1. rtracklayer
  2. Graph
Graph of rtracklayer
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  • 861e3d81 (HEAD -> master, origin/master, origin/HEAD) version bump by larman <michafla@gene.com> 2022-12-26 02:08:47 -0800;
  • 894b6699 fix <a href="#23">#23</a> by supporting any whitespace in chain data lines by larman <michafla@gene.com> 2022-12-26 02:07:51 -0800;
  • 4ee55033 Add code to handle edge case while parsing JSON by Sanchit Saini <sanchitsaini14@gmail.com> 2022-12-13 17:32:29 +0530;
  • 3dbff125 bump x.y.z version to odd y following creation of RELEASE_3_16 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2022-11-01 11:03:49 -0400;
  • 54a74972 (origin/RELEASE_3_16, RELEASE_3_16) bump x.y.z version to even y prior to creation of RELEASE_3_16 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2022-11-01 11:03:49 -0400;
  • 4c6d2201 (origin/RELEASE_3_15, RELEASE_3_15) Recent fixes from devel branch by larman <michafla@gene.com> 2022-06-22 12:10:46 -0700;
  • 05017acd Merge pull request <a href="#68">#68</a> from sanchit-saini/import.bw_long_url by Michael Lawrence <michafla@gene.com> 2022-06-22 11:32:46 -0700;
  • 2bb0b401 Fix memory leaks by Sanchit Saini <sanchitsaini14@gmail.com> 2022-05-26 00:14:31 +0530;
  • fc647bac Fix udcFileMayOpen and udcFilesCacheFiles to handle basename with query parameters by Sanchit Saini <sanchitsaini14@gmail.com> 2022-05-25 17:09:26 +0530;
  • fa2a29d0 Update size of url buffer from 1024 to 2024 by Sanchit Saini <sanchitsaini14@gmail.com> 2022-05-27 11:17:31 +0530;
  • 7f241e8d bump x.y.z version to odd y following creation of RELEASE_3_15 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2022-04-26 15:01:05 +0000;
  • 1d70f7dc bump x.y.z version to even y prior to creation of RELEASE_3_15 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2022-04-26 15:01:05 +0000;
  • 2577bc88 version bump by Michael Lawrence <michafla@gene.com> 2022-03-22 15:12:39 -0700;
  • e80c3c6a use S_alloc to become independent of <S.h> by Michael Lawrence <michafla@gene.com> 2022-03-17 13:29:03 -0700;
  • 20b5bf4e Merge pull request <a href="#60">#60</a> from sanchit-saini/fix_bigbed_incorrect_result by Michael Lawrence <michafla@gene.com> 2022-02-20 07:27:39 -0800;
  • 815dc85d Fix bigbed to get correct result & update testcase by Sanchit Saini <sanchitsaini14@gmail.com> 2022-02-20 18:26:23 +0530;
  • 4aa65701 version bump by Michael Lawrence <michafla@gene.com> 2021-12-07 13:35:29 -0800;
  • cfff0243 drop seqinfo,DNAStringSet() since made obsolete by seqinfo,List() by Michael Lawrence <michafla@gene.com> 2021-12-07 13:33:22 -0800;
  • 41013d06 doc fixes by Michael Lawrence <michafla@gene.com> 2021-12-07 13:33:00 -0800;
  • 7c5710c2 Create DFrame instance in place of a DataFrame instance by Hervé Pagès <hpages.on.github@gmail.com> 2021-11-21 02:30:45 -0800;
  • 09f1bfa6 Pass serialized S4 instances thru updateObject() by Hervé Pagès <hpages.on.github@gmail.com> 2021-11-21 00:50:52 -0500;
  • d414814c bump x.y.z version to odd y following creation of RELEASE_3_14 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-10-26 15:52:14 +0000;
  • 04cdd755 (origin/RELEASE_3_14, RELEASE_3_14) bump x.y.z version to even y prior to creation of RELEASE_3_14 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-10-26 15:52:14 +0000;
  • d9e4d166 oops by Hervé Pagès <hpages.on.github@gmail.com> 2021-08-12 12:39:31 -0700;
