R readme

Author: kcleal

.github/workflows/sync_r.yml

@@ -27,5 +27,5 @@ jobs:
       env:
         PAT_TOKEN: ${{ secrets.PAT_TOKEN }}
       run: |
-        git remote add superintervals-r https://x-access-token:${PAT_TOKEN}@github.com/kcleal/superintervals-r.git
-        git subtree push --prefix=src/R superintervals-r main
+        git remote add superintervalsr https://x-access-token:${PAT_TOKEN}@github.com/kcleal/superintervalsr.git
+        git subtree push --prefix=src/R superintervalsr main

src/R/DESCRIPTION

@@ -1,4 +1,4 @@
-Package: superintervals
+Package: superintervalsr
 Type: Package
 Title: Fast, Memory-Efficient Interval Operations for Genomics
 Version: 0.99.0
@@ -15,8 +15,8 @@ Description: Provides a fast, memory-efficient data structure for interval
     searches and SIMD-optimized counting operations. Designed for high-performance
     genomics applications where fast interval operations are essential.
 License: MIT + file LICENSE
-URL: https://github.com/yourusername/superintervals
-BugReports: https://github.com/yourusername/superintervals/issues
+URL: https://github.com/kcleal/superintervalsr
+BugReports: https://github.com/kcleal/superintervalsr/issues
 biocViews: Infrastructure, DataRepresentation, GenomeAnnotation,
            Genetics, Preprocessing, Software, Sequencing
 Depends: R (>= 4.3.0)

src/R/NAMESPACE

@@ -21,4 +21,4 @@ export(search_values)
 export(size)
 export(starts_at)
 importFrom(Rcpp,evalCpp)
-useDynLib(superintervals, .registration=TRUE)
+useDynLib(superintervalsr, .registration=TRUE)

src/R/R/RcppExports.R

@@ -2,70 +2,70 @@
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
 create_intervalmap <- function() {
-    .Call(`_superintervals_create_intervalmap`)
+    .Call(`_superintervalsr_create_intervalmap`)
 }
 
 add_interval <- function(container, start, end, value = NULL) {
-    invisible(.Call(`_superintervals_add_interval`, container, start, end, value))
+    invisible(.Call(`_superintervalsr_add_interval`, container, start, end, value))
 }
 
 build_index <- function(container) {
-    invisible(.Call(`_superintervals_build_index`, container))
+    invisible(.Call(`_superintervalsr_build_index`, container))
 }
 
 get_interval_at <- function(container, r_index) {
-    .Call(`_superintervals_get_interval_at`, container, r_index)
+    .Call(`_superintervalsr_get_interval_at`, container, r_index)
 }
 
 get_start_at <- function(container, r_index) {
-    .Call(`_superintervals_get_start_at`, container, r_index)
+    .Call(`_superintervalsr_get_start_at`, container, r_index)
 }
 
 get_end_at <- function(container, r_index) {
-    .Call(`_superintervals_get_end_at`, container, r_index)
+    .Call(`_superintervalsr_get_end_at`, container, r_index)
 }
 
 get_data_at <- function(container, r_index) {
-    .Call(`_superintervals_get_data_at`, container, r_index)
+    .Call(`_superintervalsr_get_data_at`, container, r_index)
 }
 
 clear_intervals <- function(container) {
-    invisible(.Call(`_superintervals_clear_intervals`, container))
+    invisible(.Call(`_superintervalsr_clear_intervals`, container))
 }
 
 reserve_intervals <- function(container, n) {
-    invisible(.Call(`_superintervals_reserve_intervals`, container, n))
+    invisible(.Call(`_superintervalsr_reserve_intervals`, container, n))
 }
 
 get_size <- function(container) {
-    .Call(`_superintervals_get_size`, container)
+    .Call(`_superintervalsr_get_size`, container)
 }
 
