| be10183 | Jay Hesselberth | 04 June 2018, 19:21:06 UTC | Update site [ci skip] | 04 June 2018, 19:21:06 UTC |
| 102a0d5 | Jay Hesselberth | 17 May 2018, 10:57:35 UTC | add curl to Suggests to address CRAN email | 17 May 2018, 10:57:35 UTC |
| 6349159 | kriemo | 11 May 2018, 21:44:19 UTC | add new function `bed_partition()` with cpp implementation (#336) * add new function `bed_partition()` with cpp implementation - collapses intervals into elemental intervals - calculates summaries over elemental intervals - add function to benchmarks and fix typo - add NEWS item, tests, and documentation * remove url, add partition to pkgdown, and fix typo * build site | 11 May 2018, 21:44:19 UTC |
| 163d0b5 | Jay Hesselberth | 26 April 2018, 15:23:50 UTC | update site [ci skip] | 26 April 2018, 15:23:50 UTC |
| f2c6a8f | Jay Hesselberth | 22 April 2018, 20:53:13 UTC | update site. | 22 April 2018, 20:53:13 UTC |
| 39a257a | Jay Hesselberth | 13 April 2018, 16:59:21 UTC | update docsearch config [skip ci] | 13 April 2018, 16:59:21 UTC |
| 5bfadff | Jay Hesselberth | 09 April 2018, 23:28:08 UTC | update site. | 09 April 2018, 23:28:08 UTC |
| 68e3fae | Jay Hesselberth | 04 April 2018, 15:26:00 UTC | simplify readme to improve search results | 04 April 2018, 15:26:00 UTC |
| 998755d | Jay Hesselberth | 04 April 2018, 03:02:58 UTC | update site - use custom docsearch index for debugging | 04 April 2018, 03:02:58 UTC |
| 9b2d5fa | Jay Hesselberth | 03 April 2018, 00:25:47 UTC | update site. | 03 April 2018, 00:25:47 UTC |
| cb30e6d | Jay Hesselberth | 29 March 2018, 22:50:00 UTC | update site - with new templates | 29 March 2018, 22:50:00 UTC |
| 3f647c2 | Jay Hesselberth | 27 March 2018, 22:44:49 UTC | update site - add CNAME | 27 March 2018, 22:44:49 UTC |
| 1c5016e | Jay Hesselberth | 27 March 2018, 02:25:40 UTC | update site | 27 March 2018, 02:25:40 UTC |
| a2a8c6e | Jay Hesselberth | 25 March 2018, 19:26:10 UTC | fix img res issue | 25 March 2018, 19:26:10 UTC |
| d0d811a | Jay Hesselberth | 25 March 2018, 16:31:32 UTC | add GenomicRanges comparison to vignette - news - update site - part of #292, closes #334 | 25 March 2018, 16:31:32 UTC |
| 859eb26 | Jay Hesselberth | 25 March 2018, 16:10:16 UTC | add docs for GenomicRanges part of #334 | 25 March 2018, 16:10:16 UTC |
| e55ffbc | Jay Hesselberth | 24 March 2018, 11:45:42 UTC | use docsearch-provided index | 24 March 2018, 11:45:42 UTC |
| 928e056 | Jay Hesselberth | 24 March 2018, 00:11:07 UTC | update docsearch index | 24 March 2018, 00:11:07 UTC |
| d2026f9 | Jay Hesselberth | 23 March 2018, 23:47:32 UTC | add docsearch | 23 March 2018, 23:47:32 UTC |
| f46ed46 | Jay Hesselberth | 21 March 2018, 11:48:49 UTC | update site | 21 March 2018, 11:48:49 UTC |
| 7075e2b | Jay Hesselberth | 02 March 2018, 13:20:58 UTC | ignore license.md | 02 March 2018, 13:20:58 UTC |
| a5b040d | Jay Hesselberth | 02 March 2018, 13:15:36 UTC | update license and news | 02 March 2018, 13:19:48 UTC |
| 1a8d4e6 | Jay Hesselberth | 26 February 2018, 23:39:01 UTC | update site | 26 February 2018, 23:39:01 UTC |
| 43bd72c | Jay Hesselberth | 26 January 2018, 13:14:26 UTC | astyle | 26 January 2018, 13:14:26 UTC |
