alias{length,BSgenome-method}
 \alias{mseqnames}
 \alias{mseqnames,BSgenome-method}
 \alias{names,BSgenome-method}
 \alias{masknames}
 \alias{masknames,BSgenome-method}
+\alias{masknames,MaskedBSgenome-method}
+\alias{seqnames,BSgenome-method}
 \alias{seqinfo,BSgenome-method}
 \alias{seqinfo<-,BSgenome-method}
 \alias{seqnames<-,BSgenome-method}
@@ -24,6 +32,8 @@
 
 % Other methods:
 \alias{as.list,BSgenome-method}
+\alias{coerce,BSgenome,GenomeDescription-method}
+\alias{bsgenomeName,BSgenome-method}
 \alias{show,BSgenome-method}
 \alias{[[,BSgenome-method}
 \alias{$,BSgenome-method}
@@ -42,16 +52,31 @@
 
 \section{Accessor methods}{
   In the code snippets below, \code{x} is a BSgenome object.
-  Note that, because the BSgenome class contains the
-  \link[GenomeInfoDb]{GenomeDescription} class, then all the accessor methods
-  for \link[GenomeInfoDb]{GenomeDescription} objects can also be used on
-  \code{x}.
 
   \describe{
-    \item{\code{sourceUrl(x)}}{
-      Returns the source URL i.e. the permanent URL to the place where the
-      FASTA files used to produce the sequences contained in \code{x} can
-      be found (and downloaded).
+    \item{\code{metadata(x)}}{
+      Returns a named list containing metadata associated with the BSgenome
+      object. The components of the list are:
+      \itemize{
+        \item \code{organism}: The scientific name of the organism that this
+              BSgenome object is for. E.g. \code{"Homo sapiens"},
+              \code{"Mus musculus"}, \code{"Caenorhabditis elegans"}, etc...
+        \item \code{common_name}: The common name of the organism that this
+              BSgenome object is for. E.g. \code{"Human"}, \code{"Mouse"},
+              \code{"Worm"}, etc...
+        \item \code{genome}: The name of the genome. Typically the name of
+              an NCBI assembly (e.g. \code{"GRCh38.p12"}, \code{"WBcel235"},
+              \code{"TAIR10.1"}, \code{"ARS-UCD1.2"}, etc...) or UCSC genome
+              (e.g. \code{"hg38"}, \code{"bosTau9"}, \code{"galGal6"},
+              \code{"ce11"}, etc...).
+        \item \code{provider}: The provider of this genome. E.g.
+              \code{"UCSC"}, \code{"BDGP"}, \code{"FlyBase"}, etc...
+        \item \code{release_date}:  The release date of this genome e.g.
+              \code{"Mar. 2006"}.
+        \item \code{source_url}: The permanent URL to the place where the
+              FASTA files used to produce the sequences contained in
+              \code{x} can be found (and downloaded).
+      }
     }
     \item{\code{seqnames(x)}, \code{seqnames(x) <- value}}{
       Gets or sets the names of the single sequences contained in \code{x}.
@@ -166,6 +191,8 @@
 ## into memory:
 library(BSgenome.Celegans.UCSC.ce2)
 
+metadata(Celegans)
+
 ## Number of sequences in this genome:
 length(Celegans) 
 
diff -Nru r-bioc-bsgenome-1.56.0/man/BSgenomeForge.Rd r-bioc-bsgenome-1.58.0/man/BSgenomeForge.Rd
--- r-bioc-bsgenome-1.56.0/man/BSgenomeForge.Rd	2020-04-27 20:20:26.000000000 +0000
+++ r-bioc-bsgenome-1.58.0/man/BSgenomeForge.Rd	2020-10-27 17:17:33.000000000 +0000
@@ -10,7 +10,8 @@
 \alias{forgeBSgenomeDataPkg,BSgenomeDataPkgSeed-method}
 \alias{forgeBSgenomeDataPkg,list-method}
 \alias{forgeBSgenomeDataPkg,character-method}
-\alias{forgeSeqlengthsFile}
+\alias{forgeSeqlengthsRdsFile}
+\alias{forgeSeqlengthsRdaFile}
 \alias{forgeSeqFiles}
 \alias{forgeMasksFiles}
 
@@ -28,14 +29,19 @@
 
 ## Low-level BSgenomeForge functions:
 
-forgeSeqlengthsFile(seqnames, prefix="", suffix=".fa",
-                    seqs_srcdir=".", seqs_destdir=".", verbose=TRUE)
+forgeSeqlengthsRdsFile(seqnames, prefix="", suffix=".fa",
+                       seqs_srcdir=".", seqs_destdir=".",
+                       genome=NA_character_, verbose=TRUE)
+
+forgeSeqlengthsRdaFile(seqnames, prefix="", suffix=".fa",
+                       seqs_srcdir=".", seqs_destdir=".",
+                       genome=NA_character_, verbose=TRUE)
 
-forgeSeqFiles(provider, provider_version,
+forgeSeqFiles(provider, genome,
               seqnames, mseqnames=NULL,
               seqfile_name=NA, prefix="", suffix=".fa",
               seqs_srcdir=".", seqs_destdir=".",
-              ondisk_seq_format=c("2bit", "rda", "fa.rz", "fa"),
+              ondisk_seq_format=c("2bit", "rds", "rda", "fa.rz", "fa"),
               verbose=TRUE)
 
 forgeMasksFiles(seqnames, nmask_per_seq,
@@ -74,11 +80,11 @@
     The provider of the \emph{sequence data files} e.g.
     \code{"UCSC"}, \code{"NCBI"}, \code{"BDGP"}, \code{"FlyBase"}, etc...
   }
-  \item{provider_version}{
-    The provider-side version of the genome e.g. \code{"hg38"}
-    or \code{"bosTau9"} if the genome is provided by UCSC,
-    or \code{"GRCh38.p12"} or \code{"ARS-UCD1.2"} if it's provided
-    by NCBI.
+  \item{genome}{
+    The name of the genome. Typically the name of an NCBI assembly (e.g.
+    \code{"GRCh38.p12"}, \code{"WBcel235"}, \code{"TAIR10.1"},
+    \code{"ARS-UCD1.2"}, etc...) or UCSC genome (e.g. \code{"hg38"},
+    \code{"bosTau9"}, \code{"galGal6"}, \code{"ce11"}, etc...).
   }
   \item{seqnames, mseqnames}{
     A character vector containing the names of the single (for \code{seqnames})
@@ -98,17 +104,21 @@
     serialized objects should be saved.
     These directories must already exist.
 
-    \code{forgeSeqlengthsFile} will produce a single .rda file.
+    Both \code{forgeSeqlengthsRdsFile} and \code{forgeSeqlengthsRdaFile}
+    will produce a single \code{.rds} or \code{.rda} file.
     Both \code{forgeSeqFiles} and \code{forgeMasksFiles} will produce one
-    .rda file per sequence.
+    file per sequence (all files being either \code{.rds} or \code{.rda}
+    files).
   }
   \item{ondisk_seq_format}{
     Specifies how the single sequences should be stored in the forged package.
-    Can be \code{"2bit"}, \code{"rda"}, \code{"fa.rz"}, or \code{"fa"}.
+    Can be \code{"2bit"}, \code{"rds"}, \code{"rda"}, \code{"fa.rz"},
+    or \code{"fa"}.
     If \code{"2bit"} (the default), then all the single sequences are stored
     in a single twoBit file.
-    If \code{"rda"}, then each single sequence is stored in a separated
-    serialized \link[Biostrings]{XString} object (one per single sequence).
+    If \code{"rds"} or \code{"rda"}, then each single sequence is stored in
+    a separated serialized \link[Biostrings]{XString} derivative (one per
+    single sequence).
     If \code{"fa.rz"} or \code{"fa"}, then all the single sequences are stored
     in a single FASTA file (compressed in the RAZip format if \code{"fa.rz"}).
   }
@@ -139,31 +149,31 @@
 seqs_srcdir <- system.file("extdata", package="BSgenome")
 seqnames <- c("chrX", "chrM")
 
-## Forge .rda sequence files:
+## Forge .2bit sequence files:
 forgeSeqFiles("UCSC", "ce2",
               seqnames, prefix="ce2", suffix=".fa.gz",
               seqs_srcdir=seqs_srcdir,
-              seqs_destdir=tempdir(), ondisk_seq_format="rda")
+              seqs_destdir=tempdir(), ondisk_seq_format="2bit")
 
-## Forge .2bit sequence files:
+## Forge .rds sequence files:
 forgeSeqFiles("UCSC", "ce2",
               seqnames, prefix="ce2", suffix=".fa.gz",
               seqs_srcdir=seqs_srcdir,
-              seqs_destdir=tempdir(), ondisk_seq_format="2bit")
+              seqs_destdir=tempdir(), ondisk_seq_format="rds")
 
 ## Sanity checks:
 library(BSgenome.Celegans.UCSC.ce2)
 genome <- BSgenome.Celegans.UCSC.ce2
 
-load(file.path(tempdir(), "chrX.rda"))
-stopifnot(genome$chrX == chrX)
-load(file.path(tempdir(), "chrM.rda"))
-stopifnot(genome$chrM == chrM)
-
 ce2_sequences <- import(file.path(tempdir(), "single_sequences.2bit"))
 ce2_sequences0 <- DNAStringSet(list(chrX=genome$chrX, chrM=genome$chrM))
-stopifnot(identical(names(ce2_sequences0), names(ce2_sequences)) &&
+stopifnot(identical(names(ce2_sequences0), names(ce2_sequences)),
           all(ce2_sequences0 == ce2_sequences))
+
+chrX <- readRDS(file.path(tempdir(), "chrX.rds"))
+stopifnot(genome$chrX == chrX)
+chrM <- readRDS(file.path(tempdir(), "chrM.rds"))
+stopifnot(genome$chrM == chrM)
 }
 
