Merge pull request #23 from uclahs-cds/danknight-release

v1.1.3 Release

Author: dan-knight

DESCRIPTION

@@ -2,7 +2,7 @@ Package: bedr
 Type: Package
 Title: Genomic Region Processing using Tools Such as 'BEDTools', 'BEDOPS' and 'Tabix'
 Version: 1.1.3
-Date: 2025-04-01
+Date: 2025-04-04
 Authors@R: c(
   person("Syed", "Haider", role = "aut"),
   person("Daryl", "Waggott", role = "aut"),
@@ -14,8 +14,6 @@ Authors@R: c(
   person("Melinda", "Luo", role = "ctb"),
   person("Paul", "C. Boutros", role = c("aut", "cre", "cph"), email = "[email protected]")
   )
-Author: Syed Haider [aut], Daryl Waggott [aut], Emilie Lalonde [ctb], Clement Fung [ctb], Helena Winata [ctb], Paul C. Boutros [aut, cre, cph]
-Maintainer: Paul C. Boutros <[email protected]>
 Description: Genomic regions processing using open-source command line tools such as 'BEDTools', 'BEDOPS' and 'Tabix'.
   These tools offer scalable and efficient utilities to perform genome arithmetic e.g indexing, formatting and merging.
   bedr API enhances access to these tools as well as offers additional utilities for genomic regions processing.
@@ -26,7 +24,7 @@ Suggests:
     rmarkdown (>= 0.9.5)
 VignetteBuilder: knitr
 License: GPL-2
-URL: https://github.com/uclahs-cds/pacakage-bedr
+URL: https://github.com/uclahs-cds/package-bedr
 BugReports: https://github.com/uclahs-cds/package-bedr/issues
 Imports: testthat (>= 3.0.0), VennDiagram (>= 1.6.4), data.table (>= 1.8.11), R.utils (>= 2.0.2), yaml (>= 2.1.10), parallel, grid
 Config/testthat/edition: 3

NEWS.md

@@ -1,4 +1,4 @@
-# bedr 1.1.3 (2025-04-01)
+# bedr 1.1.3 (2025-04-04)
 
 
 ## Added
@@ -9,6 +9,7 @@
 
 - Update changelog to Markdown `NEWS.md` format
 - Use updated `renv` GitHub action for `R CMD check`
+- Rename internal helper function `parse.vcf.header()` to `prep.vcf.header()` to avoid naming conflict with base R `parse()` S3 method.
 
 ## Fixed
 

R/read.vcf.R

@@ -132,7 +132,7 @@ read.vcf <- function(x, split.info = FALSE, split.samples = FALSE, nrows = -1, v
 	attr(x.df, "header") <- x.header;
 
 	# add parsed header as list in item
-	x.header.parsed <- parse.vcf.header(x.header);
+	x.header.parsed <- prep.vcf.header(x.header);
 	x.df <- list(header = x.header.parsed, vcf = x.df);
 	catv("   Done\n");
 
@@ -233,7 +233,7 @@ read.vcf <- function(x, split.info = FALSE, split.samples = FALSE, nrows = -1, v
 
 ###################################################################################################
 
-parse.vcf.header <- function(x) {
+prep.vcf.header <- function(x) {
 ### return the header as a list of key values 
 
 	if (is.null(x)) {return(NULL)}

vignettes/Using-bedr.Rmd

@@ -237,7 +237,7 @@ if (check.binary("bedtools")) {
 
 ### <a id = "jaccard-and-reldist"></a> Statistically Quantify Regions' Similarity (jaccard and reldist)
 
-When comparing (pairwise) the extent of overlap between a large collection of genomic regions, it becomes necessary to report the similarity (intersect) using a single quantitative measure. Bedtools implements two such statitics; [`jaccard`](http://bedtools.readthedocs.io/en/latest/content/tools/jaccard.html) and [`reldist`](http://bedtools.readthedocs.io/en/latest/content/tools/reldist.html) ([Favorov A et al.](https://www.ncbi.nlm.nih.gov/pubmed/22693437)) which can be called through `bedr` as shown below:
+When comparing (pairwise) the extent of overlap between a large collection of genomic regions, it becomes necessary to report the similarity (intersect) using a single quantitative measure. Bedtools implements two such statitics; [`jaccard`](http://bedtools.readthedocs.io/en/latest/content/tools/jaccard.html) and [`reldist`](http://bedtools.readthedocs.io/en/latest/content/tools/reldist.html) ([Favorov A et al.](https://pubmed.ncbi.nlm.nih.gov/22693437/)) which can be called through `bedr` as shown below:
 ```{r, results = "hold", message = TRUE, eval = TRUE, errors = TRUE}
 if (check.binary("bedtools")) {