version bump; delete parse_gff_tree

mritchielab · Feb 5, 2025 · c84efd0 · c84efd0
1 parent 2187790
commit c84efd0
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Showing 9 changed files with 9 additions and 76 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: FLAMES
 Title: FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data
-Version: 2.1.4
+Version: 2.1.5
 Date: 2023-03-27
 Authors@R: c(
        person("Luyi", "Tian", role=c("aut"),

diff --git a/NAMESPACE b/NAMESPACE
@@ -22,7 +22,6 @@ export(get_GRangesList)
 export(get_coverage)
 export(minimap2_align)
 export(minimap2_realign)
-export(parse_gff_tree)
 export(plot_coverage)
 export(plot_demultiplex)
 export(plot_isoform_heatmap)

diff --git a/R/find_isoform.R b/R/find_isoform.R
@@ -94,8 +94,6 @@ find_isoform_bambu <- function(annotation, genome_fa, genome_bam, outdir, config
     file.remove(bambuTempAnnot);
   }
 
-  # isoform_objects <- list(transcript_dict = NULL, transcript_dict_i = parse_gff_tree(isoform_gtf)$transcript_dict)
-  # isoform_objects
 }
 
 #' @importFrom reticulate import_from_path
@@ -144,6 +142,7 @@ find_isoform_flames <- function(annotation, genome_fa, genome_bam, outdir, confi
 
 #' Fake stranded GFF file
 #' @description Check if all the transcript in the annotation is stranded. If not, convert to '+'.
+#' @return Path to the temporary file with unstranded transcripts converted to '+'.
 #' @keywords internal
 fake_stranded_gff <- function(gff_file) {
   # check if all the transcript in the annotation is stranded

diff --git a/R/parse_gene_anno.R b/R/parse_gene_anno.R
diff --git a/R/sc_long_pipeline.R b/R/sc_long_pipeline.R
@@ -464,6 +464,7 @@ create_sce_from_dir <- function(outdir, annotation, quantification = "FLAMES") {
 #' Assumes rownames are transcript_ids
 #' Assumes transcript_id is present in the annotation file
 #' @importFrom SummarizedExperiment rowRanges rowRanges<-
+#' @return a \code{SummarizedExperiment} object with rowRanges added
 #' @keywords internal
 addRowRanges <- function(sce, annotation, outdir) {
   if (is.null(S4Vectors::metadata(sce)$OutputFiles)) {

diff --git a/man/addRowRanges.Rd b/man/addRowRanges.Rd
diff --git a/man/fake_stranded_gff.Rd b/man/fake_stranded_gff.Rd
diff --git a/man/parse_gff_tree.Rd b/man/parse_gff_tree.Rd
diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml
@@ -72,7 +72,6 @@ reference:
       - filter_annotation
       - get_GRangesList
       - demultiplex_sockeye
-      - parse_gff_tree
       - scmixology_lib10
       - scmixology_lib10_transcripts
       - scmixology_lib90