 \keyword{manip}
diff -Nru r-bioc-bsgenome-1.56.0/man/getSeq-methods.Rd r-bioc-bsgenome-1.58.0/man/getSeq-methods.Rd
--- r-bioc-bsgenome-1.56.0/man/getSeq-methods.Rd	2020-04-27 20:20:26.000000000 +0000
+++ r-bioc-bsgenome-1.58.0/man/getSeq-methods.Rd	2020-10-27 17:17:33.000000000 +0000
@@ -68,7 +68,6 @@
     \code{TRUE} or \code{FALSE}. Should the extracted sequences
     be returned in a standard character vector?
   }
-  \item{...}{Additional arguments. (Currently ignored.)}
 }
 
 \details{
diff -Nru r-bioc-bsgenome-1.56.0/NAMESPACE r-bioc-bsgenome-1.58.0/NAMESPACE
--- r-bioc-bsgenome-1.56.0/NAMESPACE	2020-04-27 20:20:26.000000000 +0000
+++ r-bioc-bsgenome-1.58.0/NAMESPACE	2020-10-27 17:17:33.000000000 +0000
@@ -110,6 +110,9 @@
     getRowsFromOnDiskLongTable,
     getRowsByIdFromOnDiskLongTable,
 
+    ## ODLT_SNPlocs-class.R:
+    inferRefAndAltAlleles,
+
     ## OldFashionSNPlocs-class.R:
     newSNPlocs,
 
@@ -136,7 +139,8 @@
     writeBSgenomeToTwobit,
 
     ## BSgenomeForge.R:
-    forgeSeqlengthsFile,
+    forgeSeqlengthsRdsFile,
+    forgeSeqlengthsRdaFile,
     forgeSeqFiles,
     forgeMasksFiles
 )
@@ -157,7 +161,6 @@
     referenceGenome, compatibleGenomes,
     snpcount, snplocs,
     snpsBySeqname, snpsByOverlaps, snpsById,
-    inferRefAndAltAlleles,
 
     ## OldFashionSNPlocs-class.R:
     snpid2loc, snpid2alleles, snpid2grange,
diff -Nru r-bioc-bsgenome-1.56.0/R/available.genomes.R r-bioc-bsgenome-1.58.0/R/available.genomes.R
--- r-bioc-bsgenome-1.56.0/R/available.genomes.R	2020-04-27 20:20:26.000000000 +0000
+++ r-bioc-bsgenome-1.58.0/R/available.genomes.R	2020-10-27 17:17:33.000000000 +0000
@@ -20,7 +20,7 @@
         ans <- data.frame(pkgname=character(0),
                           organism=factor(),
                           provider=factor(),
-                          provider_version=character(0),
+                          genome=character(0),
                           masked=logical(0),
                           stringsAsFactors=FALSE)
         return(ans)
@@ -54,7 +54,7 @@
     data.frame(pkgname=pkgs,
                organism=factor(uparts[idx4 - 2L]),
                provider=factor(uparts[idx4 - 1L]),
-               provider_version=uparts[idx4],
+               genome=uparts[idx4],
                masked=is_masked,
                stringsAsFactors=FALSE)
 }
@@ -99,7 +99,7 @@
 .stopOnMoreThanOneAvailablePkg <- function(genome, masked, is.source=FALSE)
     stop("Looks like there is more than one available ",
          ifelse(masked, "masked ", ""), "BSgenome data package\n",
-         "  that matches genome assembly (a.k.a. provider version): ",
+         "  that matches genome: ",
          genome, "\n",
          "  You first need to choose one (use 'available.genomes(",
          ifelse(is.source, "type=\"source\"", ""), ")' to get\n  the list). ",
@@ -108,18 +108,18 @@
          "      install(\"<pkgname>\"",
          ifelse(is.source, ", type=\"source\"", ""), ")")
 
-.getInstalledPkgnameFromProviderVersion <- function(genome, masked=FALSE)
+.getInstalledPkgnameFromGenome <- function(genome, masked=FALSE)
 {
     ## 1) Search installed packages.
     inst_pkgs <- installed.genomes(splitNameParts=TRUE)
     inst_pkgs <- inst_pkgs[inst_pkgs[ , "masked"] == masked, , drop=FALSE]
-    idx <- which(genome == inst_pkgs[ , "provider_version"])
+    idx <- which(genome == inst_pkgs[ , "genome"])
     if (length(idx) == 1L)
         return(inst_pkgs[idx , "pkgname"])
     if (length(idx) >= 2L)
         stop("Looks like you have more than one installed ",
              ifelse(masked, "masked ", ""), "BSgenome data package\n",
-             "  that matches genome assembly (a.k.a. provider version): ",
+             "  that matches genome: ",
              genome, "\n",
              "  Please disambiguate by specifying the full name of the ",
              "package you want\n  to use (use 'installed.genomes()' to ",
@@ -128,7 +128,7 @@
     ## 2) Search available packages.
     av_pkgs <- available.genomes(splitNameParts=TRUE)
     av_pkgs <- av_pkgs[av_pkgs[ , "masked"] == masked, ]
-    idx <- which(genome == av_pkgs[ , "provider_version"])
+    idx <- which(genome == av_pkgs[ , "genome"])
     if (length(idx) == 1L) {
         genome <- av_pkgs[idx , "pkgname"]
         .stopOnAvailablePkg(genome)
@@ -140,7 +140,7 @@
     if (getOption("pkgType") != "source") {
         av_srcpkgs <- available.genomes(splitNameParts=TRUE, type="source")
         av_srcpkgs <- av_srcpkgs[av_srcpkgs[ , "masked"] == masked, ]
-        idx <- which(genome == av_srcpkgs[ , "provider_version"])
+        idx <- which(genome == av_srcpkgs[ , "genome"])
         if (length(idx) == 1L) {
             genome <- av_srcpkgs[idx , "pkgname"]
             .stopOnAvailablePkg(genome, is.source=TRUE)
@@ -152,7 +152,7 @@
     ## All searches have failed.
     stop("Couldn't find a ",
          ifelse(masked, "masked ", ""), "BSgenome data package ",
-         "that matches genome assembly\n  (a.k.a. provider version): ",
+         "that matches genome assembly:\n  ",
          genome, "\n\n",
          "  Please use 'available.genomes()' ",
          "(or 'available.genomes(type=\"source\")')\n",
@@ -210,11 +210,10 @@
     if (!isSingleString(genome))
         stop("'genome' must be a BSgenome object, or the full name of an ",
              "installed\n  BSgenome data package, or a short string ",
-             "specifying a genome assembly (a.k.a.\n  provider version) ",
-             "that refers unambiguously to an installed BSgenome data\n",
-             "  package")
+             "specifying a genome assembly that\n  refers unambiguously",
+             "to an installed BSgenome data package")
     if (!.has_BSgenome_prefix(genome)) {
-        genome <- .getInstalledPkgnameFromProviderVersion(genome, masked=masked)
+        genome <- .getInstalledPkgnameFromGenome(genome, masked=masked)
     } else if (masked) {
         warning("'masked' is ignored when 'genome' is supplied as ",
                 "a full package name")
diff -Nru r-bioc-bsgenome-1.56.0/R/BSgenome-class.R r-bioc-bsgenome-1.58.0/R/BSgenome-class.R
--- r-bioc-bsgenome-1.56.0/R/BSgenome-class.R	2020-04-27 20:20:26.000000000 +0000
+++ r-bioc-bsgenome-1.58.0/R/BSgenome-class.R	2020-10-27 17:17:33.000000000 +0000
@@ -4,7 +4,16 @@
 
 
 setClass("BSgenome",
-    contains="GenomeDescription",
+    ## Expected metadata data are:
+    ## - organism
+    ## - common_name
+    ## - genome
+    ## - provider
+    ## - release_date
+    ## - source_url: permanent URL to the place where the 2bit and/or FASTA
+    ##   files used to produce the "single" and "multiple" sequences can be
+    ##   found (and downloaded).
+    contains="Annotated",
     representation(
         ## Name of the BSgenome data package where the BSgenome object is
         ## defined.
@@ -14,15 +23,11 @@
         single_sequences="OnDiskNamedSequences",
         multiple_sequences="RdaCollection",
 
-        ## Permanent URL to the place where the FASTA files that were used
-        ## to produce the "single" and "multiple" sequences above can be
-        ## found (and downloaded).
-        source_url="character",
+        ## Original seqinfo.
+        seqinfo="Seqinfo",
 
         ## Named vector representing the translation table from the original
-        ## seqnames (as stored in self@seqinfo@seqnames, the 'seqinfo' slot
-        ## being inherited from the GenomeDescription class) to the user
-        ## seqnames.
+        ## seqnames (as stored in self@seqinfo@seqnames) to the user seqnames.
         user_seqnames="character",
 
         ## For SNPs injection.
@@ -30,13 +35,7 @@
 
         ## Used for caching the single and multiple on-disk sequences.
         .seqs_cache="environment",
-        .link_counts="environment",
-
-        ## TODO: Remove the 2 slots below once all the BSgenome data packages
-        ## with masks have been split in 2 packages (naked BSgenome +
-        ## MaskedBSgenome).
-        nmask_per_seq="integer",
-        masks="RdaCollection"
+        .link_counts="environment"
     )
 )
 
@@ -137,13 +136,42 @@
 
 
 ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-### Accessors.
+### Accessors
 ###
 
