feat: R wrapper

Signed-off-by: eternal-flame-AD <yume@yumechi.jp>

.github/workflows/check.yml

@@ -181,6 +181,29 @@ jobs:
           source $(hatch env find)/bin/activate
           maturin develop --release --manifest-path Cargo.toml --features test
           hatch run test --verbose
+
+  r_port:
+    needs: [check-unix]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Rust
+        uses: actions-rs/toolchain@v1
+        with:
+          toolchain: stable
+
+      - name: Install R
+        uses: r-lib/actions/setup-r@v2
+
+      - name: Install R packages
+        run: Rscript -e 'install.packages(c("devtools", "testthat", "roxygen2", "covr", "digest"))'
+
+      - name: Install Rust R package
+        run: Rscript -e 'devtools::install_local("r/gtfsort")'
+
+      - name: Run R tests
+        run: Rscript -e 'devtools::test("r/gtfsort")'
 
   benchmark:
     needs: [check-unix, check-windows]

gtfsort/Cargo.toml

@@ -26,7 +26,6 @@ libc = "0.2.151"
 hashbrown = {version="0.14", features=["rayon"]}
 dashmap = "5.5"
 time = "0.3.36"
-libR-sys = { version = "0.7.0", optional = true }
 reqwest = { version = "0.12.5", features = ["blocking"], optional = true }
 crc = { version = "3.2.1", optional = true}
 flate2 = { version ="1.0.30" , optional = true}
@@ -53,7 +52,7 @@ opt-level = 3
 [lib]
 name = "gtfsort"
 path = "src/lib.rs"
-crate-type = ["cdylib", "rlib"]
+crate-type = ["cdylib", "rlib", "staticlib"]
 
 [[bin]]
 name = "gtfsort"

r/gtfsort/.Rbuildignore

@@ -0,0 +1,2 @@
+^src/\.cargo$
+^src/rust/gtfsort/target/

r/gtfsort/DESCRIPTION

@@ -0,0 +1,17 @@
+Package: gtfsort
+Title: An Optimized Lexicographiclexicographic Chr/Pos/Feature GTF/GFF Sorter.
+Version: 0.0.0.9000
+Authors@R: 
+    c(person("Alejandro", "Gonzales-Irribarren", , "alejandrxgzi@gmail.com", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0001-7010-8146")),
+      person("Anne", "Fu", , "anne.fu@utdallas.edu", role = "aut",
+           comment = c(ORCID = "0000-0002-9025-6071")))
+Description: While current tools (most of them GFF3-focused) have been recommended for sorting GTF files, none are directed towards chr/pos/feature ordering. This approach ensures custom sorting directionality, which is useful for reducing computation times in tools that work with sorted GTF files. Furthermore, it provides a friendly and organized visualization of gene structures (gene -> transcript -> CDS/exon -> start/stop -> UTR/Sel), allowing users to search for features more efficiently.
+License: use_mit_license()
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.1
+Config/rextendr/version: 0.3.1
+Suggests: 
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3

r/gtfsort/NAMESPACE

@@ -0,0 +1,5 @@
+# Generated by roxygen2: do not edit by hand
+
+export(sort_annotations)
+export(sort_annotations_str)
+useDynLib(gtfsort, .registration = TRUE)

r/gtfsort/R/extendr-wrappers.R

@@ -0,0 +1,41 @@
+# Generated by extendr: Do not edit by hand
+
+# nolint start
+
+#
+# This file was created with the following call:
+#   .Call("wrap__make_gtfsort_wrappers", use_symbols = TRUE, package_name = "gtfsort")
+
+#' @usage NULL
+#' @useDynLib gtfsort, .registration = TRUE
+NULL
+
+#' Sort a GTF/GFF/GFF3 file.
+#'
+#' @param input The input file path.
+#' @param output The output file path.
+#' @param threads The number of threads to use.
+#' @return a list with the input and output file paths, the number of threads used, whether the input and output were memory-mapped, the time taken to parse, index, and write the output, and the memory used before and after the operation.
+#'
+#' @examples
+#' sort_annotations("tests/data/chr1.gtf", "tests/data/chr1.sorted.gtf", 1)
+#'
+#' @export
+sort_annotations <- function(input, output, threads) .Call(wrap__sort_annotations, input, output, threads)
+
+#' Sort a string with GTF/GFF/GFF3 annotations.
+#'
+#' @param mode The mode to parse the annotations. Either "gtf" or "gff" or "gff3".
+#' @param input The string with the GTF/GFF/GFF3 annotations.
+#' @param output A function that will be called with each chunk of the sorted string. Return NULL to continue, or a string to stop.
+#' @param threads The number of threads to use.
+#' @return a list with the input and output strings, the number of threads used, whether the input and output were memory-mapped, the time taken to parse, index, and write the output, and the memory used before and after the operation.
+#'
+#' @examples
+#' sort_annotations_str("gtf", "chr1\t.\texon\t11869\t12227\t.\t+\t.\tgene_id \"ENSG00000223972.5\"; transcript_id \"ENST00000456328.2\"; exon_number \"1\";\nchr1\t.\texon\t12613\t12721\t.\t+\t.\tgene_id \"ENSG00000223972.5\"; transcript_id \"ENST00000456328.2\"; exon_number \"2\";", function(str) { cat(str); return(NULL); }, 1)
+#'
+#' @export
+sort_annotations_str <- function(mode, input, output, threads) .Call(wrap__sort_annotations_str, mode, input, output, threads)
+
+
+# nolint end

