Checks, fixes, tests

.Rbuildignore

@@ -4,3 +4,5 @@
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+^LICENSE\.md$
+^README\.Rmd$

DESCRIPTION

@@ -1,11 +1,11 @@
 Type: Package
 Package: cpp11bigwig
-Title: Read bigWig Files.
+Title: Read-only access to bigWig Files
 Version: 0.1.0
 Authors@R: 
     person("Jay", "Hesselberth", , "jay.hesselberth@gmail.com", role = c("aut", "cre"))
 Description: cpp11bigwig wraps libBigWig by @dpryan79.
-License: MIT
+License: MIT + file LICENSE
 URL: https://rnabioco.github.io/cpp11bigwig/,
     https://github.com/rnabioco/cpp11bigwig
 Suggests: 

LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2024
+COPYRIGHT HOLDER: cpp11bigwig authors

LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2024 cpp11bigwig authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

R/cpp11.R

@@ -1,5 +1,5 @@
 # Generated by cpp11: do not edit by hand
 
-read_bigwig_impl <- function(bwfname, chrom, start, end) {
-  .Call(`_cpp11bigwig_read_bigwig_impl`, bwfname, chrom, start, end)
+read_bigwig_cpp <- function(bwfname, chrom, start, end, raw) {
+  .Call(`_cpp11bigwig_read_bigwig_cpp`, bwfname, chrom, start, end, raw)
 }

R/read_bigwig.r

@@ -4,6 +4,7 @@
 #' @param chrom read data for specific chromosome
 #' @param start start position for data
 #' @param end end position for data
+#' @param raw return raw data, single-base intervals
 #'
 #' @return \code{data.frame}
 #'
@@ -15,15 +16,15 @@
 #' read_bigwig(bw)
 #'
 #' @export
-read_bigwig <- function(bwfile, chrom = "", start = -1, end = -1) {
+read_bigwig <- function(bwfile, chrom = NULL, start = NULL, end = NULL, raw = FALSE) {
 
   if (!file.exists(bwfile)) {
     stop("File does not exist: ", bwfile)
   }
 
-  # if ((!is.null(start) && start < 0) || (!is.null(end) && end < 0)) {
-  #   stop("`start` and `end` must both be >= 0")
-  # }
+  if ((!is.null(start) && start < 0) || (!is.null(end) && end < 0)) {
+    stop("`start` and `end` must both be >= 0")
+  }
 
-  read_bigwig_impl(bwfile, chrom, start, end)
+  read_bigwig_cpp(bwfile, chrom, start, end, raw)
 }

src/cpp11.cpp

@@ -6,16 +6,16 @@
 #include <R_ext/Visibility.h>
 
 // cpp11bigwig.cpp
-writable::data_frame read_bigwig_impl(std::string bwfname, std::string chrom, int start, int end);
-extern "C" SEXP _cpp11bigwig_read_bigwig_impl(SEXP bwfname, SEXP chrom, SEXP start, SEXP end) {
+writable::data_frame read_bigwig_cpp(std::string bwfname, sexp chrom, sexp start, sexp end, sexp raw);
+extern "C" SEXP _cpp11bigwig_read_bigwig_cpp(SEXP bwfname, SEXP chrom, SEXP start, SEXP end, SEXP raw) {
   BEGIN_CPP11
-    return cpp11::as_sexp(read_bigwig_impl(cpp11::as_cpp<cpp11::decay_t<std::string>>(bwfname), cpp11::as_cpp<cpp11::decay_t<std::string>>(chrom), cpp11::as_cpp<cpp11::decay_t<int>>(start), cpp11::as_cpp<cpp11::decay_t<int>>(end)));
+    return cpp11::as_sexp(read_bigwig_cpp(cpp11::as_cpp<cpp11::decay_t<std::string>>(bwfname), cpp11::as_cpp<cpp11::decay_t<sexp>>(chrom), cpp11::as_cpp<cpp11::decay_t<sexp>>(start), cpp11::as_cpp<cpp11::decay_t<sexp>>(end), cpp11::as_cpp<cpp11::decay_t<sexp>>(raw)));
   END_CPP11
 }
 
 extern "C" {
 static const R_CallMethodDef CallEntries[] = {
-    {"_cpp11bigwig_read_bigwig_impl", (DL_FUNC) &_cpp11bigwig_read_bigwig_impl, 4},
+    {"_cpp11bigwig_read_bigwig_cpp", (DL_FUNC) &_cpp11bigwig_read_bigwig_cpp, 5},
     {NULL, NULL, 0}
 };
 }

src/cpp11bigwig.cpp

@@ -1,11 +1,12 @@
 #include <cpp11.hpp>
 #include <cpp11/data_frame.hpp>
+
 using namespace cpp11;
 
 #include "bigWig.h"
 
 [[cpp11::register]]
-writable::data_frame read_bigwig_impl(std::string bwfname, std::string chrom, int start, int end) {
+writable::data_frame read_bigwig_cpp(std::string bwfname, sexp chrom, sexp start, sexp end, sexp raw) {
 