| 64eba6d | Jay Hesselberth | 26 January 2018, 02:11:49 UTC | use dev version | 26 January 2018, 02:11:49 UTC |
| 71af298 | Jay Hesselberth | 25 January 2018, 20:01:15 UTC | ignore netlify [skip ci] | 25 January 2018, 20:22:59 UTC |
| e536c06 | Jay Hesselberth | 25 January 2018, 18:58:05 UTC | bump version. | 25 January 2018, 18:58:05 UTC |
| c34472c | Jay Hesselberth | 25 January 2018, 18:47:19 UTC | prepare for release. (#332) | 25 January 2018, 18:47:19 UTC |
| 33970e6 | Ray | 25 January 2018, 18:44:27 UTC | fixes tests warnings for CRAN submission (#331) | 25 January 2018, 18:44:27 UTC |
| f75e68b | Jay Hesselberth | 25 January 2018, 13:13:12 UTC | update news. | 25 January 2018, 13:13:12 UTC |
| f76c9fa | Jay Hesselberth | 25 January 2018, 13:12:58 UTC | run styler | 25 January 2018, 13:12:58 UTC |
| 41a0e32 | Jay Hesselberth | 25 January 2018, 03:33:05 UTC | update site. | 25 January 2018, 03:33:05 UTC |
| 2586328 | Jay Hesselberth | 25 January 2018, 03:12:28 UTC | use new intersect_impl to speed-up bed_map. (#304) * use new intersect_impl to speed-up bed_map. - testing shows a speed-up of about 1 second (2680 ms before, 1680 ms current). - need to update tests * ignore profiling results * move examples to separate file * cleanup bed_map - 1 failing test. corner case where an x interval intersects 1 interval and book-ends another. The x interval is duplicated in the result. * comment * fix behavior for handling bookended intervals by tracking an interval integer id. Update tests to check for non-suffixed output colnames. * use contains() to drop passed column variable | 25 January 2018, 03:12:28 UTC |
| a23eca8 | kriemo | 25 January 2018, 02:30:32 UTC | handle generation of windows for num_win arg separately, avoids reporting more than num_win windows (#329) | 25 January 2018, 02:30:32 UTC |
| 0426c11 | Ray | 25 January 2018, 02:09:23 UTC | incorporated bedtools tests to check output parity (#328) fixed #319, fixes #320, fixes #321, fixes #323, fixes #324 | 25 January 2018, 02:09:23 UTC |
| 8f23a35 | kriemo | 24 January 2018, 18:11:34 UTC | closest behavior on book-ended intervals (#327) - closes #311 | 24 January 2018, 18:11:34 UTC |
| 2e15063 | kriemo | 24 January 2018, 16:56:36 UTC | bed_glyph: allow named x and y args (#326) - closes #318 | 24 January 2018, 16:56:36 UTC |
| d87d8f3 | kriemo | 21 January 2018, 17:51:39 UTC | require that the number of requested intervals is returned from makewindows - closes #322 | 21 January 2018, 17:51:39 UTC |
| cf5587c | kriemo | 13 January 2018, 02:08:48 UTC | bed_subtract() reports overlapping intervals in larger datasets (#316) * sort findOverlaps output prior to modifying start and end coordinates * test if all intervals are dropped * add news item | 13 January 2018, 02:08:48 UTC |
| ccaa823 | kriemo | 12 January 2018, 19:35:51 UTC | issue310 and travis/appveyor fixes (#317) * avoid rename() due to bug in dplyr v.7.4 on cran * set check_force_suggests to false https://github.com/krlmlr/r-appveyor/issues/72 * try explicity installing devtools to avoid using devtools binary https://github.com/travis-ci/travis-ci/issues/8887 | 12 January 2018, 19:35:51 UTC |