-setMethod("length", "BSgenome", function(x) length(names(x)))
-
+### Metadata.
+setMethod("organism", "BSgenome",
+    function(object) metadata(object)$organism
+)
+setMethod("commonName", "BSgenome",
+    function(object) metadata(object)$common_name
+)
+setMethod("provider", "BSgenome", function(x) metadata(x)$provider)
+setMethod("providerVersion", "BSgenome",
+    function(x)
+    {
+        msg <- c("Using providerVersion() on a ", class(x), " object ",
+                 "is deprecated. Please use 'metadata(x)$genome' instead.")
+        .Deprecated(msg=c("  ", wmsg(msg)))
+        metadata(x)$genome
+    }
+)
+setMethod("releaseDate", "BSgenome", function(x) metadata(x)$release_date)
+setMethod("releaseName", "BSgenome",
+    function(x)
+    {
+        msg <- c("Starting with Bioconductor 3.12, BSgenome objects no ",
+                 "longer have a \"release name\". As a consequence of ",
+                 "this change calling releaseName() on a BSgenome object ",
+                 "now always returns NA and is deprecated.")
+        .Deprecated(msg=c("  ", wmsg(msg)))
+        NA_character_
+    }
+)
 setGeneric("sourceUrl", function(x) standardGeneric("sourceUrl"))
-setMethod("sourceUrl", "BSgenome", function(x) x@source_url)
+setMethod("sourceUrl", "BSgenome", function(x) metadata(x)$source_url)
+
+setMethod("length", "BSgenome", function(x) length(names(x)))
 
 setGeneric("mseqnames", function(x) standardGeneric("mseqnames"))
 setMethod("mseqnames", "BSgenome",
@@ -159,13 +187,14 @@
 setMethod("names", "BSgenome", function(x) c(seqnames(x), mseqnames(x)))
 
 setGeneric("masknames", function(x) standardGeneric("masknames"))
-setMethod("masknames", "BSgenome",
+
+setMethod("masknames", "BSgenome", function(x) NULL)
+
+setMethod("masknames", "MaskedBSgenome",
     function(x)
     {
-        if (x@nmask_per_seq == 0L)
-            return(NULL)
-        ## TODO: Put this kind of checking in a validity method for BSgenome
-        ## objects (that's what validity methods are for).
+        ## TODO: Put this kind of checking in a validity method for
+        ## MaskedBSgenome objects (that's what validity methods are for).
         if (x@nmask_per_seq > length(BUILTIN_MASKNAMES))
             stop("internal anomaly: x@nmask_per_seq > ",
                  length(BUILTIN_MASKNAMES))
@@ -178,62 +207,69 @@
 ### seqinfo() accessor and related.
 ###
 
+setMethod("seqnames", "BSgenome", function(x) unname(x@user_seqnames))
+
 setMethod("seqinfo", "BSgenome",
     function(x)
     {
         ans <- x@seqinfo
-        seqlevels(ans) <- x@user_seqnames
+        seqlevels(ans) <- seqnames(x)
         ans
     }
 )
 
-### This is a restricted "seqinfo<-" method for BSgenome objects that
-### only supports replacement of the sequence names, i.e., except for their
-### sequence names, Seqinfo objects 'value' and 'seqinfo(x)' must be identical.
-setReplaceMethod("seqinfo", "BSgenome",
+### We implement a restricted seqinfo() setter for BSgenome object 'x' that
+### supports altering **only** the seqlevels and/or genome of 'seqinfo(x)'.
+### It does NOT allow subsetting 'seqinfo(x)' (by dropping/reordering some
+### of its seqlevels), or altering its seqlengths or circularity flags!
+### In other words, except for their seqnames() and genome(), Seqinfo
+### objects 'new_seqinfo' and 'old_seqinfo' must be identical. This is all
+### we need to make the seqlevelsStyle() setter work on a BSgenome object.
+.check_new2old_and_new_seqinfo <-
+    function(new2old, new_seqinfo, old_seqinfo, context="")
+{
+    if (length(new_seqinfo) != length(old_seqinfo))
+        stop(wmsg("the supplied 'seqinfo' must have the same ",
+                  "length as the current 'seqinfo'", context))
+    if (!(is.null(new2old) || identical(new2old, seq_along(new_seqinfo))))
+        stop(wmsg("'new2old' can only be set to NULL or ",
+                  "'seq_along(seqinfo(x))'", context))
+    seqnames(old_seqinfo) <- seqnames(new_seqinfo)
+    genome(old_seqinfo) <- genome(new_seqinfo)
+    if (!identical(new_seqinfo, old_seqinfo))
+        stop(wmsg("seqlengths() and isCircular() of the supplied 'seqinfo' ",
+                  "must be identical to seqlengths() and isCircular() of ",
+                  "the current 'seqinfo'", context))
+}
+
+.set_BSgenome_seqinfo <-
     function(x, new2old=NULL,
-             pruning.mode=c("error", "coarse", "fine", "tidy"),
-             value)
-    {
-        if (!is(value, "Seqinfo"))
-            stop("the supplied 'seqinfo' must be a Seqinfo object")
-        IN_THIS_CONTEXT <- paste0("when replacing the 'seqinfo' ",
-                                  "of a BSgenome object")
-        pruning.mode <- match.arg(pruning.mode)
-        if (pruning.mode != "error")
-            stop("'pruning.mode' not supported ", IN_THIS_CONTEXT)
-        x_seqinfo <- seqinfo(x)
-        if (is.null(new2old)) {
-            ## Support no-op seqinfo(x) <- seqinfo(x).
-            if (!identical(value, x_seqinfo))
-                stop("'new2old' must be specified ", IN_THIS_CONTEXT)
-            return(x)
-        }
-        if (length(value) != length(x_seqinfo))
-            stop("the supplied 'seqinfo' must have the same length ",
-                 "as the current 'seqinfo' ", IN_THIS_CONTEXT)
-        if (!identical(new2old, seq_along(value)))
-            stop("'new2old' must be NULL or equal to 'seq_along(value)' ",
-                 IN_THIS_CONTEXT)
-        new_seqnames <- seqnames(value)
-        seqnames(x_seqinfo) <- new_seqnames
-        if (!identical(value, x_seqinfo))
-            stop("the supplied and current 'seqinfo' can differ only ",
-                 "in their sequence names ", IN_THIS_CONTEXT)
-        if (any(new_seqnames %in% mseqnames(x)))
-            stop("the supplied 'seqnames' cannot match any of the ",
-                 "multiple sequence names (as returned by 'mseqnames(x)')")
-        x@user_seqnames[] <- new_seqnames  # using [] to preserve the names
-        x
-    }
-)
+                pruning.mode=c("error", "coarse", "fine", "tidy"),
+                value)
+{
+    if (!is(value, "Seqinfo"))
+        stop(wmsg("the supplied 'seqinfo' must be a Seqinfo object"))
+    context <- paste0(" when replacing the 'seqinfo' of a ",
+                      classNameForDisplay(x), " object")
+    pruning.mode <- match.arg(pruning.mode)
+    if (pruning.mode != "error")
+        stop(wmsg("'pruning.mode' is not supported", context))
+    .check_new2old_and_new_seqinfo(new2old, value, seqinfo(x), context)
+    new_seqnames <- seqnames(value)
+    if (any(new_seqnames %in% mseqnames(x)))
+        stop(wmsg("the supplied 'seqnames' cannot match any of the ",
+                  "multiple sequence names (as returned by 'mseqnames(x)')"))
+    x@user_seqnames[] <- new_seqnames  # using [] to preserve the names
+    genome(x@seqinfo) <- unname(genome(value))
+    x
+}
+
+setReplaceMethod("seqinfo", "BSgenome", .set_BSgenome_seqinfo)
 
 setReplaceMethod("seqnames", "BSgenome",
     function(x, value)
     {
-        x_seqinfo <- seqinfo(x)
-        seqnames(x_seqinfo) <- value
-        seqinfo(x, new2old=seq_along(x_seqinfo)) <- x_seqinfo
+        seqnames(seqinfo(x)) <- value
         x
     }
 )
@@ -261,9 +297,8 @@
 ###
 
 ### 'seqnames' only used for sanity check.
-.makeBSgenomeSeqinfo <- function(single_sequences,
-                                 circ_seqs, provider_version,
-                                 seqnames)
+.make_BSgenome_seqinfo <- function(single_sequences, circ_seqs,
+                                   genome, seqnames)
 {
     seqlengths <- seqlengths(single_sequences)
     if (length(seqnames) == 0L) {
@@ -282,73 +317,53 @@
     Seqinfo(seqnames=seqnames,
             seqlengths=seqlengths,
             isCircular=is_circ,
-            genome=provider_version)
+            genome=genome)
 }
 
 ### NOTES:
-### - In BioC 2.14, the 'seqs_pkgname' and 'masks_pkgname' BSgenome slots
-###   were replaced with the 'pkgname' slot but the 2 corresponding
-###   arguments were kept for backward compatibility with existing
-###   BSgenome packages.
+### - In BioC 2.14, the 'seqs_pkgname' BSgenome slot was renamed 'pkgname'
+###   but the corresponding argument was not renamed for backward
+###   compatibility with existing BSgenome packages.
 ### - In BioC 3.1, the 'species' argument was replaced with the 'common_name'
 ###   argument but the former was kept for backward compatibility with
 ###   existing BSgenome packages.
-BSgenome <- function(organism, common_name, provider, provider_version,
+### - In BioC 3.12, the 'provider_version' argument was replaced with the
+###   'genome' argument, and the 'release_name' became ignored and was only
+###   kept for backward compatibility.
+BSgenome <- function(organism, common_name, genome,
+                     provider, provider_version,
                      release_date, release_name, source_url,
                      seqnames, circ_seqs=NA, mseqnames,
                      seqs_pkgname, seqs_dirpath,
-                     nmask_per_seq=0, masks_pkgname=NA, masks_dirpath=NA,
                      species=NA_character_)
 {
-    twobit_filename <- "single_sequences.2bit"
-    twobit_filepath <- file.path(seqs_dirpath, twobit_filename)
-    if (file.exists(twobit_filepath)) {
-        single_sequences <- TwobitNamedSequences(twobit_filepath)
-    } else {
-        fa_filename <- "single_sequences.fa"
-        fa_filepath <- file.path(seqs_dirpath, fa_filename)
-        farz_filename <- paste0(fa_filename, ".rz")
-        farz_filepath <- file.path(seqs_dirpath, farz_filename)
-        if (file.exists(farz_filepath)) {
-            single_sequences <- FastaNamedSequences(farz_filepath)
-        } else if (file.exists(fa_filepath)) {
-            single_sequences <- FastaNamedSequences(fa_filepath)
-        } else {
-            single_sequences <- RdaNamedSequences(seqs_dirpath, seqnames)
-        }
-    }
-    seqinfo <- .makeBSgenomeSeqinfo(single_sequences,
-                                    circ_seqs, provider_version,
-                                    seqnames)
+    single_sequences <- OnDiskNamedSequences(seqs_dirpath, seqnames=seqnames)
+    if (missing(genome))
+        genome <- provider_version
+    seqinfo <- .make_BSgenome_seqinfo(single_sequences, circ_seqs,
+                                      genome, seqnames)
     seqnames <- seqnames(seqinfo)
     if (missing(common_name))
         common_name <- species
-    genome_description <- GenomeDescription(organism, common_name,
-                                            provider, provider_version,
-                                            release_date, release_name,
-                                            seqinfo)
+    metadata <- list(organism=organism,
+                     common_name=common_name,
+                     genome=genome,
+                     provider=provider,
+                     release_date=release_date,
+                     source_url=source_url)
     if (is.null(mseqnames))
         mseqnames <- character(0)
     multiple_sequences <- RdaCollection(seqs_dirpath, mseqnames)
     names(user_seqnames) <- user_seqnames <- seqnames
-    nmask_per_seq <- as.integer(nmask_per_seq)
-    masks_dirpath <- as.character(masks_dirpath)
-    if (nmask_per_seq == 0L || length(seqnames) == 0L) {
-        masks <- RdaCollection(masks_dirpath, character(0))
-    } else {
-        masks <- RdaCollection(masks_dirpath, paste0(seqnames, ".masks"))
-    }
 
