| 7f85dd3 | Kent Riemondy | 04 April 2024, 20:40:11 UTC | Increment version number to 0.8.0.9000 | 04 April 2024, 20:40:11 UTC |
| e9bfcb6 | Kent Riemondy | 04 April 2024, 18:13:12 UTC | Increment version number to 0.8.0 | 04 April 2024, 18:13:12 UTC |
| ad01d5e | Kent Riemondy | 04 April 2024, 17:04:51 UTC | update cran comments | 04 April 2024, 17:04:51 UTC |
| 94e3387 | Kent Riemondy | 04 April 2024, 14:45:06 UTC | polish news | 04 April 2024, 14:45:06 UTC |
| e0f6e9e | Kent Riemondy | 04 April 2024, 14:44:12 UTC | remove docType package from ivl_df docs and redoc | 04 April 2024, 14:44:12 UTC |
| a4093ef | Kent Riemondy | 11 October 2023, 17:53:42 UTC | add genomecov (#411) * add genomecov functionality, closes #410 * change column output, depth -> .depth, for consistency with other valr outputs * styler::style_pkg() * fix note | 11 October 2023, 17:53:42 UTC |
| 69a2b8f | Kent Riemondy | 18 September 2023, 19:42:19 UTC | Increment version number to 0.7.0.9000 | 18 September 2023, 19:42:19 UTC |
| cad2178 | Kent Riemondy | 18 September 2023, 16:40:32 UTC | Increment version number to 0.7.0 | 18 September 2023, 16:40:32 UTC |
| 9c550a0 | Kent Riemondy | 18 September 2023, 16:38:48 UTC | update cran comments | 18 September 2023, 16:38:48 UTC |
| f2ce10b | Jay Hesselberth | 17 September 2023, 15:17:19 UTC | update main vignette | 17 September 2023, 15:17:19 UTC |
| 905b404 | Jay Hesselberth | 16 September 2023, 20:48:29 UTC | use base pipe | 16 September 2023, 20:51:22 UTC |
| 7a8a359 | Jay Hesselberth | 14 June 2023, 20:34:58 UTC | sniff n_fields in read functions (#408) and deprecate the `n_fields` param | 14 June 2023, 20:34:58 UTC |
| a68a797 | Jay Hesselberth | 19 May 2023, 12:57:41 UTC | update actions | 19 May 2023, 12:57:41 UTC |
| 991a485 | Kent Riemondy | 16 May 2023, 14:50:05 UTC | Increment version number to 0.6.8.9000 | 16 May 2023, 14:50:05 UTC |
| 3847504 | Kent Riemondy | 16 May 2023, 13:29:34 UTC | Increment version number to 0.6.8 | 16 May 2023, 13:29:34 UTC |
| 547d4ce | Kent Riemondy | 16 May 2023, 13:20:10 UTC | update news and cran comments | 16 May 2023, 13:20:10 UTC |
| e39efc3 | Kent Riemondy | 15 May 2023, 14:56:11 UTC | update shiny url | 15 May 2023, 14:56:11 UTC |
| 512331b | Jay Hesselberth | 08 April 2023, 21:43:40 UTC | remove `r_index` from df subset fxns (#406) | 08 April 2023, 21:43:40 UTC |
| 29cf177 | Kent Riemondy | 08 April 2023, 15:53:49 UTC | reimplement closest (#404) * working impl * working reimplementation * add debug utility for ivl-tree * more docs * update news, docs, and tests * remove old closest interval-tree code * report bookend ivl as 1 and polish tests * minor refactor * 5 back to 10 | 08 April 2023, 15:53:49 UTC |
| db30567 | Kent Riemondy | 06 April 2023, 18:22:59 UTC | Merge pull request #403 from rnabioco/issue-401-2 simplify merge logic and add more tests | 06 April 2023, 18:22:59 UTC |
| bedf84e | Kent Riemondy | 06 April 2023, 16:41:16 UTC | simplify merge logic and add more tests | 06 April 2023, 18:01:19 UTC |
| 75c437b | Kent Riemondy | 05 April 2023, 19:43:57 UTC | Merge pull request #402 from rnabioco/issue_401 fix OB1 bug when max_dist argument supplied | 05 April 2023, 19:43:57 UTC |
| b47a57a | Kent Riemondy | 05 April 2023, 18:29:29 UTC | fix OB1 error | 05 April 2023, 18:29:29 UTC |
| 810afe0 | Kent Riemondy | 18 February 2023, 22:48:48 UTC | Increment version number to 0.6.7.9000 | 18 February 2023, 22:48:48 UTC |
| b8e9dfb | Kent Riemondy | 18 February 2023, 17:12:22 UTC | Increment version number to 0.6.7 | 18 February 2023, 17:12:22 UTC |
| f824e4b | Kent Riemondy | 18 February 2023, 17:11:31 UTC | update cran comments [skip ci] | 18 February 2023, 17:11:31 UTC |