| 02ac966 | kriemo | 17 December 2017, 20:01:21 UTC | issue312: prevent infinite loop and drop intervals shorter than num_win (#313) * add warnings to make_windows - warn and skip interval if num_win is greater than interval size - deprecate genome argument to bed - add test for warning and skipped intervals - remove genome argument from examples and vignettes * update docs and fix genome warning argument parsing * handle win_size passed as positional argument * update warning message, test, and add news | 17 December 2017, 20:01:21 UTC |
| 08138a6 | Jay Hesselberth | 09 December 2017, 21:48:01 UTC | ignore netlify | 09 December 2017, 21:48:01 UTC |
| af18b3d | Jay Hesselberth | 16 November 2017, 12:55:33 UTC | add github links to news [skip ci] | 16 November 2017, 12:55:33 UTC |
| 335be49 | Jay Hesselberth | 12 November 2017, 00:52:40 UTC | make interval_spacing behave more like bedtools - don't merge intervals - port test form bedtools | 12 November 2017, 00:52:40 UTC |
| 9e59610 | Jay Hesselberth | 01 November 2017, 11:38:04 UTC | add orcid | 01 November 2017, 11:38:04 UTC |
| dfedefd | Jay Hesselberth | 26 October 2017, 12:18:36 UTC | use https to suppress js warnings | 26 October 2017, 12:18:36 UTC |
| 81500af | Jay Hesselberth | 21 October 2017, 13:45:25 UTC | add search to docs [ci skip] | 21 October 2017, 13:45:25 UTC |
| d90b7d9 | Jay Hesselberth | 19 October 2017, 15:12:42 UTC | add GA tracking info | 19 October 2017, 15:12:42 UTC |
| a4f4284 | Jay Hesselberth | 19 October 2017, 15:03:54 UTC | fix scrolling | 19 October 2017, 15:03:54 UTC |
| d5e24e4 | Jay Hesselberth | 15 October 2017, 18:55:34 UTC | add lab link | 15 October 2017, 18:55:34 UTC |
| caf6a7d | Jay Hesselberth | 14 October 2017, 14:37:30 UTC | add ORCID ID | 14 October 2017, 14:37:30 UTC |
| 22b9e41 | Jay Hesselberth | 08 September 2017, 11:23:56 UTC | add unmatched x intervals to intersect when invert = TRUE (#305) * add unmatched x intervals to intersect when invert = TRUE - add test * fast finish on travis - uptime on their osx builds is not good | 08 September 2017, 11:23:56 UTC |
| cea988c | Jay Hesselberth | 06 September 2017, 19:48:11 UTC | update bed_substract to use new intersect_impl | 06 September 2017, 19:48:11 UTC |
| c5f7a32 | Jay Hesselberth | 06 September 2017, 17:52:32 UTC | return non-intersecting from intersect_impl (#303) * return non-intersecting from intersect_impl - update bed_intersect to remove join-based approach * styler * news [skip ci] | 06 September 2017, 17:52:32 UTC |
| 92a538f | Jay Hesselberth | 06 September 2017, 15:23:38 UTC | run styler (#302) | 06 September 2017, 15:23:38 UTC |
| 34e78d7 | Jay Hesselberth | 22 August 2017, 21:46:04 UTC | Merge branch 'master' of github.com:rnabioco/valr | 22 August 2017, 21:46:04 UTC |
| b33a501 | Jay Hesselberth | 22 August 2017, 21:45:55 UTC | re-pkg [ci skip] | 22 August 2017, 21:45:55 UTC |
| d20ec2a | kriemo | 09 August 2017, 22:39:31 UTC | bed_cluster: reorder ids in R to match chromosome ordering (#299) * reorder ids on the R side to match chromosome ordering * change test to behavior expected with input sorted by chrom, start and end | 09 August 2017, 22:39:31 UTC |