-    new("BSgenome", genome_description,
-        pkgname=seqs_pkgname,
-        single_sequences=single_sequences,
-        multiple_sequences=multiple_sequences,
-        source_url=source_url,
-        user_seqnames=user_seqnames,
-        .seqs_cache=new.env(parent=emptyenv()),
-        .link_counts=new.env(parent=emptyenv()),
-        nmask_per_seq=nmask_per_seq,
-        masks=masks
+    new("BSgenome", metadata=metadata,
+                    pkgname=seqs_pkgname,
+                    single_sequences=single_sequences,
+                    multiple_sequences=multiple_sequences,
+                    seqinfo=seqinfo,
+                    user_seqnames=user_seqnames,
+                    .seqs_cache=new.env(parent=emptyenv()),
+                    .link_counts=new.env(parent=emptyenv())
     )
 }
 
@@ -376,11 +391,46 @@
                function(seqname) x[[seqname]])
 )
 
+setAs("BSgenome", "GenomeDescription",
+    function(from)
+    {
+        metadata <- metadata(from)
+        GenomeDescription(organism=metadata$organism,
+                          common_name=metadata$common_name,
+                          provider=metadata$provider,
+                          provider_version=metadata$genome,
+                          release_date=metadata$release_date,
+                          release_name=NA_character_,
+                          seqinfo=seqinfo(from))
+    }
+)
+
+
+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+### bsgenomeName()
+###
+
+setMethod("bsgenomeName", "BSgenome",
+    function(x) bsgenomeName(as(x, "GenomeDescription"))
+)
+
 
 ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 ### The "show" method
 ###
 
+.print_BSgenome_metadata <- function(metadata, prefix="")
+{
+    common_name <- metadata$common_name
+    if (!is.na(common_name))
+        cat(common_name, "genome:\n")
+    cat(prefix, "organism: ", metadata$organism,
+                " (", common_name, ")\n", sep="")
+    cat(prefix, "genome: ", metadata$genome, "\n", sep="")
+    cat(prefix, "provider: ", metadata$provider, "\n", sep="")
+    cat(prefix, "release date: ", metadata$release_date, "\n", sep="")
+}
+
 .SHOW_BSGENOME_PREFIX <- "# "
 .SHOW_SEQSECTION_PREFIX <- "#   "
 
@@ -390,10 +440,7 @@
         mystrwrap <- function(line)
             writeLines(strwrap(line, width=getOption("width")+1,
                                exdent=0L, prefix=.SHOW_BSGENOME_PREFIX))
-        if (!is.na(object@common_name))
-            cat(object@common_name, "genome:\n")
-        GenomeInfoDb:::showGenomeDescription(object,
-                                             margin=.SHOW_BSGENOME_PREFIX)
+        .print_BSgenome_metadata(metadata(object), prefix=.SHOW_BSGENOME_PREFIX)
         if (!is.null(SNPlocs_pkgname(object)))
             cat(.SHOW_BSGENOME_PREFIX, "with SNPs injected from package: ", SNPlocs_pkgname(object), "\n", sep="")
         if (length(mseqnames(object)) == 0L) {
@@ -466,7 +513,7 @@
         return(ans)
     }
     # single sequence
-    ans <- x@single_sequences[[seqname]]
+    ans <- getListElement(x@single_sequences, seqname)
     ## Check the length of the sequence
     if (length(ans) != seqlengths(x)[[user_seqname]]) {
         stop(user_seqname, " sequence does not have the expected length. ",
@@ -482,17 +529,17 @@
         masks_objname <- paste0(seqname, ".masks")
         builtinmasks <- x@masks[[masks_objname]]
         if (length(builtinmasks) < nmask_per_seq) {
-            masks_filepath <- rdaPath(x@masks, masks_objname)
+            masks_path <- rdaPath(x@masks, masks_objname)
             stop("expecting ", nmask_per_seq, " built-in masks per ",
                  "single sequence, found only ", length(builtinmasks),
-                 " in file '", masks_filepath, "'. ",
+                 " in file '", masks_path, "'. ",
                  "May be the data on disk is corrupted?")
         }
         if (length(builtinmasks) > nmask_per_seq)
             builtinmasks <- builtinmasks[seq_len(nmask_per_seq)]
         if (!identical(names(builtinmasks), masknames(x))) {
-            masks_filepath <- rdaPath(x@masks, masks_objname)
-            stop("mask names found in file '", masks_filepath, "' are not ",
+            masks_path <- rdaPath(x@masks, masks_objname)
+            stop("mask names found in file '", masks_path, "' are not ",
                  "identical to the names returned by masknames(). ",
                  "May be the data on disk is corrupted?")
         }
@@ -555,10 +602,10 @@
         ## to be of length <= 1
         if (length(subscripts) == 0L)
             stop("no index specified")
-        i <- subscripts[[1]]
-        if (length(i) < 1)
+        i <- subscripts[[1L]]
+        if (length(i) < 1L)
             stop("attempt to select less than one element")
-        if (length(i) > 1)
+        if (length(i) > 1L)
             stop("attempt to select more than one element")
         if (is.character(i)) {
             user_seqname <- try(match.arg(i, names(x)), silent=TRUE)
diff -Nru r-bioc-bsgenome-1.56.0/R/BSgenomeForge.R r-bioc-bsgenome-1.58.0/R/BSgenomeForge.R
--- r-bioc-bsgenome-1.56.0/R/BSgenomeForge.R	2020-04-27 20:20:26.000000000 +0000
+++ r-bioc-bsgenome-1.58.0/R/BSgenomeForge.R	2020-10-27 17:17:33.000000000 +0000
@@ -3,30 +3,32 @@
 ### -------------------------------------------------------------------------
 
 
-.get_circ_seqs <- function(provider, provider_version, circ_seqs)
-{
-    if (provider == "UCSC") {
-        UCSC_genomes <- registered_UCSC_genomes()
-        if (provider_version %in% UCSC_genomes[ , "genome"]) {
-            chrom_info <- getChromInfoFromUCSC(provider_version)
-            circ_idx <- which(chrom_info[ , "circular"])
-            circ_seqs <- deparse(chrom_info[circ_idx, "chrom"])
-        }
-    }
-    circ_seqs
-}
-
 .getMasksObjname <- function(seqnames)
 {
     if (length(seqnames) == 0)
         return(character(0))
-    paste(seqnames, ".masks", sep="")
+    paste0(seqnames, ".masks")
 }
 
-.saveObject <- function(object, objname, destdir=".", verbose=TRUE)
+.saveObjectToRdsFile <- function(object, objname, destdir=".", verbose=TRUE)
+{
+    destfile <- file.path(destdir, paste0(objname, ".rds"))
+    if (verbose)
+        cat("Saving '", objname, "' object to compressed data file '",
+            destfile, "' ... ", sep="")
+    ## Using compress="xz" (instead of compress="gzip") would produce a .rds
+    ## file that is about 20% smaller on disk but it would also take almost 3x
+    ## longer to load it later on with load(). Tested on hg19 chr1 with R-2.14
+    ## (2011-09-20 r57033). This is why we stick to compress="gzip".
+    saveRDS(object, file=destfile, compress="gzip")
+    if (verbose)
+        cat("DONE\n")
+}
+
+.saveObjectToRdaFile <- function(object, objname, destdir=".", verbose=TRUE)
 {
     assign(objname, object)
-    destfile <- file.path(destdir, paste(objname, ".rda", sep=""))
+    destfile <- file.path(destdir, paste0(objname, ".rda"))
     if (verbose)
         cat("Saving '", objname, "' object to compressed data file '",
             destfile, "' ... ", sep="")
@@ -49,9 +51,9 @@
 {
     if (!is.null(seqnames) && !is.character(seqnames))
         stop("'seqnames' must be a character vector (or NULL)")
-    if (length(seqnames) == 0) {
+    if (length(seqnames) == 0L) {
         warning("'seqnames' is empty")
-        return(character(0))
+        return(setNames(character(0), character(0)))
     }
     if (!isSingleString(prefix))
         stop("'prefix' must be a single string")
@@ -59,7 +61,7 @@
         stop("'suffix' must be a single string")
     if (!isSingleString(seqs_srcdir))
         stop("'seqs_srcdir' must be a single string")
-    srcfiles <- paste(prefix, seqnames, suffix, sep="")
+    srcfiles <- paste0(prefix, seqnames, suffix)
     ans <- file.path(seqs_srcdir, srcfiles)
     is_OK <- file.exists(ans)
     if (!all(is_OK)) {
@@ -72,53 +74,93 @@
 
