diff --git a/pkgdown.yml b/pkgdown.yml
index 375c2ce..5839653 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,7 +2,7 @@ pandoc: 3.1.11
pkgdown: 2.1.1
pkgdown_sha: ~
articles: {}
-last_built: 2024-12-29T14:58Z
+last_built: 2024-12-30T13:56Z
urls:
reference: https://rnabioco.github.io/cpp11bigwig/reference
article: https://rnabioco.github.io/cpp11bigwig/articles
diff --git a/reference/cpp11bigwig-package.html b/reference/cpp11bigwig-package.html
index 3cd7027..e1504dc 100644
--- a/reference/cpp11bigwig-package.html
+++ b/reference/cpp11bigwig-package.html
@@ -49,7 +49,7 @@ cpp11bigwig: read data from bigWig files
See also
@@ -60,7 +60,7 @@
diff --git a/search.json b/search.json
index c819850..5410e1a 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"https://rnabioco.github.io/cpp11bigwig/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 cpp11bigwig authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://rnabioco.github.io/cpp11bigwig/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Jay Hesselberth. Author, maintainer. RNA Bioscience Initiative. Funder, copyright holder. Devon Ryan. Copyright holder.","code":""},{"path":"https://rnabioco.github.io/cpp11bigwig/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Hesselberth J (2024). cpp11bigwig: Read bigWig bigBed Files. R package version 0.1.0, https://github.com/rnabioco/cpp11bigwig, https://rnabioco.github.io/cpp11bigwig/.","code":"@Manual{, title = {cpp11bigwig: Read bigWig and bigBed Files}, author = {Jay Hesselberth}, year = {2024}, note = {R package version 0.1.0, https://github.com/rnabioco/cpp11bigwig}, url = {https://rnabioco.github.io/cpp11bigwig/}, }"},{"path":"https://rnabioco.github.io/cpp11bigwig/index.html","id":"cpp11bigwig","dir":"","previous_headings":"","what":"Read bigWig and bigBed Files","title":"Read bigWig and bigBed Files","text":"cpp11bigwig provides read-access bigWig bigBed files using libBigWig https://github.com/dpryan79/libBigWig.","code":""},{"path":"https://rnabioco.github.io/cpp11bigwig/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Read bigWig and bigBed Files","text":"","code":"# Install development version from GitHub # install.packages(\"pak\") pak::pak(\"rnabioco/cpp11bigwig\") library(cpp11bigwig) bw <- system.file(\"extdata\", \"test.bw\", package = \"cpp11bigwig\") read_bigwig(bw) #> # A tibble: 6 × 4 #> chrom start end value #> #> 1 1 0 1 0.100 #> 2 1 1 2 0.200 #> 3 1 2 3 0.300 #> 4 1 100 150 1.40 #> 5 1 150 151 1.5 #> 6 10 200 300 2 bb <- system.file(\"extdata\", \"test.bb\", package = \"cpp11bigwig\") read_bigbed(bb) #> # A tibble: 3 × 12 #> chrom start end name score strand thickStart thickEnd reserved blockCount #> #> 1 chr1 4.80e6 4.80e6 test… 1 + 4797973 4836816 1 9 #> 2 chr10 4.85e6 4.85e6 diff… 1 + 4848118 4880877 1 6 #> 3 chr20 5.07e6 5.07e6 negs… 1 - 5073253 5152630 1 14 #> # ℹ 2 more variables: blockSizes , chromStarts "},{"path":"https://rnabioco.github.io/cpp11bigwig/reference/cpp11bigwig-package.html","id":null,"dir":"Reference","previous_headings":"","what":"cpp11bigwig: read data from bigWig files — cpp11bigwig-package","title":"cpp11bigwig: read data from bigWig files — cpp11bigwig-package","text":"bigwig provides methods read data bigWig files. bigwig uses cpp11 wrap libBigWig @dpryan79.","code":""},{"path":"https://rnabioco.github.io/cpp11bigwig/reference/cpp11bigwig-package.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"cpp11bigwig: read data from bigWig files — cpp11bigwig-package","text":"","code":""},{"path":[]},{"path":"https://rnabioco.github.io/cpp11bigwig/reference/cpp11bigwig-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"cpp11bigwig: read data from bigWig files — cpp11bigwig-package","text":"Jay Hesselberth ","code":""},{"path":"https://rnabioco.github.io/cpp11bigwig/reference/read_bigbed.html","id":null,"dir":"Reference","previous_headings":"","what":"Read data from bigBed files. — read_bigbed","title":"Read data from bigBed files. — read_bigbed","text":"Read data bigBed