| 42825ec | Jay Hesselberth | 08 August 2017, 14:24:57 UTC | clean up args to random_impl | 08 August 2017, 14:24:57 UTC |
| 51c61da | Jay Hesselberth | 07 August 2017, 04:51:36 UTC | ensure start ties in bed_sort are sorted by end. | 07 August 2017, 04:51:36 UTC |
| 48394b9 | Jay Hesselberth | 06 August 2017, 02:50:49 UTC | Update dplyr headers to v0.7 (#296) * migrate to dplyr v0.7 headers - copy complete set of headers from v0.7.2 - delay inclusion of GroupedDataFrame to fix missing build_index_cpp (modified dplyr_types.h; see unmerged dplyr/#2687) - updated to GroupedSlicingIndex and .names() form - use SymbolVector - use GroupedSlicingIndex and .names() - inline copied util functions. - add NEWS bullet | 06 August 2017, 02:50:49 UTC |
| eec7de0 | Jay Hesselberth | 04 August 2017, 03:43:11 UTC | test cluster output | 04 August 2017, 03:43:11 UTC |
| 55404a0 | Jay Hesselberth | 29 July 2017, 19:23:40 UTC | update jaccard docs. | 29 July 2017, 19:23:40 UTC |
| 13114b4 | Jay Hesselberth | 23 July 2017, 21:03:31 UTC | calculate jaccard for grouped inputs (#293) * calculate jaccard for grouped inputs - fixes #216, closes #260 * qualify group_by in example and update globals | 23 July 2017, 21:03:31 UTC |
| e4d1419 | Jay Hesselberth | 23 July 2017, 14:25:01 UTC | update site [ci skip] | 23 July 2017, 14:25:01 UTC |
| 79009d1 | Jay Hesselberth | 22 July 2017, 14:33:36 UTC | return tbl_intervals | 22 July 2017, 14:33:36 UTC |
| f6145b5 | Jay Hesselberth | 22 July 2017, 04:22:11 UTC | bump version | 22 July 2017, 04:22:11 UTC |
| ffcc13c | Jay Hesselberth | 22 July 2017, 02:21:33 UTC | prepare cran submission | 22 July 2017, 02:21:33 UTC |
| f6fd93d | Jay Hesselberth | 22 July 2017, 00:17:59 UTC | move README figure to man/figures - update Rbuildignore | 22 July 2017, 00:17:59 UTC |
| 3378585 | Jay Hesselberth | 21 July 2017, 22:53:41 UTC | update travis config | 21 July 2017, 22:53:41 UTC |
| c5a8c99 | kriemo | 21 July 2017, 18:04:54 UTC | WIP: simplifying returning DataFrames from Rcpp Issue192 (#283) * implement DataFrameBuilder class to simplify returning cpp objects * clean up src function outputs * overload .add_df member function to store df without suffixes * run astyle * rename writer.h to DataFrameBuilder.h - update source code registration to match latest Rcpp version registration - remove unused variable in merge_impl | 21 July 2017, 18:04:54 UTC |
| 2f6c8c0 | Jay Hesselberth | 21 July 2017, 17:51:40 UTC | fix appveyor failure config | 21 July 2017, 17:51:40 UTC |
| 286f1ee | Jay Hesselberth | 21 July 2017, 17:42:56 UTC | allow appveyor devel to fail - bioconductor is not yet available for 3.5.0 | 21 July 2017, 17:42:56 UTC |
| 126ca88 | Jay Hesselberth | 21 July 2017, 17:08:16 UTC | new as.tbl_interval and as.tbl_genome S3 generics (#291) - closes #224 | 21 July 2017, 17:08:16 UTC |
| 5df1cd5 | Jay Hesselberth | 20 July 2017, 14:34:11 UTC | skip vignette for CHECK/BUILD | 20 July 2017, 14:34:11 UTC |
| 917cdde | Jay Hesselberth | 20 July 2017, 14:33:50 UTC | cleanup examples | 20 July 2017, 14:33:50 UTC |
| d391aca | Jay Hesselberth | 18 July 2017, 11:52:06 UTC | return tibble from bed_sort | 18 July 2017, 11:52:06 UTC |