 
 ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-### The getSeqlengths() and forgeSeqlengthsFile() functions.
+### getSeqlengths(), forgeSeqlengthsRdsFile(), and forgeSeqlengthsRdaFile()
 ###
 
-getSeqlengths <- function(seqnames, prefix="", suffix=".fa", seqs_srcdir=".")
+getSeqlengths <- function(seqnames, prefix="", suffix=".fa", seqs_srcdir=".",
+                          genome=NA_character_)
 {
-    if (length(seqnames) == 0) {
-        warning("'seqnames' is empty")
-        return(integer(0))
-    }
     srcpaths <- getSeqSrcpaths(seqnames, prefix=prefix, suffix=suffix,
                                seqs_srcdir=seqs_srcdir)
-    sapply(seqnames, function(seqname)
-           {
-               srcpath <- srcpaths[[seqname]]
-               ans <- fasta.seqlengths(srcpath)
-               if (length(ans) == 0)
-                   stop("In file '", srcpath, "': no sequence found")
-               if (length(ans) > 1)
-                   warning("In file '", srcpath, "': ", length(ans),
-                           " sequences found, using first sequence only")
-               if (names(ans)[1] != seqname)
-                   warning("In file '", srcpath, "': sequence description \"",
-                           names(ans), "\" doesn't match user-specified ",
-                           "sequence name \"", seqname, "\"")
-               ans[[1]]
-           },
-           USE.NAMES=TRUE
+    ans <- vapply(seqnames,
+        function(seqname) {
+            srcpath <- srcpaths[[seqname]]
+            ans <- fasta.seqlengths(srcpath)
+            if (length(ans) == 0L)
+                stop("In file '", srcpath, "': no sequence found")
+            if (length(ans) > 1L)
+                warning("In file '", srcpath, "': ", length(ans),
+                        " sequences found, using first sequence only")
+            if (names(ans)[[1L]] != seqname)
+                warning("In file '", srcpath, "': sequence description \"",
+                        names(ans), "\" doesn't match user-specified ",
+                        "sequence name \"", seqname, "\"")
+            ans[[1L]]
+        },
+        integer(1),
+        USE.NAMES=TRUE
     )
+    if (!is.na(genome)) {
+        expected <- seqlengths(Seqinfo(genome=genome))
+        if (!identical(expected[names(ans)], ans))
+            stop("the sequences in the files have lengths that don't match ",
+                 "the lengths reported by 'Seqinfo(genome=\"", genome, "\")'")
+    }
+    ans
 }
 
-forgeSeqlengthsFile <- function(seqnames, prefix="", suffix=".fa",
-                                seqs_srcdir=".", seqs_destdir=".",
-                                verbose=TRUE)
+forgeSeqlengthsRdsFile <- function(seqnames, prefix="", suffix=".fa",
+                                   seqs_srcdir=".", seqs_destdir=".",
+                                   genome=NA_character_, verbose=TRUE)
 {
+    if (!isSingleString(seqs_destdir))
+        stop("'seqs_destdir' must be a single string")
     seqlengths <- getSeqlengths(seqnames, prefix=prefix, suffix=suffix,
-                                seqs_srcdir=seqs_srcdir)
+                                seqs_srcdir=seqs_srcdir, genome=genome)
+    .saveObjectToRdsFile(seqlengths, "seqlengths", destdir=seqs_destdir,
+                         verbose=verbose)
+}
+
+forgeSeqlengthsRdaFile <- function(seqnames, prefix="", suffix=".fa",
+                                   seqs_srcdir=".", seqs_destdir=".",
+                                   genome=NA_character_, verbose=TRUE)
+{
     if (!isSingleString(seqs_destdir))
         stop("'seqs_destdir' must be a single string")
-    .saveObject(seqlengths, "seqlengths", destdir=seqs_destdir,
-                verbose=verbose)
+    seqlengths <- getSeqlengths(seqnames, prefix=prefix, suffix=suffix,
+                                seqs_srcdir=seqs_srcdir, genome=genome)
+    .saveObjectToRdaFile(seqlengths, "seqlengths", destdir=seqs_destdir,
+                         verbose=verbose)
 }
 
 
 ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-### The "forgeSeqFiles" function.
+### forgeSeqFiles()
 ###
 
+.forgeRdsSeqFile <- function(name, prefix, suffix, seqs_srcdir, seqs_destdir,
+                             is.single.seq=TRUE, verbose=TRUE)
+{
+    if (!isSingleString(name))
+        stop("'name' must be a single string")
+    srcpath <- getSeqSrcpaths(name, prefix=prefix, suffix=suffix,
+                              seqs_srcdir=seqs_srcdir)
+    if (verbose)
+        cat("Loading FASTA file '", srcpath, "' ... ", sep="")
+    seq <- readDNAStringSet(srcpath, "fasta")
+    if (verbose)
+        cat("DONE\n")
+    if (is.single.seq) {
+        if (length(seq) == 0L)
+            stop("file contains no DNA sequence")
+        if (length(seq) > 1L)
+            warning("file contains ", length(seq), " sequences, ",
+                    "using the first sequence only")
+        seq <- seq[[1L]] # now 'seq' is a DNAString object
+    }
+    .saveObjectToRdsFile(seq, name, destdir=seqs_destdir, verbose=verbose)
+}
+
 .forgeRdaSeqFile <- function(name, prefix, suffix, seqs_srcdir, seqs_destdir,
                              is.single.seq=TRUE, verbose=TRUE)
 {
@@ -133,14 +175,14 @@
     if (verbose)
         cat("DONE\n")
     if (is.single.seq) {
-        if (length(seq) == 0)
+        if (length(seq) == 0L)
             stop("file contains no DNA sequence")
-        if (length(seq) > 1)
+        if (length(seq) > 1L)
             warning("file contains ", length(seq), " sequences, ",
                     "using the first sequence only")
         seq <- seq[[1]] # now 'seq' is a DNAString object
     }
-    .saveObject(seq, name, destdir=seqs_destdir, verbose=verbose)
+    .saveObjectToRdaFile(seq, name, destdir=seqs_destdir, verbose=verbose)
 }
 
 .forgeFastaRzFileFromFastaFiles <- function(seqnames, prefix, suffix,
@@ -300,12 +342,12 @@
         cat("DONE\n")
 }
 
-.sortUCSCTwobitFile <- function(provider_version, seqs_dir, verbose=TRUE)
+.sortUCSCTwobitFile <- function(genome, seqs_dir, verbose=TRUE)
 {
     if (verbose)
         cat("Getting chrom info from UCSC with 'getChromInfoFromUCSC(\"",
-            provider_version, "\")' ... ", sep="")
-    chrom_info <- getChromInfoFromUCSC(provider_version)
+            genome, "\")' ... ", sep="")
+    chrom_info <- getChromInfoFromUCSC(genome)
     if (verbose)
         cat("DONE\n")
     filename <- "single_sequences.2bit"
@@ -318,10 +360,10 @@
     m <- match(chrom_info[ , "chrom"], names(seqs))
     if (nrow(chrom_info) != length(seqs) || anyNA(m))
         stop(wmsg("nb of sequences in 'chromInfo' table and 2bit file ",
-                  "don't match for UCSC genome ", provider_version))
+                  "don't match for UCSC genome ", genome))
     if (verbose)
         cat("Sorting sequences as in 'getChromInfoFromUCSC(\"",
-            provider_version, "\")' ... ", sep="")
+            genome, "\")' ... ", sep="")
     seqs <- seqs[m]
     if (verbose)
         cat("DONE\n")
@@ -329,7 +371,7 @@
         cat("Checking the sequence lengths ... ")
     if (!identical(chrom_info[ , "size"], width(seqs)))
         stop(wmsg("sequence lengths in 'chromInfo' table and 2bit file ",
-                  "don't match for UCSC genome ", provider_version))
+                  "don't match for UCSC genome ", genome))
     if (verbose)
         cat("OK\n")
     if (verbose)
@@ -339,11 +381,11 @@
         cat("DONE\n")
 }
 
-forgeSeqFiles <- function(provider, provider_version,
+forgeSeqFiles <- function(provider, genome,
                           seqnames, mseqnames=NULL,
                           seqfile_name=NA, prefix="", suffix=".fa",
                           seqs_srcdir=".", seqs_destdir=".",
-                          ondisk_seq_format=c("2bit", "rda", "fa.rz", "fa"),
+                          ondisk_seq_format=c("2bit", "rds", "rda", "fa.rz", "fa"),
                           verbose=TRUE)
 {
     if (length(seqnames) == 0L && is.na(seqfile_name))
@@ -353,7 +395,12 @@
     if (!isSingleString(seqs_destdir))
         stop("'seqs_destdir' must be a single string")
     ondisk_seq_format <- match.arg(ondisk_seq_format)
-    if (ondisk_seq_format == "rda") {  # "rda" format
+    if (ondisk_seq_format == "rds") {          # "rds" format
+        for (name in seqnames) {
+            .forgeRdsSeqFile(name, prefix, suffix, seqs_srcdir, seqs_destdir,
+                             is.single.seq=TRUE, verbose=verbose)
+        }
+    } else if (ondisk_seq_format == "rda") {   # "rda" format
         for (name in seqnames) {
             .forgeRdaSeqFile(name, prefix, suffix, seqs_srcdir, seqs_destdir,
                              is.single.seq=TRUE, verbose=verbose)
@@ -373,8 +420,8 @@
                             verbose=verbose)
             if (provider == "UCSC") {
                 UCSC_genomes <- registered_UCSC_genomes()
-                if (provider_version %in% UCSC_genomes[ , "genome"])
-                    .sortUCSCTwobitFile(provider_version, seqs_destdir,
+                if (genome %in% UCSC_genomes[ , "genome"])
+                    .sortUCSCTwobitFile(genome, seqs_destdir,
                                         verbose=verbose)
             }
         }
@@ -391,7 +438,7 @@
 
