├── .Rbuildignore ├── .clang-format ├── .github ├── .gitignore ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── ISSUE_TEMPLATE.md └── workflows │ ├── check-standard.yaml │ ├── clang-format.yaml │ ├── format-suggest.yaml │ ├── pkgdown.yaml │ ├── pr-commands.yaml │ ├── rhub.yaml │ └── test-coverage.yaml ├── .gitignore ├── .vscode ├── extensions.json └── settings.json ├── CLAUDE.md ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── bed12_to_exons.r ├── bed_absdist.r ├── bed_closest.r ├── bed_cluster.r ├── bed_complement.r ├── bed_coverage.r ├── bed_fisher.r ├── bed_flank.r ├── bed_genomecov.r ├── bed_glyph.r ├── bed_intersect.r ├── bed_jaccard.r ├── bed_makewindows.r ├── bed_map.r ├── bed_merge.r ├── bed_partition.r ├── bed_projection.r ├── bed_random.r ├── bed_reldist.r ├── bed_shift.r ├── bed_shuffle.r ├── bed_slop.r ├── bed_sort.r ├── bed_subtract.r ├── bed_window.r ├── cpp11.R ├── db.r ├── features.r ├── import-standalone-obj-type.R ├── import-standalone-types-check.R ├── read_bed.r ├── read_genome.r ├── read_vcf.r ├── reexport-cpp11bigwig.r ├── reexport-tibble.r ├── spacing.r ├── strands.r ├── tbls.r ├── utils-external.r ├── utils.r └── valr-package.r ├── README.Rmd ├── README.md ├── air.toml ├── bench ├── benchmarks.Rmd └── quick_bench.R ├── codecov.yml ├── cran-comments.md ├── inst ├── CITATION ├── example │ └── bed_map.r ├── extdata │ ├── 12fields.bed.gz │ ├── 3fields.bed.gz │ ├── 6fields.bed.gz │ ├── bug254_e.bed │ ├── genes.hg19.chr22.bed.gz │ ├── genome.txt.gz │ ├── hela.h3k4.chip.bg.gz │ ├── hg19.chrom.sizes.gz │ ├── hg19.dnase1.bw │ ├── hg19.gencode.gtf.gz │ ├── hg19.refGene.chr22.bed.gz │ ├── hg19.rmsk.chr22.bed.gz │ ├── hg19.snps147.chr22.bed.gz │ ├── mm9.refGene.bed.gz │ ├── sample.broadPeak.gz │ ├── sample.narrowPeak.gz │ ├── test.bb │ ├── test.bg.gz │ └── test.vcf.gz └── include │ ├── valr.h │ └── valr │ ├── dataframe.hpp │ ├── genome.hpp │ ├── intervals.hpp │ └── random.hpp ├── man-roxygen ├── groups.R ├── min_overlap.R └── stats.R ├── man ├── bed12_to_exons.Rd ├── bed_absdist.Rd ├── bed_closest.Rd ├── bed_cluster.Rd ├── bed_complement.Rd ├── bed_coverage.Rd ├── bed_fisher.Rd ├── bed_flank.Rd ├── bed_genomecov.Rd ├── bed_glyph.Rd ├── bed_intersect.Rd ├── bed_jaccard.Rd ├── bed_makewindows.Rd ├── bed_map.Rd ├── bed_merge.Rd ├── bed_partition.Rd ├── bed_projection.Rd ├── bed_random.Rd ├── bed_reldist.Rd ├── bed_shift.Rd ├── bed_shuffle.Rd ├── bed_slop.Rd ├── bed_sort.Rd ├── bed_subtract.Rd ├── bed_window.Rd ├── bound_intervals.Rd ├── create_introns.Rd ├── create_tss.Rd ├── create_utrs3.Rd ├── create_utrs5.Rd ├── db.Rd ├── figures │ ├── README-intersect_glyph-1.png │ ├── lifecycle-deprecated.svg │ ├── lifecycle-experimental.svg │ ├── lifecycle-stable.svg │ ├── lifecycle-superseded.svg │ └── logo.png ├── flip_strands.Rd ├── gr_to_bed.Rd ├── id.Rd ├── id_var.Rd ├── interval_spacing.Rd ├── ivl_df.Rd ├── read_bed.Rd ├── read_genome.Rd ├── read_gtf.Rd ├── read_vcf.Rd ├── reexports.Rd ├── valr-package.Rd ├── valr.Rd └── valr_example.Rd ├── pkgdown ├── _pkgdown.yml └── favicon │ ├── apple-touch-icon-120x120.png │ ├── apple-touch-icon-60x60.png │ ├── apple-touch-icon-76x76.png │ ├── apple-touch-icon.png │ ├── favicon-16x16.png │ ├── favicon-32x32.png │ └── favicon.ico ├── revdep ├── .gitignore ├── README.md ├── cran.md ├── failures.md └── problems.md ├── src ├── .gitignore ├── Makevars ├── Makevars.win ├── bed12toexons.cpp ├── closest.cpp ├── complement.cpp ├── coverage.cpp ├── cpp11.cpp ├── dist.cpp ├── flank.cpp ├── gcoverage.cpp ├── intersect.cpp ├── makewindows.cpp ├── merge.cpp ├── partition.cpp ├── random.cpp ├── shuffle.cpp └── subtract.cpp ├── tests ├── testthat.R └── testthat │ ├── _snaps │ ├── bed12_to_exons.md │ ├── genome.md │ ├── glyph.md │ ├── glyph │ │ ├── intersect-glyph-is-ok.svg │ │ └── merge-glyph-is-ok.svg │ ├── intersect.md │ ├── makewindows.md │ ├── merge.md │ ├── random.md │ ├── read_bed.md │ ├── shuffle.md │ ├── strands.md │ └── types.md │ ├── helper-astyle.r │ ├── helper-vdiffr.R │ ├── test-db.r │ ├── test_absdist.r │ ├── test_bed12_to_exons.r │ ├── test_closest.r │ ├── test_cluster.r │ ├── test_complement.r │ ├── test_coverage.r │ ├── test_features.r │ ├── test_fisher.r │ ├── test_flank.r │ ├── test_genome.r │ ├── test_genomecov.R │ ├── test_glyph.r │ ├── test_groups.r │ ├── test_intersect.r │ ├── test_jaccard.r │ ├── test_makewindows.r │ ├── test_map.r │ ├── test_merge.r │ ├── test_partition.r │ ├── test_projection.r │ ├── test_random.r │ ├── test_read_bed.r │ ├── test_read_vcf.r │ ├── test_reldist.r │ ├── test_shift.r │ ├── test_shuffle.r │ ├── test_slop.r │ ├── test_sort.r │ ├── test_spacing.r │ ├── test_strands.r │ ├── test_stress.r │ ├── test_subtract.r │ ├── test_tbls.r │ ├── test_types.R │ ├── test_utils.r │ └── test_window.r └── vignettes ├── .gitignore ├── interval-stats.Rmd └── valr.Rmd /.Rbuildignore: -------------------------------------------------------------------------------- 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