| f52b7fd | Jay Hesselberth | 18 July 2017, 03:29:31 UTC | De-deprecate bed_sort (#290) * de-deprecate bed_sort() - to be able to use throughout library instead of numerous calls to arrange. * use bed_sort instead of arrange calls | 18 July 2017, 03:29:31 UTC |
| d3b1893 | Jay Hesselberth | 16 July 2017, 17:50:42 UTC | add dbplyr to Suggests - fixes #241 | 16 July 2017, 17:50:42 UTC |
| 7bcbb1b | Jay Hesselberth | 16 July 2017, 17:45:28 UTC | report start/end cols when spec is provided to bed_merge() (#289) - fixes #288 | 16 July 2017, 17:45:28 UTC |
| f8947c8 | Jay Hesselberth | 16 July 2017, 14:22:22 UTC | update vignettes | 16 July 2017, 14:22:22 UTC |
| 43e5a22 | Jay Hesselberth | 16 July 2017, 12:01:14 UTC | update rcpp | 16 July 2017, 12:01:14 UTC |
| a0e9c78 | Jay Hesselberth | 15 July 2017, 22:00:52 UTC | link tbl_interval in docs | 15 July 2017, 22:00:52 UTC |
| ed6dc24 | Jay Hesselberth | 15 July 2017, 21:34:26 UTC | add bound_intervals to utilities | 15 July 2017, 21:34:26 UTC |
| e2b4fa3 | Jay Hesselberth | 15 July 2017, 16:00:17 UTC | thorough doc update. | 15 July 2017, 16:00:17 UTC |
| 782f976 | Jay Hesselberth | 14 July 2017, 12:38:16 UTC | more complex examples for ivl stats - closes #286 | 14 July 2017, 12:38:16 UTC |
| eee5fbe | Jay Hesselberth | 01 July 2017, 14:13:33 UTC | benchmark vignette (#284) - render benchmark and interval stat vignettes for site but ignore for R CMD BUILD/CHECK - improve display of plots / tables in interval stats vignette - closes #284, closes #279, closes #259, closes #239 | 01 July 2017, 14:13:33 UTC |
| 6887c6c | Jay Hesselberth | 29 June 2017, 14:05:53 UTC | update citation | 29 June 2017, 14:05:53 UTC |
| 8da547c | Jay Hesselberth | 29 June 2017, 12:08:19 UTC | add zenodo badge [ci skip] | 29 June 2017, 12:08:19 UTC |
| f944b4a | Jay Hesselberth | 29 June 2017, 11:58:08 UTC | drop index.Rmd in favor of README.Rmd [ci skip] | 29 June 2017, 11:58:08 UTC |
| 15abb03 | Jay Hesselberth | 26 June 2017, 20:59:08 UTC | ok fine build on appveyor | 26 June 2017, 20:59:08 UTC |
| 060a37a | Jay Hesselberth | 25 June 2017, 20:38:08 UTC | don't build vignettes on ci platforms | 25 June 2017, 20:38:08 UTC |
| 392d817 | Jay Hesselberth | 24 June 2017, 14:43:26 UTC | new create_tss() - add @family tag for feature functions - update tests, NEWS and site | 24 June 2017, 14:43:26 UTC |
| 0ce7276 | Jay Hesselberth | 24 June 2017, 12:55:06 UTC | add site to DESCRIPTION URLs | 24 June 2017, 12:55:06 UTC |
| 4a9acca | Jay Hesselberth | 23 June 2017, 11:37:00 UTC | update site. [ci skip] | 23 June 2017, 11:37:00 UTC |
| 41df001 | Jay Hesselberth | 18 June 2017, 14:43:26 UTC | lint package (#282) | 18 June 2017, 14:43:26 UTC |
| e9bb675 | kriemo | 16 June 2017, 20:17:35 UTC | merge absdist and reldist cpp code Issue200 (#281) * merge absdist.cpp and reldist.cpp * update filename | 16 June 2017, 20:17:35 UTC |
| e1ab0f5 | Jay Hesselberth | 15 June 2017, 14:54:51 UTC | update site [ci skip] | 15 June 2017, 14:54:51 UTC |
| 632c5ef | Jay Hesselberth | 15 June 2017, 14:53:01 UTC | update site [ci skip] | 15 June 2017, 14:53:01 UTC |
| 1f72cc8 | Jay Hesselberth | 15 June 2017, 14:12:30 UTC | tag release | 15 June 2017, 14:12:30 UTC |