 
 ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-### The "forgeMasksFiles" function.
+### forgeMasksFiles()
 ###
 
 ## AGAPS is the mask of "assembly gaps" (inter-contig Ns).
@@ -417,7 +464,7 @@
         desc(ans) <- "assembly gaps (empty)"
     } else {
         if (is.na(filename))
-            filename <- paste(fileprefix, seqname, filesuffix, sep="")
+            filename <- paste0(fileprefix, seqname, filesuffix)
         filepath <- file.path(masks_srcdir, filename)
         if (filetype == "gap")
             ans <- read.gapMask(filepath, seqname=seqname, mask.width=mask_width)
@@ -441,7 +488,7 @@
     ans <- collapse(masks(seq)[-1])
     desc(ans) <- "intra-contig ambiguities"
     if (isEmpty(ans))
-        desc(ans) <- paste(desc(ans), "(empty)")
+        desc(ans) <- paste0(desc(ans), " (empty)")
     active(ans) <- TRUE
     names(ans) <- "AMB"
     ans
@@ -459,7 +506,7 @@
     if (!isSingleStringOrNA(filesuffix))
         stop("'filesuffix' must be a single string or NA")
     if (is.na(filename))
-        filename <- paste(fileprefix, seqname, filesuffix, sep="")
+        filename <- paste0(fileprefix, seqname, filesuffix)
     filepath <- file.path(masks_srcdir, filename)
     if (file.exists(filepath)) {
         ans <- read.rmMask(filepath, seqname=seqname, mask.width=mask_width)
@@ -486,7 +533,7 @@
     if (!isSingleStringOrNA(filesuffix))
         stop("'filesuffix' must be a single string or NA")
     if (is.na(filename))
-        filename <- paste(fileprefix, seqname, filesuffix, sep="")
+        filename <- paste0(fileprefix, seqname, filesuffix)
     filepath <- file.path(masks_srcdir, filename)
     if (file.exists(filepath)) {
         ans <- read.trfMask(filepath, seqname=seqname, mask.width=mask_width)
@@ -528,7 +575,7 @@
     ## Load the sequence.
     ondisk_seq_format <- match.arg(ondisk_seq_format)
     if (ondisk_seq_format == "rda") {  # "rda" format
-        seqfile <- file.path(seqs_destdir, paste(seqname, ".rda", sep=""))
+        seqfile <- file.path(seqs_destdir, paste0(seqname, ".rda"))
         load(seqfile)
         seq <- get(seqname)
         remove(list=seqname)
@@ -576,7 +623,7 @@
         masks <- append(masks, TRFmask)
     }
     objname <- .getMasksObjname(seqname)
-    .saveObject(masks, objname, destdir=masks_destdir, verbose=verbose)
+    .saveObjectToRdaFile(masks, objname, destdir=masks_destdir, verbose=verbose)
 }
 
 forgeMasksFiles <- function(seqnames, nmask_per_seq,
@@ -589,7 +636,7 @@
                             TRFfiles_name=NA, TRFfiles_prefix="", TRFfiles_suffix=".bed",
                             verbose=TRUE)
 {
-    if (length(seqnames) == 0)
+    if (length(seqnames) == 0L)
         warning("'seqnames' is empty")
     for (seqname in seqnames) {
         .forgeMasksFile(seqname, nmask_per_seq,
@@ -622,10 +669,13 @@
         License="character",
         organism="character",
         common_name="character",
+        ## Should be accepted by 'Seqinfo(genome=genome)' e.g. "TAIR10.1",
+        ## "hg38", "ce11" etc...
+        genome="character",
         provider="character",
-        provider_version="character",
+        provider_version="character", # deprecated in favor of 'genome'
         release_date="character",
-        release_name="character",
+        release_name="character",    # deprecated (not replaced by anything)
         source_url="character",
         organism_biocview="character",
         BSgenomeObjname="character",
@@ -645,9 +695,12 @@
         Maintainer="Bioconductor Package Maintainer <maintainer@bioconductor.org>",
         Suggests="",
         License="Artistic-2.0",
+        genome=NA_character_,
+        provider_version=NA_character_,
+        release_name=NA_character_,
         source_url="-- information not available --",
-        seqnames="NULL",             # equivalent to "character(0)"
-        circ_seqs="NULL",            # equivalent to "character(0)"
+        seqnames=NA_character_,
+        circ_seqs=NA_character_,
         mseqnames="NULL",            # equivalent to "character(0)"
         PkgDetails="",
         SrcDataFiles="-- information not available --",
@@ -760,7 +813,34 @@
         template_path <- system.file("pkgtemplates", "BSgenome_datapkg",
                                      package="BSgenome")
         BSgenome_version <- installed.packages()['BSgenome','Version']
-        circ_seqs <- .get_circ_seqs(x@provider, x@provider_version, x@circ_seqs)
+        if (is.na(x@genome)) {
+            if (is.na(x@provider_version))
+                stop("'genome' field is missing in seed file")
+            warning("field 'provider_version' is deprecated ",
+                    "in favor of 'genome'")
+            x@genome <- x@provider_version
+        }
+        if (!is.na(x@release_name))
+            warning("field 'release_name' is deprecated")
+        seqnames <- x@seqnames
+        if (!is.na(seqnames)) {
+            .seqnames <- eval(parse(text=seqnames))
+        } else {
+            if (is.na(x@seqfile_name)) {
+                .seqnames <- seqlevels(Seqinfo(genome=x@genome))
+            } else {
+                .seqnames <- NULL
+            }
+            seqnames <- deparse(.seqnames)
+	}
+        circ_seqs <- x@circ_seqs
+        if (!is.na(circ_seqs)) {
+            .circ_seqs <- eval(parse(text=circ_seqs))
+        } else {
+            si <- Seqinfo(genome=x@genome)
+	    .circ_seqs <- seqlevels(si)[isCircular(si)]
+            circ_seqs <- deparse(.circ_seqs)
+        }
         symvals <- list(
             PKGTITLE=x@Title,
             PKGDESCRIPTION=x@Description,
@@ -772,14 +852,13 @@
             LICENSE=x@License,
             ORGANISM=x@organism,
             COMMONNAME=x@common_name,
+            GENOME=x@genome,
             PROVIDER=x@provider,
-            PROVIDERVERSION=x@provider_version,
             RELEASEDATE=x@release_date,
-            RELEASENAME=x@release_name,
             SOURCEURL=x@source_url,
             ORGANISMBIOCVIEW=x@organism_biocview,
             BSGENOMEOBJNAME=x@BSgenomeObjname,
-            SEQNAMES=ifelse(is.na(x@seqfile_name), x@seqnames, "NULL"),
+            SEQNAMES=seqnames,
             CIRCSEQS=circ_seqs,
             MSEQNAMES=x@mseqnames,
             PKGDETAILS=x@PkgDetails,
@@ -800,20 +879,30 @@
         Biobase::createPackage(x@Package, destdir, template_path, symvals)
         pkgdir <- file.path(destdir, x@Package)
 
-        .seqnames <- eval(parse(text=x@seqnames))
         .mseqnames <- eval(parse(text=x@mseqnames))
         seqs_destdir <- file.path(pkgdir, "inst", "extdata")
-        if (x@ondisk_seq_format == "rda") {
+        if (x@ondisk_seq_format == "rds") {
+            ## Forge the "seqlengths.rds" file
+            forgeSeqlengthsRdsFile(.seqnames,
+                                   prefix=x@seqfiles_prefix,
+                                   suffix=x@seqfiles_suffix,
+                                   seqs_srcdir=seqs_srcdir,
+                                   seqs_destdir=seqs_destdir,
+                                   genome=x@genome,
+                                   verbose=verbose)
+        } else if (x@ondisk_seq_format == "rda") {
             ## Forge the "seqlengths.rda" file
-            forgeSeqlengthsFile(.seqnames,
-                                prefix=x@seqfiles_prefix,
-                                suffix=x@seqfiles_suffix,
-                                seqs_srcdir=seqs_srcdir,
-                                seqs_destdir=seqs_destdir,
-                                verbose=verbose)
+            forgeSeqlengthsRdaFile(.seqnames,
+                                   prefix=x@seqfiles_prefix,
+                                   suffix=x@seqfiles_suffix,
+                                   seqs_srcdir=seqs_srcdir,
+                                   seqs_destdir=seqs_destdir,
+                                   genome=x@genome,
+                                   verbose=verbose)
         }
-        ## Forge the sequence files (either "2bit", "rda", "fa.rz", or "fa")
-        forgeSeqFiles(x@provider, x@provider_version,
+        ## Forge the sequence files (either "2bit", "rds", "rda", "fa.rz",
+        ## or "fa").
+        forgeSeqFiles(x@provider, x@genome,
                       .seqnames, mseqnames=.mseqnames,
                       seqfile_name=x@seqfile_name,
                       prefix=x@seqfiles_prefix,
@@ -879,7 +968,7 @@
         seed_dir <- system.file("extdata", "GentlemanLab", package="BSgenome")
         file <- file.path(seed_dir, file)
         if (!file.exists(file)) {
-            file <- paste(file, "-seed", sep="")
+            file <- paste0(file, "-seed")
             if (!file.exists(file))
                 stop("seed file '", file0, "' not found")
         }
@@ -943,12 +1032,11 @@
             REFPKGNAME=x@RefPkgname,
             SUGGESTS=x@Suggests,
             LICENSE=x@License,
-            ORGANISM=organism(ref_bsgenome),
-            COMMONNAME=commonName(ref_bsgenome),
-            PROVIDER=provider(ref_bsgenome),
-            PROVIDERVERSION=providerVersion(ref_bsgenome),
-            RELEASEDATE=releaseDate(ref_bsgenome),
-            RELEASENAME=releaseName(ref_bsgenome),
+            ORGANISM=metadata(ref_bsgenome)$organism,
+            COMMONNAME=metadata(ref_bsgenome)$common_name,
+            GENOME=metadata(ref_bsgenome)$genome,
+            PROVIDER=metadata(ref_bsgenome)$provider,
+            RELEASEDATE=metadata(ref_bsgenome)$release_date,
             SOURCEURL=x@source_url,
             ORGANISMBIOCVIEW=x@organism_biocview,
             NMASKPERSEQ=as.character(x@nmask_per_seq),
diff -Nru r-bioc-bsgenome-1.56.0/R/OnDiskNamedSequences-class.R r-bioc-bsgenome-1.58.0/R/OnDiskNamedSequences-class.R
--- r-bioc-bsgenome-1.56.0/R/OnDiskNamedSequences-class.R	2020-04-27 20:20:26.000000000 +0000
+++ r-bioc-bsgenome-1.58.0/R/OnDiskNamedSequences-class.R	2020-10-27 17:17:33.000000000 +0000
@@ -12,7 +12,7 @@
 ###   - seqlengthsFilepath()
 ###   - seqinfo API (implementing seqinfo() is enough to make seqlengths(),
 ###                  seqlevels(), etc... work)
-###   - [[ -- load full sequence as XString object
+###   - getListElement() -- load full sequence as XString derivative
 ### Default methods are provided for the following:
 ###   - length()
 ###   - seqnames()
@@ -30,18 +30,28 @@
 