  • 20a38310 (origin/RELEASE_3_13, RELEASE_3_13) Increase max line length supported by readGFF() from 65536 to 200000 by Hervé Pagès <hpages.on.github@gmail.com> 2021-08-12 12:31:12 -0700;
  • 5027b8e0 Increase max line length supported by readGFF() from 65536 to 200000 by Hervé Pagès <hpages.on.github@gmail.com> 2021-08-12 12:31:12 -0700;
  • b11616f3 bump x.y.z version to odd y following creation of RELEASE_3_13 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-05-19 15:40:44 +0000;
  • 51e5a2c5 bump x.y.z version to even y prior to creation of RELEASE_3_13 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-05-19 15:40:43 +0000;
  • 2c493686 Merge pull request <a href="#49">#49</a> from sanchit-saini/parseURI-fix by Michael Lawrence <michafla@gene.com> 2021-05-11 07:38:01 -0700;
  • 245e6cc9 Update code according to updated .parseURI() implementation by Sanchit Saini <sanchitsaini14@gmail.com> 2021-05-11 09:11:37 +0530;
  • 72f981da Remove duplicate code already present in BiocIO by Sanchit Saini <sanchitsaini14@gmail.com> 2021-05-10 22:34:30 +0530;
  • 28d5aeaf drop extra '/' in file URL to fix <a href="#48">#48</a> by Michael Lawrence <michafla@gene.com> 2021-05-04 19:06:19 -0700;
  • d4c1733a Merge pull request <a href="#47">#47</a> from sanchit-saini/windows-checks-fix by Michael Lawrence <michafla@gene.com> 2021-05-04 07:41:59 -0700;
  • 6062183a Update bed tests remove file scheme uri by Sanchit Saini <sanchitsaini14@gmail.com> 2021-05-04 19:51:19 +0530;
  • 0ef8b82a Update ucsc tests to avoid check on windows by Sanchit Saini <sanchitsaini14@gmail.com> 2021-05-04 19:49:52 +0530;
  • 93d88534 Merge pull request <a href="#46">#46</a> from sanchit-saini/windows-fixes by Michael Lawrence <michafla@gene.com> 2021-04-13 10:16:33 -0700;
  • 67b9a46e Move ret & udcCacheEnabled() out of #ifndef WIN32 by Sanchit Saini <sanchitsaini14@gmail.com> 2021-04-12 06:24:07 +0530;
  • 1c705c6f Remove linux dependent code to fix windows build by Sanchit Saini <sanchitsaini14@gmail.com> 2021-04-12 06:19:10 +0530;
  • d5321c71 Update kent library code to support URL redirection by Sanchit Saini <sanchitsaini14@gmail.com> 2021-03-16 02:48:45 +0530;
  • 22bac8e7 version bump by Michael Lawrence <michafla@gene.com> 2021-03-02 13:58:09 -0800;
  • b3db0253 Merge pull request <a href="#40">#40</a> from sanchit-saini/table_query_improvements by Michael Lawrence <michafla@gene.com> 2021-02-01 10:43:33 -0800;
  • 0d8250af Update '=' to '<-' for consistency in track method by Sanchit Saini <sanchitsaini14@gmail.com> 2021-02-02 00:08:58 +0530;
  • 98a61577 Update JSON response parsing approach by Sanchit Saini <sanchitsaini14@gmail.com> 2021-01-29 06:27:41 +0530;
  • 1851134d Update tableNames() of UCSCTableQuery class to make it backward compatible by Sanchit Saini <sanchitsaini14@gmail.com> 2021-01-29 05:19:48 +0530;
  • f99d9fb5 Fix tableNames() of UCSCTableQuery class to list correct table names by Sanchit Saini <sanchitsaini14@gmail.com> 2021-01-29 04:57:01 +0530;
  • 1d59f7ea Merge pull request <a href="#39">#39</a> from sanchit-saini/trackhub_windows_patch by Michael Lawrence <michafla@gene.com> 2021-01-20 12:18:11 -0800;
  • 346ad732 Fix windows build by removing scheme from the URI by Sanchit Saini <sanchitsaini14@gmail.com> 2021-01-21 01:19:18 +0530;
  • 456b44a4 Update function call from parseURI() to .parseURI() by Sanchit Saini <sanchitsaini14@gmail.com> 2021-01-21 00:45:31 +0530;
