move single generic into annot_rse

R/annot_rse.R

@@ -1,3 +1,56 @@
+#' Annotate known SNP positions
+#'
+#' @description This function will annotate a [GRanges] or the rowRanges of
+#' a [SummarizedExperiment] with SNPs from a SNP package.
+#'
+#' @param obj GRanges or SummarizedExperiment  object
+#' @param dbsnp SNPlocs package, see available packages from
+#' [BSgenome::available.SNPs()]
+#' @param chrom only operate on a specified chromosome
+#' @param col_to_aggr column from SNPlocs package to add to
+#' input. If multiple SNPs overlap these values will be concatenated
+#' as comma separated values.
+#' @param genome A BSgenome object, which if supplied, will be used to provide
+#' additional `snp_ref_allele` and `snp_alt_alleles` columns containing the
+#' reference and alt allele sequences, with respect to the positive strand.
+#' Additionally the snp sequences will be checked against the allele at the site
+#' if a column named `ALT` is present in object. The strand of the site will be
+#' used to determine if the `ALT` allele needs to be complemented prior to
+#' comparing against the SNP db (which always returns sequences w.r.t the
+#' plus strand).
+#' @param drop If TRUE, remove sites overlapping SNPs
+#' @param RLE If TRUE, columns added will returned as [S4Vectors::Rle()] vectors
+#' to reduce memory
+#'
+#' @param ... For the generic, further arguments to pass to specific methods.
+#' Unused for now.
+#'
+#' @return Either a GRanges or SummarizedExperiment object with
+#' a new column added with information from `col_to_aggr` and optionally
+#' `snp_ref_allele`, `snp_alt_alleles`, and `snp_matches_site` annotations.
+#'
+#' @examples
+#' if (require(SNPlocs.Hsapiens.dbSNP144.GRCh38)) {
+#'     gr <- GRanges(rep("22", 10),
+#'         IRanges(
+#'             seq(10510077,
+#'                 10610077,
+#'                 by = 1000
+#'             )[1:10],
+#'             width = 250
+#'         ),
+#'         strand = "+"
+#'     )
+#'     genome(gr) <- "GRCh38.p2"
+#'     annot_snps(gr, SNPlocs.Hsapiens.dbSNP144.GRCh38)
+#' }
+#' @seealso [SNPlocs.Hsapiens.dbSNP144.GRCh38](https://bioconductor.org/packages/release/data/annotation/html/SNPlocs.Hsapiens.dbSNP144.GRCh38.html)
+#' @export
+annot_snps <- function(obj, ...) {
+    UseMethod("annot_snps", obj)
+}
+
+
 #' @rdname annot_snps
 #' @importFrom BSgenome snpsByOverlaps
 #' @export

R/pileup.R

@@ -151,12 +151,7 @@ pileup_sites <- function(bamfiles,
 
     ## set default bam flags if not supplied
     if (identical(param@bam_flags, Rsamtools::scanBamFlag())) {
-        param@bam_flags <- Rsamtools::scanBamFlag(
-            isSecondaryAlignment = FALSE,
-            isNotPassingQualityCont = FALSE,
-            isDuplicate = FALSE,
-            isSupplementaryAlignment = FALSE
-        )
+        param@bam_flags <- defaultBulkBamFlags
     }
 
     fp <- cfilterParam(param, n_files)
@@ -304,6 +299,14 @@ setup_valid_regions <- function(bam, chroms, region = NULL, fasta = NULL) {
 # IRanges/GRanges are limited to this max int
 MAX_INT <- 536870912
 
+defaultBulkBamFlags <- Rsamtools::scanBamFlag(
+        isSecondaryAlignment = FALSE,
+        isNotPassingQualityCont = FALSE,
+        isDuplicate = FALSE,
+        isSupplementaryAlignment = FALSE
+)
+
+
 # parses a region string (e.g. "chr1:456-567" or "chr1")
 # using htslib into chrom, start, and end (0-based start)
 # returns a list with chrom, start, and end entries

R/sc-pileup.R

@@ -155,15 +155,10 @@ pileup_cells <- function(bamfiles,
 
     ## set default bam flags if not supplied
     if (identical(param@bam_flags, Rsamtools::scanBamFlag())) {
-        param@bam_flags <- Rsamtools::scanBamFlag(
-            isSecondaryAlignment = FALSE,
-            isSupplementaryAlignment = FALSE,
-            isNotPassingQualityControls = FALSE
-        )
+        param@bam_flags <- defaultScBamFlags
     }
 
     cell_barcodes <- cell_barcodes[!is.na(cell_barcodes)]
-
     cb_tag <- check_tag(cb_tag)
     umi_tag <- check_tag(umi_tag)
 
@@ -255,6 +250,12 @@ pileup_cells <- function(bamfiles,
     res
 }
 
+defaultScBamFlags <- Rsamtools::scanBamFlag(
+    isSecondaryAlignment = FALSE,
+    isSupplementaryAlignment = FALSE,
+    isNotPassingQualityControls = FALSE
+)
+
 get_sc_pileup <- function(bamfn, index, id, sites, barcodes,
                           outfile_prefix, chrom,
                           umi_tag, cb_tag, param,