| 00f506e | Kent Riemondy | 17 February 2023, 18:52:15 UTC | drop remaining references to c++11 | 17 February 2023, 18:52:15 UTC |
| 4eb781f | Kent Riemondy | 15 February 2023, 20:33:33 UTC | update cran comments | 15 February 2023, 20:33:33 UTC |
| 0006d38 | Kent Riemondy | 11 February 2023, 03:16:44 UTC | specify multiple = "all" argument added in dplyr 1.1.0 (#400) We can safely specify multiple = "all" in bed_absdist() to silence this warning. There may be other conditions in other code that trigger this, but I don't see this warning in other tests, examples, or vignettes. Note that you need to set Sys.setenv(TESTTHAT_PKG = "valr") to see the warning during interactive use. closes #399 | 11 February 2023, 03:16:44 UTC |
| 597fb9f | Jay Hesselberth | 09 February 2023, 11:14:15 UTC | update readme and news | 09 February 2023, 11:14:15 UTC |
| 6c5fa61 | Jay Hesselberth | 09 February 2023, 11:06:38 UTC | remove SystemRequirements from DESCRIPTION (#397) Addresses new CRAN note: cloud.r-project.org/web/checks/check_results_valr.html We have a Makevars specifying CXX_STD=CXX11, which is best practice and doesn't require SystemRequirements specification: cran.r-project.org/doc/manuals/r-release/R-exts.html#Using-C_002b_002b-code | 09 February 2023, 11:06:38 UTC |
| 13c397c | Jay Hesselberth | 05 February 2023, 20:52:59 UTC | styler::style_pkg() and re-document | 05 February 2023, 20:52:59 UTC |
| 0e00aa3 | Kent Riemondy | 04 February 2023, 23:04:00 UTC | Merge pull request #396 from rnabioco/issue395 Issue395 | 04 February 2023, 23:04:00 UTC |
| 3a0f003 | Kent Riemondy | 04 February 2023, 19:59:28 UTC | fix typo and add get_id_col to bed_map | 04 February 2023, 19:59:28 UTC |
| cf47bde | Kent Riemondy | 04 February 2023, 17:54:50 UTC | update news and glyph tests (insignificant changes) | 04 February 2023, 17:54:50 UTC |
| 09bb36d | Kent Riemondy | 04 February 2023, 17:43:22 UTC | update test to account for sorted output | 04 February 2023, 17:43:22 UTC |
| d83ff9b | Kent Riemondy | 04 February 2023, 17:37:24 UTC | return all input ivls | 04 February 2023, 17:37:24 UTC |
| 2966368 | Jay Hesselberth | 03 February 2023, 23:43:18 UTC | update gh actions | 03 February 2023, 23:43:18 UTC |
| c129dad | Jay Hesselberth | 07 December 2022, 14:49:55 UTC | update db tests | 07 December 2022, 14:49:55 UTC |
| 7e3c606 | Jay Hesselberth | 27 November 2022, 16:16:44 UTC | use tidy eval in `aes` fixes warnings for soft deprecation of `aes_` and `aes_string` | 27 November 2022, 16:16:44 UTC |
| 6978eff | Kent Riemondy | 11 October 2022, 18:19:59 UTC | Increment version number to 0.6.6.9000 | 11 October 2022, 18:19:59 UTC |
| 5a00f02 | Kent Riemondy | 11 October 2022, 17:21:58 UTC | Increment version number to 0.6.6 | 11 October 2022, 17:21:58 UTC |
| bde702f | Kent Riemondy | 11 October 2022, 17:19:51 UTC | update cran comments | 11 October 2022, 17:19:51 UTC |
| 92e5d8e | Jay Hesselberth | 05 October 2022, 18:10:35 UTC | update readme | 05 October 2022, 18:10:35 UTC |
| 9060783 | Kent Riemondy | 05 October 2022, 17:53:34 UTC | Merge pull request #391 from rnabioco/ivl-tree update intervaltree | 05 October 2022, 17:53:34 UTC |
| a5f80ca | Kent Riemondy | 05 October 2022, 17:34:11 UTC | move into copyright statement | 05 October 2022, 17:34:11 UTC |
| c7a30a0 | Kent Riemondy | 05 October 2022, 17:31:02 UTC | sync with main, add additional comments about intervalTree source. Merge branch 'main' into ivl-tree # Conflicts: # NEWS.md | 05 October 2022, 17:31:02 UTC |
| 4b9c506 | Jay Hesselberth | 05 October 2022, 13:32:18 UTC | improvements for interactive use (#393) use cli for msg/warn/info and use `check_required` to improve interactive use. update testthat and tests closes #392 | 05 October 2022, 13:32:18 UTC |
