Subject: [bug#66914] [PATCH 1/2] gnu: Add r-bsgenome-hsapiens-ucsc-hg38-masked.

From: Mădălin Ionel Patrașcu<[email-masked]>
Date: Fri, 3 Nov 2023 14:40:59 +0100

* gnu/packages/bioconductor.scm
  (r-bsgenome-hsapiens-ucsc-hg38-masked): New variable.

Change-Id: Ic1b646a3bd3b7262dd82f0972961c2e89628e90b
---
 gnu/packages/bioconductor.scm | 36 +++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d79236ea26..ac09a079b4 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -68,6 +68,42 @@ (define-module (gnu packages bioconductor)
 
 ;;; Annotations
 
+(define-public r-bsgenome-hsapiens-ucsc-hg38-masked
+  (package
+    (name "r-bsgenome-hsapiens-ucsc-hg38-masked")
+    (version "1.4.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38.masked" version
+                              'annotation))
+       (sha256
+        (base32 "0j71hdxqvvc0s8mc6jp6zk502mrf095qazj95yzzb4rm6sjvd20m"))))
+    (properties `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38.masked")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg38
+                             r-genomeinfodb))
+    (home-page
+     "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38.masked")
+    (synopsis
+     "Full masked genomic sequences for Homo sapiens (UCSC version hg38)")
+    (description
+     "This package provides the complete genome sequences for Homo sapiens as
+provided by UCSC (genome hg38, based on assembly GRCh38.p14 since 2023/01/31).
+The sequences are the same as in BSgenome.Hsapiens.UCSC.hg38, except that each
+of them has the 4 following masks on top:
+
+@enumerate
+@item the mask of assembly gaps (AGAPS mask);
+@item the mask of intra-contig ambiguities (AMB mask);
+@item the mask of repeats from @code{RepeatMasker} (RM mask);
+@item the mask of repeats from Tandem Repeats Finder (TRF mask).
+@end enumerate
+
+Only the AGAPS and AMB masks are \"active\" by default.  The sequences are stored
+in @code{MaskedDNAString} objects.")
+    (license license:artistic2.0)))
+
 (define-public r-mafh5-gnomad-v3-1-2-grch38
   (package
     (name "r-mafh5-gnomad-v3-1-2-grch38")

base-commit: a0a377fdd6c873aeb6340afeddcd23b4ead7657d
-- 
2.41.0