files.","code":""},{"path":"https://rnabioco.github.io/cpp11bigwig/reference/read_bigbed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read data from bigBed files. — read_bigbed","text":"","code":"read_bigbed(bbfile, chrom = NULL, start = NULL, end = NULL, convert = TRUE)"},{"path":"https://rnabioco.github.io/cpp11bigwig/reference/read_bigbed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read data from bigBed files. — read_bigbed","text":"bbfile filename bigBed file chrom read data specific chromosome start start position data end end position data convert convert bigBed values individual columns","code":""},{"path":"https://rnabioco.github.io/cpp11bigwig/reference/read_bigbed.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read data from bigBed files. — read_bigbed","text":"tibble","code":""},{"path":[]},{"path":"https://rnabioco.github.io/cpp11bigwig/reference/read_bigbed.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read data from bigBed files. — read_bigbed","text":"","code":"bb <- system.file(\"extdata\", \"test.bb\", package = \"cpp11bigwig\") read_bigbed(bb) #> # A tibble: 3 × 12 #> chrom start end name score strand thickStart thickEnd reserved blockCount #> #> 1 chr1 4.80e6 4.80e6 test… 1 + 4797973 4836816 1 9 #> 2 chr10 4.85e6 4.85e6 diff… 1 + 4848118 4880877 1 6 #> 3 chr20 5.07e6 5.07e6 negs… 1 - 5073253 5152630 1 14 #> # ℹ 2 more variables: blockSizes , chromStarts read_bigbed(bb, chrom = \"chr10\") #> # A tibble: 1 × 12 #> chrom start end name score strand thickStart thickEnd reserved blockCount #> #> 1 chr10 4.85e6 4.85e6 diff… 1 + 4848118 4880877 1 6 #> # ℹ 2 more variables: blockSizes , chromStarts "},{"path":"https://rnabioco.github.io/cpp11bigwig/reference/read_bigwig.html","id":null,"dir":"Reference","previous_headings":"","what":"Read data from bigWig files. — read_bigwig","title":"Read data from bigWig files. — read_bigwig","text":"Read data bigWig files.","code":""},{"path":"https://rnabioco.github.io/cpp11bigwig/reference/read_bigwig.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read data from bigWig files. — read_bigwig","text":"","code":"read_bigwig(bwfile, chrom = NULL, start = NULL, end = NULL, as = NULL)"},{"path":"https://rnabioco.github.io/cpp11bigwig/reference/read_bigwig.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read data from bigWig files. — read_bigwig","text":"bwfile filename bigWig file chrom read data specific chromosome start start position data end end position data return data specific type. default tibble (`tbl`) GRanges (`gr`)","code":""},{"path":"https://rnabioco.github.io/cpp11bigwig/reference/read_bigwig.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read data from bigWig files. — read_bigwig","text":"tibble","code":""},{"path":[]},{"path":"https://rnabioco.github.io/cpp11bigwig/reference/read_bigwig.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read data from bigWig files. — read_bigwig","text":"","code":"bw <- system.file(\"extdata\", \"test.bw\", package = \"cpp11bigwig\") read_bigwig(bw) #> # A tibble: 6 × 4 #> chrom start end value #> #> 1 1 0 1 0.100 #> 2 1 1 2 0.200 #> 3 1 2 3 0.300 #> 4 1 100 150 1.40 #> 5 1 150 151 1.5 #> 6 10 200 300 2 read_bigwig(bw, chrom = \"10\") #> # A tibble: 1 × 4 #> chrom start end value #> #> 1 10 200 300 2 read_bigwig(bw, chrom = \"1\", start = 100, end = 130) #> # A tibble: 1 × 4 #> chrom start end value #> #> 1 1 100 130 1.40 read_bigwig(bw, as = \"GRanges\") #> GRanges object with 6 ranges and 1 metadata column: #> seqnames ranges strand | score #> | #> [1] 1 0-1 * | 0.1 #> [2] 1 1-2 * | 0.2 #> [3] 1 2-3 * | 0.3 #> [4] 1 100-150 * | 1.4 #> [5] 1 150-151 * | 1.5 #> [6] 10 200-300 * | 2.0 #> ------- #> seqinfo: 2 sequences from an unspecified genome; no seqlengths"},{"path":"https://rnabioco.github.io/cpp11bigwig/news/index.html","id":"cpp11bigwig-010","dir":"Changelog","previous_headings":"","what":"cpp11bigwig 0.1.0","title":"cpp11bigwig 0.1.0","text":"Initial CRAN submission.","code":""},{"path":"https://rnabioco.github.io/cpp11bigwig/news/index.html","id":"cpp11bigwig-0009000","dir":"Changelog","previous_headings":"","what":"cpp11bigwig 0.0.0.9000","title":"cpp11bigwig 0.0.0.9000","text":"libBigWig mostly untouched excpect removal fprintf statements (R won’t allow linked libraries) fixups ASAN errors, mostly GNU-specific pointer arithmetic. cpp11bigwig passes ASAN valgrind checks (via rhub).","code":""}]