   //http://stackoverflow.com/questions/347949/how-to-convert-a-stdstring-to-const-char-or-char
   std::vector<char> bwfile(bwfname.begin(), bwfname.end()) ;
@@ -14,11 +15,12 @@ writable::data_frame read_bigwig_impl(std::string bwfname, std::string chrom, in
   const char mode = 'r' ;
 
   bigWigFile_t *bwf = NULL;
-  // XXX change NULL to a CURL callback. see libBigWig demos
+
+  // NULL can be a CURL callback. see libBigWig demos
   bwf = bwOpen(&bwfile[0], NULL, &mode) ;
 
   if (!bwf)
-    stop("Failed to open file: %s\n", bwfname.c_str()) ;
+    stop("Failed to open file: '%s'\n", bwfname.c_str()) ;
 
   std::vector<std::string> chroms ;
   std::vector<int> starts ;
@@ -30,19 +32,22 @@ writable::data_frame read_bigwig_impl(std::string bwfname, std::string chrom, in
   int nchrom = bwf->cl->nKeys ;
   for (int nc = 0; nc<nchrom; ++nc) {
 
-    char* cur_chrom = bwf->cl->chrom[nc] ;
-    std::string cur_chrom_c = cur_chrom ;
+    char* bw_chrom = bwf->cl->chrom[nc] ;
+    std::string bw_chrom_c(bw_chrom) ;
 
-    if (!chrom.empty() && chrom != cur_chrom_c) continue ;
+    if (!Rf_isNull(chrom)) {
+      std::string r_chrom = as_cpp<std::string>(chrom) ;
+      if (r_chrom != bw_chrom_c) continue ;
+    }
 
     // set maximum boundaries if start / end are not specified
-    if (start == -1) start = 0 ;
-    if (end == -1) end = bwf->cl->len[nc];
+    int bw_start = Rf_isNull(start) ? 0 : as_cpp<int>(start) ;
+    int bw_end = Rf_isNull(end) ? bwf->cl->len[nc] : as_cpp<int>(end) ;
 
-    intervals = bwGetValues(bwf, cur_chrom, start, end, 0) ;
+    intervals = bwGetValues(bwf, bw_chrom, bw_start, bw_end, 0) ;
 
     if (!intervals)
-      stop("Failed to retreived intervals for %s\n", chrom.c_str()) ;
+      stop("Failed to retreived intervals for %s\n", bw_chrom) ;
 
     int nint = intervals->l ;
     for(int i=0; i<nint; ++i) {
@@ -56,17 +61,20 @@ writable::data_frame read_bigwig_impl(std::string bwfname, std::string chrom, in
       ends.push_back(end) ;
       vals.push_back(val) ;
 
-      chroms.push_back(cur_chrom_c) ;
+      chroms.push_back(bw_chrom_c) ;
     }
 
     bwDestroyOverlappingIntervals(intervals) ;
   }
 
+  bwClose(bwf) ;
+  bwCleanup() ;
+
   return writable::data_frame({
-    "chrom"_nm = chroms,
-    "start"_nm = starts,
-    "end"_nm = ends,
-    "value"_nm = vals
-  }) ;
+      "chrom"_nm = chroms,
+      "start"_nm = starts,
+      "end"_nm = ends,
+      "value"_nm = vals
+    }) ;
 
 }

tests/testthat/_snaps/read.md

@@ -0,0 +1,16 @@
+# results have expected shape
+
+    Expected string vector of length 1
+
+# missing file causes error
+
+    File does not exist: missing.bw
+
+# negative coords causes error
+
+    `start` and `end` must both be >= 0
+
+---
+
+    `start` and `end` must both be >= 0
+

tests/testthat/test-read.R

@@ -1,15 +1,41 @@
 
-test_that("output have expected shape", {
-  out <- read_bigwig(test_path("data/test.bw"))
-  expect_equal(ncol(out), 4)
-  expect_equal(nrow(out), 154)
+test_that("results have expected shape", {
+  # -- raw output -------
+  bw <- test_path("data/test.bw")
+
+  res <- read_bigwig(bw)
+  expect_equal(ncol(res), 4)
+  expect_equal(nrow(res), 154)
+
+  # chrom
+  expect_equal(nrow(read_bigwig(bw, chrom = "1")), 54)
+  expect_equal(nrow(read_bigwig(bw, chrom = "10")), 100)
+
+  # `chrom` must be a string
+  expect_snapshot_error(read_bigwig(bw, chrom = 10))
+
+  # 0 rows, chrom doesn't exist
+  expect_equal(nrow(read_bigwig(bw, chrom = "100")), 0)
+
+  # start/end
+  expect_equal(nrow(read_bigwig(bw, chrom = "1", start = 1, end = 100)), 2)
+  expect_equal(nrow(read_bigwig(bw, chrom = "1", start = 100, end = 100)), 0)
+  expect_equal(nrow(read_bigwig(bw, chrom = "10", start = 100, end = 1000)), 100)
+  expect_equal(nrow(read_bigwig(bw, chrom = "10", start = 200, end = 250)), 50)
+
+  # values
+  res <- read_bigwig(bw, chrom = "10", start = 100, end = 1000)
+  expect_equal(length(unique(res$value)), 1)
+  expect_equal(unique(res$value), 2)
+
+  # -- bedgraph output -----
 })
 
 test_that("missing file causes error", {
-  expect_error(read_bigwig("missing.bw"))
+  expect_snapshot_error(read_bigwig("missing.bw"))
 })
 
 test_that("negative coords causes error", {
-  expect_error(read_bigwig(test_path("data/test.bw"), start = -1))
-  expect_error(read_bigwig(test_path("data/test.bw"), end = -1))
+  expect_snapshot_error(read_bigwig(test_path("data/test.bw"), start = -1))
+  expect_snapshot_error(read_bigwig(test_path("data/test.bw"), end = -1))
 })