 ### Low-level utilities
 
-### Works on an XString object or any object 'x' for which seqlengths() is
-### defined.
+.check_getListElement_index <- function(i, what)
+{
+    if (!is.character(i))
+        stop(wmsg(what, " can only be subsetted by name"))
+    if (length(i) < 1L)
+        stop(wmsg("attempt to select less than one element"))
+    if (length(i) > 1L)
+        stop(wmsg("attempt to select more than one element"))
+}
+
+### Works on an XString derivative or any object 'x' for which seqlengths()
+### is defined.
 .get_seqlength <- function(x, seqname)
 {
     if (!isSingleString(seqname))
-        stop("'seqname' must be a single string")
+        stop(wmsg("'seqname' must be a single string"))
     if (is(x, "XString"))
         return(length(x))
     x_seqlengths <- seqlengths(x)
     idx <- match(seqname, names(x_seqlengths))
     if (is.na(idx))
-        stop("invalid sequence name: ", seqname)
+        stop(wmsg("invalid sequence name: ", seqname))
     x_seqlengths[[idx]]
 }
 
@@ -60,7 +70,7 @@
     }
 )
 
-### Load regions from a single sequence as an XStringSet object.
+### Load regions from a single sequence as an XStringSet derivative.
 
 ### 'seqname' is ignored.
 setMethod("loadSubseqsFromLinearSequence", "XString",
@@ -70,15 +80,104 @@
 
 setMethod("loadSubseqsFromLinearSequence", "OnDiskNamedSequences",
     function(x, seqname, ranges)
-        loadSubseqsFromLinearSequence(x[[seqname]], seqname, ranges)
+    {
+        seq <- getListElement(x, seqname)
+        loadSubseqsFromLinearSequence(seq, seqname, ranges)
+    }
+)
+
+
+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+### RdsNamedSequences objects
+###
+### The 'dirpath' slot should point to a directory that contains one .rds
+### file per XString derivative + a seqlengths.rds file that contains a
+### serialized named integer vector with the sequence names and lengths.
+###
+
+setClass("RdsNamedSequences",
+    contains=c("RdsCollection", "OnDiskNamedSequences"),
+    prototype=prototype(
+        elementType="XString"
+    )
+)
+
+setMethod("seqlevels", "RdsNamedSequences", function(x) names(x))
+
+setMethod("seqlengthsFilepath", "RdsNamedSequences",
+    function(x) file.path(path(x), "seqlengths.rds")
+)
+
+.read_seqlengths_from_file <- function(x) readRDS(seqlengthsFilepath(x))
+
+setMethod("seqlengths", "RdsNamedSequences",
+    function(x)
+    {
+        noext_ends <- nchar(x@filenames) - nchar(".rds")
+        noext_filenames <- substr(x@filenames, 1L, noext_ends)
+        setNames(.read_seqlengths_from_file(x)[noext_filenames], names(x))
+    }
+)
+
+setMethod("seqinfo", "RdsNamedSequences",
+    function(x)
+    {
+        x_seqlengths <- seqlengths(x)
+        Seqinfo(names(x_seqlengths), unname(x_seqlengths))
+    }
+)
+
+setAs("RdsCollection", "RdsNamedSequences",
+    function(from)
+    {
+        ans <- new2("RdsNamedSequences", from, elementType="XString",
+                                         check=FALSE)
+        seqlengths_from_file <- .read_seqlengths_from_file(ans)
+        if (!is.integer(seqlengths_from_file))
+            stop(wmsg("object serialized in ",
+                      "file '", seqlengthsFilepath(ans), "' ",
+                      "must be a named integer vector"))
+        if (!all(names(from) %in% names(seqlengths_from_file)))
+            stop(wmsg("the names on the RdsCollection object to coerce ",
+                      "to RdsNamedSequences must be a subset of ",
+                      "the names on the integer vector serialized ",
+                      "in file '", seqlengthsFilepath(ans), "'"))
+        ans
+    }
+)
+
+### Constructor.
+RdsNamedSequences <- function(path, seqnames)
+{
+    filenames <- paste0(seqnames, ".rds")
+    as(RdsCollection(path, filenames), "RdsNamedSequences")
+}
+
+### Load a full sequence as an XString derivative.
+setMethod("getListElement", "RdsNamedSequences",
+    function(x, i, exact=TRUE)
+    {
+        .check_getListElement_index(i, "an RdsNamedSequences object")
+        ans <- callNextMethod()
+        if (!is(ans, "XString")) {
+            filepath <- file.path(path(x), x@filenames[[i]])
+            stop(wmsg("serialized object in file '", filepath, "' ",
+                      "must be an XString derivative"))
+        }
+        updateObject(ans)
+    }
 )
 
 
 ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 ### RdaNamedSequences objects
 ###
-### The "dirpath" slot should contain 1 serialized XString object per
-### sequence + a serialized named integer vector ('seqlengths.rda')
+### June 2020: THE RdaNamedSequences CLASS IS SUPERSEDED BY THE
+### RdsNamedSequences CLASS!
+### TODO: Deprecate the RdaNamedSequences class.
+###
+### The "dirpath" slot should contain 1 serialized XString derivative
+### per sequence + a serialized named integer vector ('seqlengths.rda')
 ### containing the sequence names and lengths.
 ###
 
@@ -100,8 +199,8 @@
     {
         ans <- x@seqlengths[["seqlengths"]]
         if (!is.integer(ans) || is.null(names(ans)))
-            stop("serialized object in file '", seqlengthsFilepath(x), "' ",
-                 "must be a named integer vector")
+            stop(wmsg("serialized object in file '", seqlengthsFilepath(x),
+                      "' must be a named integer vector"))
         ans
     }
 )
@@ -123,14 +222,15 @@
     new("RdaNamedSequences", sequences, seqlengths=seqlengths)
 }
 
-### Load a full sequence as an XString object.
-setMethod("[[", "RdaNamedSequences",
-    function(x, i, j, ...)
+### Load a full sequence as an XString derivative.
+setMethod("getListElement", "RdaNamedSequences",
+    function(x, i, exact=TRUE)
     {
-        ans <- callNextMethod()
+        .check_getListElement_index(i, "an RdaNamedSequences object")
+        ans <- x[[i]]
         if (!is(ans, "XString"))
-            stop("serialized object in file '", rdaPath(x, i), "' ",
-                 "must be an XString object")
+            stop(wmsg("serialized object in file '", rdaPath(x, i), "' ",
+                      "must be an XString derivative"))
         updateObject(ans)
     }
 )
@@ -165,19 +265,11 @@
     new("FastaNamedSequences", fafile=fafile)
 }
 
-### We only support subetting by name.
 ### Load a full sequence as a DNAString object.
-setMethod("[[", "FastaNamedSequences",
-    function(x, i, j, ...)
+setMethod("getListElement", "FastaNamedSequences",
+    function(x, i, exact=TRUE)
     {
-        if (!missing(j) || length(list(...)) > 0L)
-            stop("invalid subsetting")
-        if (!is.character(i))
-            stop("a FastaNamedSequences object can only be subsetted by name")
-        if (length(i) < 1L)
-            stop("attempt to select less than one element")
-        if (length(i) > 1L)
-            stop("attempt to select more than one element")
+        .check_getListElement_index(i, "a FastaNamedSequences object")
         fafile <- x@fafile
         seqlength <- .get_seqlength(fafile, i)
         param <- GRanges(i, IRanges(1L, seqlength))
@@ -193,13 +285,13 @@
     function(x, seqname, ranges)
     {
         if (!is(ranges, "IntegerRanges"))
-            stop("'ranges' must be an IntegerRanges object")
+            stop(wmsg("'ranges' must be an IntegerRanges object"))
         fafile <- x@fafile
         seqlength <- .get_seqlength(fafile, seqname)
         if (length(ranges) != 0L &&
             (min(start(ranges)) < 1L || max(end(ranges)) > seqlength))
-            stop("trying to load regions beyond the boundaries ",
-                 "of non-circular sequence \"", seqname, "\"")
+            stop(wmsg("trying to load regions beyond the boundaries ",
+                      "of non-circular sequence \"", seqname, "\""))
         param <- GRanges(seqname, ranges)
         scanFa(fafile, param=param)
     }
@@ -234,19 +326,11 @@
     new("TwobitNamedSequences", twobitfile=twobitfile)
 }
 