+[{"path":"https://rnabioco.github.io/cpp11bigwig/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 cpp11bigwig authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://rnabioco.github.io/cpp11bigwig/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Jay Hesselberth. Author, maintainer. RNA Bioscience Initiative. Funder, copyright holder. Devon Ryan. Copyright holder.","code":""},{"path":"https://rnabioco.github.io/cpp11bigwig/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Hesselberth J (2024). cpp11bigwig: Read bigWig bigBed Files. R package version 0.1.0, https://github.com/rnabioco/cpp11bigwig, https://rnabioco.github.io/cpp11bigwig/.","code":"@Manual{, title = {cpp11bigwig: Read bigWig and bigBed Files}, author = {Jay Hesselberth}, year = {2024}, note = {R package version 0.1.0, https://github.com/rnabioco/cpp11bigwig}, url = {https://rnabioco.github.io/cpp11bigwig/}, }"},{"path":"https://rnabioco.github.io/cpp11bigwig/index.html","id":"cpp11bigwig","dir":"","previous_headings":"","what":"Read bigWig and bigBed Files","title":"Read bigWig and bigBed Files","text":"cpp11bigwig provides read-access bigWig bigBed files using libBigWig https://github.com/dpryan79/libBigWig.","code":""},{"path":"https://rnabioco.github.io/cpp11bigwig/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Read bigWig and bigBed Files","text":"","code":"# Install development version from GitHub # install.packages(\"pak\") pak::pak(\"rnabioco/cpp11bigwig\") library(cpp11bigwig) bw <- system.file(\"extdata\", \"test.bw\", package = \"cpp11bigwig\") read_bigwig(bw) #> # A tibble: 6 × 4 #> chrom start end value #> #> 1 1 0 1 0.100 #> 2 1 1 2 0.200 #> 3 1 2 3 0.300 #> 4 1 100 150 1.40 #> 5 1 150 151 1.5 #> 6 10 200 300 2 bb <- system.file(\"extdata\", \"test.bb\", package = \"cpp11bigwig\") read_bigbed(bb) #> # A tibble: 3 × 12 #> chrom start end name score strand thickStart thickEnd reserved blockCount #> #> 1 chr1 4.80e6 4.80e6 test… 1 + 4797973 4836816 1 9 #> 2 chr10 4.85e6 4.85e6 diff… 1 + 4848118 4880877 1 6 #> 3 chr20 5.07e6 5.07e6 negs… 1 - 5073253 5152630 1 14 #> # ℹ 2 more variables: blockSizes , chromStarts "},{"path":"https://rnabioco.github.io/cpp11bigwig/reference/cpp11bigwig-package.html","id":null,"dir":"Reference","previous_headings":"","what":"cpp11bigwig: read data from bigWig files — cpp11bigwig-package","title":"cpp11bigwig: read data from bigWig files — cpp11bigwig-package","text":"bigwig provides methods read data bigWig files. bigwig uses cpp11 wrap libBigWig @dpryan79.","code":""},{"path":"https://rnabioco.github.io/cpp11bigwig/reference/cpp11bigwig-package.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"cpp11bigwig: read data from bigWig files — cpp11bigwig-package","text":"https://github.com/dpryan79/libBigWig","code":""},{"path":[]},{"path":"https://rnabioco.github.io/cpp11bigwig/reference/cpp11bigwig-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"cpp11bigwig: read data from bigWig files — cpp11bigwig-package","text":"Jay Hesselberth jay.hesselberth@gmail.com","code":""},{"path":"https://rnabioco.github.io/cpp11bigwig/reference/read_bigbed.html","id":null,"dir":"Reference","previous_headings":"","what":"Read data from bigBed files. — read_bigbed","title":"Read data from bigBed files. — read_bigbed","text":"Read data bigBed files.","code":""},{"path":"https://rnabioco.github.io/cpp11bigwig/reference/read_bigbed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read data from bigBed files. — read_bigbed","text":"","code":"read_bigbed(bbfile, chrom = NULL, start = NULL, end = NULL, convert = TRUE)"},{"path":"https://rnabioco.github.io/cpp11bigwig/reference/read_bigbed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read data from bigBed files. — read_bigbed","text":"bbfile filename bigBed file chrom read data specific chromosome start start position data end end position data convert convert bigBed values individual columns","code":""},{"path":"https://rnabioco.github.io/cpp11bigwig/reference/read_bigbed.