| 3a6c04d | Kent Riemondy | 24 August 2022, 14:32:48 UTC | remove SEXP type from dataframe builder, can crash R during gc() call. Also remove add_vec, instead add to df builder class manually, avoids needing templates for each Rcpp vector class | 24 August 2022, 14:32:48 UTC |
| 805a1d3 | Kent Riemondy | 23 August 2022, 18:35:48 UTC | use template function definition and call via wrapper | 23 August 2022, 18:35:48 UTC |
| 83a1f5e | Kent Riemondy | 20 August 2022, 20:58:40 UTC | rename file in git | 20 August 2022, 20:58:58 UTC |
| 9a2e59f | Kent Riemondy | 20 August 2022, 20:37:03 UTC | add news and update copyright for modified files | 20 August 2022, 20:37:03 UTC |
| d5281c6 | Kent Riemondy | 20 August 2022, 16:18:41 UTC | updated interval tree: - added friend declaration for findClosest into external header - moved findClosest definition out of external header - uses std::move to build tree - commit id from ekg/intervaltree f0c404 | 20 August 2022, 16:18:41 UTC |
| 0aa9418 | Kent Riemondy | 19 August 2022, 14:54:17 UTC | Increment version number to 0.6.5.9000 | 19 August 2022, 14:54:17 UTC |
| 7f112d6 | Kent Riemondy | 19 August 2022, 14:47:28 UTC | v 0.6.5 release | 19 August 2022, 14:47:28 UTC |
| bc62d91 | Kent Riemondy | 18 August 2022, 21:00:11 UTC | update revdep and cran comments | 18 August 2022, 21:00:11 UTC |
| 6234b4c | Jay Hesselberth | 16 August 2022, 15:46:50 UTC | Re-build readme | 16 August 2022, 15:46:50 UTC |
| 695d497 | Jay Hesselberth | 16 August 2022, 15:44:57 UTC | Polish news | 16 August 2022, 15:44:57 UTC |
| 3fc7393 | Kent Riemondy | 04 August 2022, 20:41:07 UTC | Merge pull request #389 from rnabioco/issue388 ensure that first interval per group is part of cluster in bed_cluster | 04 August 2022, 20:41:07 UTC |
| a6e4dc6 | Kent Riemondy | 04 August 2022, 20:01:03 UTC | ensure that first interval per group is part of cluster in bed_cluster. | 04 August 2022, 20:01:03 UTC |
| 7a654f3 | Jay Hesselberth | 10 July 2022, 12:17:29 UTC | update url in readme | 10 July 2022, 12:17:29 UTC |
| 4437d30 | Jay Hesselberth | 05 July 2022, 20:54:00 UTC | update tests | 05 July 2022, 20:54:00 UTC |
| f54ee31 | Jay Hesselberth | 05 July 2022, 20:12:54 UTC | styler::style_pkg() | 05 July 2022, 20:12:54 UTC |
| dc87c2c | Jay Hesselberth | 03 July 2022, 19:46:57 UTC | fix vignette error | 03 July 2022, 19:46:57 UTC |
| 54d8423 | Jay Hesselberth | 03 July 2022, 16:12:09 UTC | Merge branch 'main' of github.com:rnabioco/valr | 03 July 2022, 16:12:09 UTC |
| 004d0ec | Jay Hesselberth | 03 July 2022, 16:11:23 UTC | update workflows | 03 July 2022, 16:11:23 UTC |
| 0be99f1 | Henry Miller | 02 July 2022, 19:27:54 UTC | Corrected user feedback for stop() in bed_random. Now it correctly indicates that the issue is "length" being larger than some chrom.sizes. (#386) | 02 July 2022, 19:27:54 UTC |
| e9c1fc0 | Jay Hesselberth | 02 July 2022, 19:03:27 UTC | update actions | 02 July 2022, 19:04:14 UTC |
| 01e1d66 | Jay Hesselberth | 19 June 2022, 16:01:14 UTC | Add cph role to RBI | 19 June 2022, 16:01:14 UTC |
| c5717f0 | Jay Hesselberth | 21 February 2022, 01:59:36 UTC | add package | 21 February 2022, 01:59:36 UTC |
| de39657 | Jay Hesselberth | 21 February 2022, 01:50:54 UTC | rebuild pkgdown site | 21 February 2022, 01:50:54 UTC |
| b8a887b | Jay Hesselberth | 21 February 2022, 01:25:49 UTC | use rbitemplate for pkgdown site | 21 February 2022, 01:26:51 UTC |
| aff74d6 | Kent Riemondy | 08 December 2021, 23:14:30 UTC | increment version number to development version | 08 December 2021, 23:14:30 UTC |
| d956433 | Kent Riemondy | 08 December 2021, 16:44:51 UTC | fix spelling errors | 08 December 2021, 16:44:51 UTC |