-### We only support subetting by name.
 ### Load a full sequence as a DNAString object.
-setMethod("[[", "TwobitNamedSequences",
-    function(x, i, j, ...)
+setMethod("getListElement", "TwobitNamedSequences",
+    function(x, i, exact=TRUE)
     {
-        if (!missing(j) || length(list(...)) > 0L)
-            stop("invalid subsetting")
-        if (!is.character(i))
-            stop("a FastaNamedSequences object can only be subsetted by name")
-        if (length(i) < 1L)
-            stop("attempt to select less than one element")
-        if (length(i) > 1L)
-            stop("attempt to select more than one element")
+        .check_getListElement_index(i, "a TwobitNamedSequences object")
         twobitfile <- x@twobitfile
         seqlength <- .get_seqlength(twobitfile, i)
         which <- GRanges(i, IRanges(1L, seqlength))
@@ -259,13 +343,13 @@
     function(x, seqname, ranges)
     {
         if (!is(ranges, "IntegerRanges"))
-            stop("'ranges' must be an IntegerRanges object")
+            stop(wmsg("'ranges' must be an IntegerRanges object"))
         twobitfile <- x@twobitfile
         seqlength <- .get_seqlength(twobitfile, seqname)
         if (length(ranges) != 0L &&
             (min(start(ranges)) < 1L || max(end(ranges)) > seqlength))
-            stop("trying to load regions beyond the boundaries ",
-                 "of non-circular sequence \"", seqname, "\"")
+            stop(wmsg("trying to load regions beyond the boundaries ",
+                      "of non-circular sequence \"", seqname, "\""))
         which <- GRanges(seqname, ranges)
         import(twobitfile, which=which)
     }
@@ -279,7 +363,7 @@
 .loadSubseqsFromCircularSequence <- function(x, seqname, ranges)
 {
     if (!is(ranges, "IntegerRanges"))
-        stop("'ranges' must be an IntegerRanges object")
+        stop(wmsg("'ranges' must be an IntegerRanges object"))
     seqlength <- .get_seqlength(x, seqname)
     LRranges <- splitLRranges(ranges, seqlength, seqname)
     Lans <- loadSubseqsFromLinearSequence(x, seqname, LRranges$L)
@@ -291,9 +375,9 @@
                                             is_circular=NA)
 {
     if (length(ranges) != length(strand))
-        stop("'ranges' and 'strand' must have the same length")
+        stop(wmsg("'ranges' and 'strand' must have the same length"))
     if (!is.logical(is_circular) || length(is_circular) != 1L)
-        stop("'is_circular' must be a single logical")
+        stop(wmsg("'is_circular' must be a single logical"))
     if (is_circular %in% c(NA, FALSE)) {
         loadFUN <- loadSubseqsFromLinearSequence
     } else {
@@ -301,7 +385,43 @@
     }
     ans <- loadFUN(x, seqname, ranges)
     idx <- which(strand == "-")
-    ans[idx] <- reverseComplement(ans[idx])
+    if (length(idx) != 0L)
+        ans[idx] <- reverseComplement(ans[idx])
     ans
 }
 
+
+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+### OnDiskNamedSequences() constructor
+###
+
+OnDiskNamedSequences <- function(dirpath, seqnames=NULL)
+{
+    filename <- "seqlengths.rds"
+    filepath <- file.path(dirpath, filename)
+    if (file.exists(filepath))
+        return(RdsNamedSequences(dirpath, seqnames))
+
+    filename <- "seqlengths.rda"
+    filepath <- file.path(dirpath, filename)
+    if (file.exists(filepath))
+        return(RdaNamedSequences(dirpath, seqnames))
+
+    filename <- "single_sequences.fa"
+    filepath <- file.path(dirpath, filename)
+    if (file.exists(filepath))
+        return(FastaNamedSequences(filepath))
+
+    filename <- "single_sequences.fa.rz"
+    filepath <- file.path(dirpath, filename)
+    if (file.exists(filepath))
+        return(FastaNamedSequences(filepath))
+
+    filename <- "single_sequences.2bit"
+    filepath <- file.path(dirpath, filename)
+    if (file.exists(filepath))
+        return(TwobitNamedSequences(filepath))
+
+    stop(wmsg("invalid directory content at ", dirpath))
+}
+
diff -Nru r-bioc-bsgenome-1.56.0/vignettes/BSgenomeForge.Rnw r-bioc-bsgenome-1.58.0/vignettes/BSgenomeForge.Rnw
--- r-bioc-bsgenome-1.56.0/vignettes/BSgenomeForge.Rnw	2020-04-27 20:20:26.000000000 +0000
+++ r-bioc-bsgenome-1.58.0/vignettes/BSgenomeForge.Rnw	2020-10-27 17:17:33.000000000 +0000
@@ -75,13 +75,6 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 
-IMPORTANT NOTE: Starting with Bioconductor 2.14, the
-\Rfunction{forgeBSgenomeDataPkg} function doesn't handle masks anymore
-i.e. now it produces a \term{BSgenome data package} that contains only
-the bare sequences. A new function \Rfunction{forgeMaskedBSgenomeDataPkg}
-has been added to forge a \term{BSgenome data package} with masked
-sequences. This vignette has been updated to reflect these changes.
-
 This vignette describes the process of forging a \term{BSgenome data package}.
 It is intended for Bioconductor users who want to make a new \term{BSgenome
 data package}, not for regular users of these packages.
@@ -128,9 +121,12 @@
 \Rpackage{Biostrings} or \Rpackage{BSgenome} packages.
 
 Questions, comments or bug reports about this vignette or about the
-BSgenomeForge functions are welcome. Please address them to the author
-(\code{hpages@fredhutch.org}) or post them on the Bioconductor support
-site \footnote{\url{https://support.bioconductor.org/}}.
+BSgenomeForge functions are welcome. Please use the Bioconductor support
+site \footnote{\url{https://support.bioconductor.org/}} if you have
+questions or need help about forging a \term{BSgenome data package},
+or about anything related to the \Rpackage{BSgenome} package. For bug
+reports or feature requests, please open an issue on GitHub at
+\url{https://github.com/Bioconductor/BSgenome/issues}.
 
 In the next section (``How to forge a BSgenome data package with bare
 sequences''), we describe how to forge a \term{BSgenome data package}
@@ -318,27 +314,24 @@
       the \textit{List of UCSC genome releases} table
       \footnote{\url{http://genome.ucsc.edu/FAQ/FAQreleases\#release1}}.
 
-\item \code{provider}: The provider of the \term{sequence data files} e.g.
-      \code{UCSC}, \code{NCBI}, \code{BDGP}, \code{FlyBase}, etc...
-      Should preferably match part 3 of the package name (field \code{Package}).
-
-\item \code{provider\_version}: The provider-side version of the genome.
+\item \code{genome}: The name of the genome. Typically the name of an NCBI
+      assembly (e.g. \code{GRCh38.p12}, \code{WBcel235}, \code{TAIR10.1},
+      \code{ARS-UCD1.2}, etc...) or UCSC genome (e.g. \code{hg38},
+      \code{bosTau9}, \code{galGal6}, \code{ce11}, etc...).
       Should preferably match part 4 of the package name (field \code{Package}).
       For the packages built by the Bioconductor project from a UCSC genome,
       this field corresponds to the \code{UCSC VERSION} field of the
       \textit{List of UCSC genome releases} table.
 
+\item \code{provider}: The provider of the \term{sequence data files} e.g.
+      \code{UCSC}, \code{NCBI}, \code{BDGP}, \code{FlyBase}, etc...
+      Should preferably match part 3 of the package name (field \code{Package}).
+
 \item \code{release\_date}: When this assembly of the genome was released.
       For the packages built by the Bioconductor project from a UCSC genome,
       this field corresponds to the \code{RELEASE DATE} field of the
       \textit{List of UCSC genome releases} table.
 
-\item \code{release\_name}: The release name or build number of this assembly
-      of the genome.
-      For the packages built by the Bioconductor project from a UCSC genome,
-      this field corresponds to the \code{RELEASE NAME} field of the
-      \textit{List of UCSC genome releases} table.
-
 \item \code{source\_url}: The permanent URL where the \term{sequence data
       files} used to forge the \term{target package} can be found.
 
diff -Nru r-bioc-bsgenome-1.56.0/vignettes/GenomeSearching.Rnw r-bioc-bsgenome-1.58.0/vignettes/GenomeSearching.Rnw
--- r-bioc-bsgenome-1.56.0/vignettes/GenomeSearching.Rnw	2020-04-27 20:20:26.000000000 +0000
+++ r-bioc-bsgenome-1.58.0/vignettes/GenomeSearching.Rnw	2020-10-27 17:17:33.000000000 +0000
@@ -123,17 +123,15 @@
 @
 
 When displayed, some basic information about the origin of the
-genome is shown (organism, provider, provider version, etc...)
+genome is shown (organism, genome, provider, etc...)
 followed by the index of {\it single} sequences and eventually
 an additional index of {\it multiple} sequences.
 Methods (adequately called {\it accessor methods}) are defined
 for individual access to this information:
 <<b3>>=
-organism(genome)
-provider(genome)
-providerVersion(genome)
+metadata(genome)
 seqnames(genome)
-mseqnames(genome)
+seqinfo(genome)
 @
 
 See the man page for the \Rclass{BSgenome} class (\Rfunction{?BSgenome})
@@ -328,7 +326,7 @@
     genome <- BSgenome.Celegans.UCSC.ce2
     seqnames <- seqnames(genome)
     seqnames_in1string <- paste(seqnames, collapse=", ")
-    cat("Target:", providerVersion(genome),
+    cat("Target:", metadata(genome)$genome,
         "chromosomes", seqnames_in1string, "\n")
     append <- FALSE
     for (seqname in seqnames) {
@@ -737,7 +735,7 @@
 runOneStrandAnalysis <- function(dict0, bsgenome, seqnames, strand,
                                  outfile="", append=FALSE)
 {
-    cat("\nTarget: strand", strand, "of", providerVersion(bsgenome),
+    cat("\nTarget: strand", strand, "of", metadata(bsgenome)$genome,
         "chromosomes", paste(seqnames, collapse=", "), "\n")
     if (strand == "-")
         dict0 <- reverseComplement(dict0)