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read data from bigBed files. — read_bigbed","text":"tibble","code":""},{"path":[]},{"path":"https://rnabioco.github.io/cpp11bigwig/reference/read_bigbed.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read data from bigBed files. — read_bigbed","text":"","code":"bb <- system.file(\"extdata\", \"test.bb\", package = \"cpp11bigwig\") read_bigbed(bb) #> # A tibble: 3 × 12 #> chrom start end name score strand thickStart thickEnd reserved blockCount #> #> 1 chr1 4.80e6 4.80e6 test… 1 + 4797973 4836816 1 9 #> 2 chr10 4.85e6 4.85e6 diff… 1 + 4848118 4880877 1 6 #> 3 chr20 5.07e6 5.07e6 negs… 1 - 5073253 5152630 1 14 #> # ℹ 2 more variables: blockSizes , chromStarts read_bigbed(bb, chrom = \"chr10\") #> # A tibble: 1 × 12 #> chrom start end name score strand thickStart thickEnd reserved blockCount #> #> 1 chr10 4.85e6 4.85e6 diff… 1 + 4848118 4880877 1 6 #> # ℹ 2 more variables: blockSizes , chromStarts "},{"path":"https://rnabioco.github.io/cpp11bigwig/reference/read_bigwig.html","id":null,"dir":"Reference","previous_headings":"","what":"Read data from bigWig files. — read_bigwig","title":"Read data from bigWig files. — read_bigwig","text":"Read data bigWig files.","code":""},{"path":"https://rnabioco.github.io/cpp11bigwig/reference/read_bigwig.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read data from bigWig files. — read_bigwig","text":"","code":"read_bigwig(bwfile, chrom = NULL, start = NULL, end = NULL, as = NULL)"},{"path":"https://rnabioco.github.io/cpp11bigwig/reference/read_bigwig.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read data from bigWig files. — read_bigwig","text":"bwfile filename bigWig file chrom read data specific chromosome start start position data end end position data return data specific type. default tibble (tbl) GRanges (gr)","code":""},{"path":"https://rnabioco.github.io/cpp11bigwig/reference/read_bigwig.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read data from bigWig files. — read_bigwig","text":"tibble","code":""},{"path":[]},{"path":"https://rnabioco.github.io/cpp11bigwig/reference/read_bigwig.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read data from bigWig files. — read_bigwig","text":"","code":"bw <- system.file(\"extdata\", \"test.bw\", package = \"cpp11bigwig\") read_bigwig(bw) #> # A tibble: 6 × 4 #> chrom start end value #> #> 1 1 0 1 0.100 #> 2 1 1 2 0.200 #> 3 1 2 3 0.300 #> 4 1 100 150 1.40 #> 5 1 150 151 1.5 #> 6 10 200 300 2 read_bigwig(bw, chrom = \"10\") #> # A tibble: 1 × 4 #> chrom start end value #> #> 1 10 200 300 2 read_bigwig(bw, chrom = \"1\", start = 100, end = 130) #> # A tibble: 1 × 4 #> chrom start end value #> #> 1 1 100 130 1.40 read_bigwig(bw, as = \"GRanges\") #> GRanges object with 6 ranges and 1 metadata column: #> seqnames ranges strand | score #> | #> [1] 1 0-1 * | 0.1 #> [2] 1 1-2 * | 0.2 #> [3] 1 2-3 * | 0.3 #> [4] 1 100-150 * | 1.4 #> [5] 1 150-151 * | 1.5 #> [6] 10 200-300 * | 2.0 #> ------- #> seqinfo: 2 sequences from an unspecified genome; no seqlengths"},{"path":"https://rnabioco.github.io/cpp11bigwig/news/index.html","id":"cpp11bigwig-010","dir":"Changelog","previous_headings":"","what":"cpp11bigwig 0.1.0","title":"cpp11bigwig 0.1.0","text":"Initial CRAN submission.","code":""},{"path":"https://rnabioco.github.io/cpp11bigwig/news/index.html","id":"cpp11bigwig-0009000","dir":"Changelog","previous_headings":"","what":"cpp11bigwig 0.0.0.9000","title":"cpp11bigwig 0.0.0.9000","text":"libBigWig mostly untouched excpect removal fprintf statements (R won’t allow linked libraries) fixups ASAN errors, mostly GNU-specific pointer arithmetic. cpp11bigwig passes ASAN valgrind checks (via rhub).","code":""}]