 cpp_has_overlaps <- function(container, start, end) {
-    .Call(`_superintervals_cpp_has_overlaps`, container, start, end)
+    .Call(`_superintervalsr_cpp_has_overlaps`, container, start, end)
 }
 
 count_overlaps <- function(container, start, end) {
-    .Call(`_superintervals_count_overlaps`, container, start, end)
+    .Call(`_superintervalsr_count_overlaps`, container, start, end)
 }
 
 cpp_search_values <- function(container, start, end) {
-    .Call(`_superintervals_cpp_search_values`, container, start, end)
+    .Call(`_superintervalsr_cpp_search_values`, container, start, end)
 }
 
 search_indexes <- function(container, start, end) {
-    .Call(`_superintervals_search_indexes`, container, start, end)
+    .Call(`_superintervalsr_search_indexes`, container, start, end)
 }
 
 cpp_search_keys <- function(container, start, end) {
-    .Call(`_superintervals_cpp_search_keys`, container, start, end)
+    .Call(`_superintervalsr_cpp_search_keys`, container, start, end)
 }
 
 cpp_search_items <- function(container, start, end) {
-    .Call(`_superintervals_cpp_search_items`, container, start, end)
+    .Call(`_superintervalsr_cpp_search_items`, container, start, end)
 }
 
 get_coverage <- function(container, start, end) {
-    .Call(`_superintervals_get_coverage`, container, start, end)
+    .Call(`_superintervalsr_get_coverage`, container, start, end)
 }
 

src/R/R/superintervals.R src/R/R/superintervalsr.Rsrc/R/R/superintervals.R renamed to src/R/R/superintervalsr.R

@@ -1,4 +1,4 @@
-#' @useDynLib superintervals, .registration=TRUE
+#' @useDynLib superintervalsr, .registration=TRUE
 #' @importFrom Rcpp evalCpp
 NULL
 

src/R/README.md

@@ -1,7 +1,7 @@
 # SuperIntervals
 
-The R Bioconductor package `superintervals` provides a fast, memory-efficient data structure for interval intersection queries in R.
-Built on a novel superset-index approach, SuperIntervals maintains intervals in position-sorted order,
+The R Bioconductor package `superintervalsr` provides a fast, memory-efficient data structure for interval intersection queries in R.
+Built on a novel superset-index approach that maintains intervals in position-sorted order,
 enabling cache-friendly searches and SIMD-optimized counting operations.
 
 ## Key Features
@@ -17,8 +17,10 @@ enabling cache-friendly searches and SIMD-optimized counting operations.
 
 Build and install:
 ```r
-cd superintervals/src/R
 bash ./build.sh
+
+# Run a small benchmark vs IRanges
+Rscript benchmark.R
 ```
 
 ## Quick Start
@@ -121,7 +123,7 @@ clear(imap)
 ## Example: Genomic Analysis
 
 ```r
-library(superintervals)
+library(superintervalsr)
 
 # Create interval map for gene annotations
 genes <- IntervalMap()

src/R/benchmark.R

@@ -1,8 +1,8 @@
 #!/usr/bin/env Rscript
-# benchmark.R - SuperIntervals vs IRanges (NCLS algorithm)
+# benchmark.R - SuperIntervals-r vs IRanges (NCLS algorithm)
 
 suppressPackageStartupMessages({
-  library(superintervals)
+  library(superintervalsr)
   library(IRanges)
   library(microbenchmark)
 })

src/R/build.sh

@@ -17,11 +17,11 @@ echo "=== Building package ==="
 R CMD build .
 
 echo "=== Running R CMD check ==="
-TARBALL=$(ls -t superintervals_*.tar.gz | head -n1)
+TARBALL=$(ls -t superintervalsr_*.tar.gz | head -n1)
 R CMD check "$TARBALL" --no-manual
 
-# echo "=== Build complete ==="
-# echo "Package tarball: $TARBALL"
+echo "=== Build complete ==="
+echo "Package tarball: $TARBALL"
 
 echo "=== Installing ==="
 R CMD INSTALL .