| 9bf5781 | Kent Riemondy | 08 December 2021, 16:37:00 UTC | drop rhub windows comments | 08 December 2021, 16:37:00 UTC |
| 3da16d2 | Kent Riemondy | 08 December 2021, 16:26:37 UTC | update cran comments | 08 December 2021, 16:26:37 UTC |
| 3398685 | Kent Riemondy | 08 December 2021, 16:24:28 UTC | increment version number | 08 December 2021, 16:24:28 UTC |
| d086cba | Kent Riemondy | 08 December 2021, 16:24:12 UTC | add revdep directory but ignore in build | 08 December 2021, 16:24:12 UTC |
| 8704555 | Jay Hesselberth | 05 December 2021, 15:30:23 UTC | Move benchmarks to internal directory | 05 December 2021, 15:30:23 UTC |
| b1a3aea | Jay Hesselberth | 04 December 2021, 20:25:24 UTC | restore coverage badge | 04 December 2021, 20:25:24 UTC |
| 9ffdb03 | Jay Hesselberth | 04 December 2021, 20:03:45 UTC | suppress benchmark vignette | 04 December 2021, 20:03:45 UTC |
| 8cb1f78 | Jay Hesselberth | 04 December 2021, 20:01:29 UTC | fix some urls | 04 December 2021, 20:01:29 UTC |
| 2a45d30 | Jay Hesselberth | 04 December 2021, 19:53:37 UTC | Update news and readme | 04 December 2021, 19:53:37 UTC |
| 5007f6a | Jay Hesselberth | 04 December 2021, 19:51:41 UTC | Kent Riemondy is now maintainer. cc @kriemo | 04 December 2021, 19:51:41 UTC |
| f027e5a | Jay Hesselberth | 04 December 2021, 19:49:59 UTC | pkgdown fix (take 2) | 04 December 2021, 19:49:59 UTC |
| 2568158 | Jay Hesselberth | 04 December 2021, 19:22:46 UTC | pkgdown fix | 04 December 2021, 19:22:46 UTC |
| 7929f8b | Jay Hesselberth | 04 December 2021, 19:07:30 UTC | Updates for new pkgdown Update actions, README, DESCCRIPTION Renamed master -> main | 04 December 2021, 19:07:30 UTC |
| a2f8f99 | Kent Riemondy | 20 October 2021, 19:34:43 UTC | Merge pull request #382 from rnabioco/issue379 - add read_gtf and read_bigwig fxns - modify gh actions to build on release only | 20 October 2021, 19:34:43 UTC |
| 360995c | Kent Riemondy | 20 October 2021, 18:29:04 UTC | only build on release, there are missing binaries for older releases | 20 October 2021, 18:29:04 UTC |
| c4bafa8 | Kent Riemondy | 20 October 2021, 15:41:54 UTC | conditionally run tests/examples for read_bigwig on windows due to known rtracklayer issues | 20 October 2021, 15:41:54 UTC |
| 1ecefa8 | Kent Riemondy | 20 October 2021, 14:30:18 UTC | add read_gtf and read_bigwig fxns - add rtracklayer to imports - add unit tests - add example data files - update gh actions to install rtracklayer | 20 October 2021, 14:30:18 UTC |
| 7f0672e | Kent Riemondy | 20 October 2021, 13:28:10 UTC | Merge pull request #381 from rnabioco/intersect-input fix list handling bug, closes #380 | 20 October 2021, 13:28:10 UTC |
| 5e721d4 | Kent Riemondy | 19 October 2021, 22:03:29 UTC | don't build on devel due to bioc and R version mismatch | 19 October 2021, 22:03:29 UTC |
| 8289335 | Kent Riemondy | 19 October 2021, 18:06:49 UTC | test on latest ubuntu | 19 October 2021, 18:06:49 UTC |
| 4ff37ea | Kent Riemondy | 15 October 2021, 23:25:41 UTC | fix list handling bug | 15 October 2021, 23:25:41 UTC |
| 799dd74 | Jay Hesselberth | 03 September 2021, 14:30:05 UTC | Update URL | 03 September 2021, 14:30:05 UTC |
| 3d3efbd | Kent Riemondy | 09 June 2021, 20:27:14 UTC | Merge pull request #378 from rnabioco/create_introns create_introns numbering bug | 09 June 2021, 20:27:14 UTC |
| 84bd893 | Kent Riemondy | 09 June 2021, 19:40:30 UTC | add test for duplicated intron score and news item (closes #378) | 09 June 2021, 19:43:36 UTC |
| 9f9d0e5 | rmsheridan@cassini | 09 June 2021, 17:27:21 UTC | create_introns numbering bug | 09 June 2021, 17:27:21 UTC |
| c1e48cf | Jay Hesselberth | 15 May 2021, 12:53:48 UTC | Increment version number | 15 May 2021, 12:53:48 UTC |