  • 410167a3 Clean Up track() of TrackHubGenome class by Sanchit Saini <sanchitsaini14@gmail.com> 2021-01-21 00:42:08 +0530;
  • 456c9ce7 version bump by Michael Lawrence <michafla@gene.com> 2021-01-13 13:52:33 -0800;
  • e1d0a003 Merge pull request <a href="#37">#37</a> from sanchit-saini/ucsc_track_patch by Michael Lawrence <michafla@gene.com> 2021-01-13 13:50:54 -0800;
  • eb506f38 Add documentation for ucscTables() by Sanchit Saini <sanchitsaini14@gmail.com> 2021-01-13 06:58:54 +0530;
  • 63b7fa75 Rename parseBwDf() and parseBbDf() to parseBigWigDf(),parseBigBedDf() by Sanchit Saini <sanchitsaini14@gmail.com> 2021-01-13 06:33:02 +0530;
  • 8f4023aa Clean handleResponseForOutputTypes() to make it more modular by Sanchit Saini <sanchitsaini14@gmail.com> 2021-01-13 05:25:21 +0530;
  • 60a02700 Update seqlengths() of UCSCSession to avoid call stackoverflow by Sanchit Saini <sanchitsaini14@gmail.com> 2021-01-13 05:15:42 +0530;
  • 1efb84e2 Add ucscTables() to get the list of tables for a track by Sanchit Saini <sanchitsaini14@gmail.com> 2021-01-13 05:02:56 +0530;
  • 6dff5694 Add support for genePred format for ucscTableQuery by Sanchit Saini <sanchitsaini14@gmail.com> 2021-01-07 03:36:11 +0530;
  • 3d6ce983 Update deprecation warning of ucscTableQuery() for 'track' parameter by Sanchit Saini <sanchitsaini14@gmail.com> 2021-01-07 03:32:46 +0530;
  • ab6ee70a Fix track to table conversion logic by Sanchit Saini <sanchitsaini14@gmail.com> 2021-01-07 03:27:11 +0530;
  • efde695e Update ucscTableQuery() to be able to instantiate only with the identifier by Sanchit Saini <sanchitsaini14@gmail.com> 2021-01-07 03:11:33 +0530;
  • 6362beec path() is a method (on RTLFile) again by Michael Lawrence <michafla@gene.com> 2021-01-04 14:07:12 -0800;
  • b81097a4 Move scraper logic into a separate function by Sanchit Saini <sanchitsaini14@gmail.com> 2021-01-03 20:13:15 +0530;
  • c381ad69 Issue a deprecation warning when a track parameter is used by Sanchit Saini <sanchitsaini14@gmail.com> 2021-01-03 20:09:38 +0530;
  • 7247f546 Add support for track parameter for ucscTableQuery by Sanchit Saini <sanchitsaini14@gmail.com> 2021-01-03 02:11:06 +0530;
  • ce7efb66 actually import restfulr by Michael Lawrence <michafla@gene.com> 2020-12-23 21:49:39 -0800;
  • e68d6d16 move restfulr to imports by Michael Lawrence <michafla@gene.com> 2020-12-23 18:03:07 -0800;
  • 7b794d0f fix browseGenome() by Michael Lawrence <michafla@gene.com> 2020-12-23 18:02:42 -0800;
  • f5a62ee1 Merge pull request <a href="#31">#31</a> from sanchit-saini/rest_migration by Michael Lawrence <michafla@gene.com> 2020-12-14 09:07:11 -0800;
  • 8fe8f48d Update documentation of UCSCSchema and UCSCTableQuery class by Sanchit Saini <sanchitsaini14@gmail.com> 2020-12-14 21:17:59 +0530;
  • 5c72eb26 Add accessor method for UCSCTableQuery class by Sanchit Saini <sanchitsaini14@gmail.com> 2020-12-14 21:15:21 +0530;
  • 5cbccaf2 Remove unnecessary check from ucscTableQuery character constructor by Sanchit Saini <sanchitsaini14@gmail.com> 2020-12-14 21:11:49 +0530;
  • 8eaae14e version bump by Michael Lawrence <michafla@gene.com> 2020-12-09 13:46:23 -0800;
  • d12a5c30 Merge pull request <a href="#34">#34</a> from mtmorgan/BiocIO-additional-updates by Michael Lawrence <michafla@gene.com> 2020-12-09 13:44:07 -0800;
  • 3aff923d Add unit tests for UCSCTableQuery class by Sanchit Saini <sanchitsaini14@gmail.com> 2020-12-07 15:05:50 +0530;