r/gtfsort/src/.gitignore

@@ -0,0 +1,5 @@
+*.o
+*.so
+*.dll
+target
+.cargo

r/gtfsort/src/Makevars

@@ -0,0 +1,30 @@
+TARGET_DIR = ./rust/target
+LIBDIR = $(TARGET_DIR)/release
+STATLIB = $(LIBDIR)/libgtfsort.a
+PKG_LIBS = -L$(LIBDIR) -lgtfsort
+
+all: C_clean
+
+$(SHLIB): $(STATLIB)
+
+CARGOTMP = $(CURDIR)/.cargo
+
+$(STATLIB):
+	# In some environments, ~/.cargo/bin might not be included in PATH, so we need
+	# to set it here to ensure cargo can be invoked. It is appended to PATH and
+	# therefore is only used if cargo is absent from the user's PATH.
+	if [ "$(NOT_CRAN)" != "true" ]; then \
+		export CARGO_HOME=$(CARGOTMP); \
+	fi && \
+		export PATH="$(PATH):$(HOME)/.cargo/bin" && \
+		cargo build --lib --release --manifest-path=./rust/Cargo.toml --target-dir $(TARGET_DIR)
+	if [ "$(NOT_CRAN)" != "true" ]; then \
+		rm -Rf $(CARGOTMP) && \
+		rm -Rf $(LIBDIR)/build; \
+	fi
+
+C_clean:
+	rm -Rf $(SHLIB) $(STATLIB) $(OBJECTS)
+
+clean:
+	rm -Rf $(SHLIB) $(STATLIB) $(OBJECTS) rust/target

r/gtfsort/src/Makevars.ucrt

@@ -0,0 +1,5 @@
+# Rtools42 doesn't have the linker in the location that cargo expects, so we
+# need to overwrite it via configuration.
+CARGO_LINKER = x86_64-w64-mingw32.static.posix-gcc.exe
+
+include Makevars.win

r/gtfsort/src/Makevars.win

@@ -0,0 +1,40 @@
+TARGET = $(subst 64,x86_64,$(subst 32,i686,$(WIN)))-pc-windows-gnu
+
+TARGET_DIR = ./rust/target
+LIBDIR = $(TARGET_DIR)/$(TARGET)/release
+STATLIB = $(LIBDIR)/libgtfsort.a
+PKG_LIBS = -L$(LIBDIR) -lgtfsort -lws2_32 -ladvapi32 -luserenv -lbcrypt -lntdll
+
+all: C_clean
+
+$(SHLIB): $(STATLIB)
+
+CARGOTMP = $(CURDIR)/.cargo
+
+$(STATLIB):
+	mkdir -p $(TARGET_DIR)/libgcc_mock
+	# `rustc` adds `-lgcc_eh` flags to the compiler, but Rtools' GCC doesn't have
+	# `libgcc_eh` due to the compilation settings. So, in order to please the
+	# compiler, we need to add empty `libgcc_eh` to the library search paths.
+	#
+	# For more details, please refer to
+	# https://github.com/r-windows/rtools-packages/blob/2407b23f1e0925bbb20a4162c963600105236318/mingw-w64-gcc/PKGBUILD#L313-L316
+	touch $(TARGET_DIR)/libgcc_mock/libgcc_eh.a
+
+	# CARGO_LINKER is provided in Makevars.ucrt for R >= 4.2
+	if [ "$(NOT_CRAN)" != "true" ]; then \
+		export CARGO_HOME=$(CARGOTMP); \
+	fi && \
+		export CARGO_TARGET_X86_64_PC_WINDOWS_GNU_LINKER="$(CARGO_LINKER)" && \
+		export LIBRARY_PATH="$${LIBRARY_PATH};$(CURDIR)/$(TARGET_DIR)/libgcc_mock" && \
+		cargo build --target=$(TARGET) --lib --release --manifest-path=./rust/Cargo.toml --target-dir $(TARGET_DIR)
+	if [ "$(NOT_CRAN)" != "true" ]; then \
+		rm -Rf $(CARGOTMP) && \
+		rm -Rf $(LIBDIR)/build; \
+	fi
+
+C_clean:
+	rm -Rf $(SHLIB) $(STATLIB) $(OBJECTS)
+
+clean:
+	rm -Rf $(SHLIB) $(STATLIB) $(OBJECTS) $(TARGET_DIR)

r/gtfsort/src/entrypoint.c

@@ -0,0 +1,8 @@
+// We need to forward routine registration from C to Rust
+// to avoid the linker removing the static library.
+
+void R_init_gtfsort_extendr(void *dll);
+
+void R_init_gtfsort(void *dll) {
+    R_init_gtfsort_extendr(dll);
+}

r/gtfsort/src/gtfsort-win.def

@@ -0,0 +1,2 @@
+EXPORTS
+R_init_gtfsort