  • ab971217 Update getTable() of UCSCTableQuery class for better name filtering support by Sanchit Saini <sanchitsaini14@gmail.com> 2020-12-07 14:58:27 +0530;
  • d835c817 Update bigDataUrl of trackhub test data and testcase by Sanchit Saini <sanchitsaini14@gmail.com> 2020-12-07 12:22:48 +0530;
  • 172ad956 Update test data of a TrackHub by Sanchit Saini <sanchitsaini14@gmail.com> 2020-12-07 12:09:44 +0530;
  • 8d3da659 Add genome() accessor for UCSCTableQuery class by Sanchit Saini <sanchitsaini14@gmail.com> 2020-12-07 12:06:41 +0530;
  • 977b9c0a Update normGenomeRange() to normalize range with seqinfo instead of UCSCSession by Sanchit Saini <sanchitsaini14@gmail.com> 2020-12-07 11:57:55 +0530;
  • 47f3bfb7 revert change to normURI() in 064ae63 by Martin Morgan <Martin.Morgan@RoswellPark.org> 2020-12-05 16:20:27 -0500;
  • ec57795c don't use RTLFile by Martin Morgan <Martin.Morgan@RoswellPark.org> 2020-12-05 16:16:35 -0500;
  • d2956a64 don't define or export CompressedFile() by Martin Morgan <Martin.Morgan@RoswellPark.org> 2020-12-05 16:13:03 -0500;
  • 561cc87b initial clean-up by Martin Morgan <Martin.Morgan@RoswellPark.org> 2020-12-05 16:09:50 -0500;
  • c51c0745 add liftOver method for Pairs objects by Michael Lawrence <michafla@gene.com> 2020-12-01 14:46:27 -0800;
  • 7ebdb9b3 force C locale when parsing last modified date with strptime() by Michael Lawrence <michafla@gene.com> 2020-11-30 16:12:09 -0800;
  • 5290ff02 Removed 'rtracklayer:::' from BiocFileList reference by Daniel Van Twisk <daniel.vantwisk@roswellpark.org> 2020-07-07 13:38:43 -0400;
  • 064ae63f merge BiocIO stuff by Michael Lawrence <michafla@gene.com> 2020-12-01 15:48:39 -0800;
  • c516a20e merge BiocIO stuff by Michael Lawrence <michafla@gene.com> 2020-12-01 15:47:41 -0800;
  • 2b9348d8 Deprecated functions by Daniel Van Twisk <daniel.vantwisk@roswellpark.org> 2020-06-26 11:03:47 -0400;
  • 29e42bc0 Changes in conjunction with BiocIO changes by Daniel Van Twisk <daniel.vantwisk@roswellpark.org> 2020-06-24 09:27:47 -0400;
  • 59f5f759 merge more BiocIO stuff by Michael Lawrence <michafla@gene.com> 2020-12-01 15:44:48 -0800;
  • 688b8b7c BiocIO merge by Michael Lawrence <michafla@gene.com> 2020-12-01 15:34:57 -0800;
  • 3ef684b7 Remove unintented setting of genome on the session by Sanchit Saini <sanchitsaini14@gmail.com> 2020-11-30 20:53:00 +0530;
  • 65130899 Remove GPos support from track() of UCSCTableQuery by Sanchit Saini <sanchitsaini14@gmail.com> 2020-11-23 21:06:59 +0530;
  • dfcd8b9b Fix condition to identify table may have more than 100,000 elements by Sanchit Saini <sanchitsaini14@gmail.com> 2020-11-23 21:03:37 +0530;
  • caf2dae6 Clean Up normGenomeRange() and other related methods by Sanchit Saini <sanchitsaini14@gmail.com> 2020-11-23 20:44:38 +0530;
  • e733af43 Add show() for UCSCSchema by Sanchit Saini <sanchitsaini14@gmail.com> 2020-11-02 22:03:36 +0530;
  • 2307e944 Update getTable() of UCSCSession with parameterized call to ucscTableQuery() by Sanchit Saini <sanchitsaini14@gmail.com> 2020-11-02 22:00:33 +0530;
  • fdf4835c Update track() and getTable() to handle different outputTypes from API by Sanchit Saini <sanchitsaini14@gmail.com> 2020-11-02 21:56:02 +0530;
  • dbeaded6 Add wrapper on TrackHub API to query on TrackHubs using UCSCTableQuery by Sanchit Saini <sanchitsaini14@gmail.com> 2020-11-02 21:25:20 +0530;