Bioconductor Code: rtracklayer

Graph of rtracklayer

2f6627c0 (HEAD -> devel, origin/master, origin/devel, origin/HEAD) bump x.y.z version to odd y following creation of RELEASE_3_18 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2023-10-24 09:39:43 -0400;
58efbf9c (origin/RELEASE_3_18, RELEASE_3_18) bump x.y.z version to even y prior to creation of RELEASE_3_18 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2023-10-24 09:39:43 -0400;
da7456ef Merge pull request <a href="#100">#100</a> from sanchit-saini/browseGenome by Michael Lawrence <michafla@gene.com> 2023-10-23 09:45:03 -0700;
59915dfd Merge pull request <a href="#99">#99</a> from sanchit-saini/ucsc_tracks by Michael Lawrence <michafla@gene.com> 2023-10-23 09:43:50 -0700;
04712de2 Change GRangesList to GRanges in browseGenome() to avoid error in normGenomeRange() by Sanchit Saini <sanchitsaini14@gmail.com> 2023-10-21 13:05:26 +0530;
f358cff9 Refactor normArgTrack() to make it more readable by Sanchit Saini <sanchitsaini14@gmail.com> 2023-10-21 09:49:23 +0530;
c566f663 Update url in ucscTableTracks() by Sanchit Saini <sanchitsaini14@gmail.com> 2023-10-21 09:43:11 +0530;
07ed9800 another take at the "hub_xxx_genome" issue, fixing <a href="#84">#84</a> by Michael Lawrence <michafla@gene.com> 2023-10-20 10:23:15 -0700;
1de3bf57 Merge pull request <a href="#97">#97</a> from hpages/https_ucsc by Michael Lawrence <michafla@gene.com> 2023-10-20 10:22:49 -0700;
b5d2e0f9 one more tweak suggested by Sanchit Saini by Hervé Pagès <hpages.on.github@gmail.com> 2023-10-19 23:13:55 -0700;
8f85d70f Address more potential annoying messages from readGFF() by Hervé Pagès <hpages.on.github@gmail.com> 2023-10-19 21:41:28 -0700;
49b7e39d Switch from HTTP to HTTPS for requests to *.ucsc.edu by Hervé Pagès <hpages.on.github@gmail.com> 2023-10-19 17:53:42 -0700;
5a681a29 Merge pull request <a href="#79">#79</a> from svengato/master by Michael Lawrence <michafla@gene.com> 2023-10-17 20:11:10 -0700;
4c4f8f65 Merge pull request <a href="#93">#93</a> from sanchit-saini/genome_names_fix by Michael Lawrence <michafla@gene.com> 2023-10-17 20:06:07 -0700;
b9533db9 Update to handle UCSC genome names for hs1 & mpxvRivers by Sanchit Saini <sanchitsaini14@gmail.com> 2023-09-28 17:59:48 +0530;
a93a1c0f Merge pull request <a href="#92">#92</a> from sanchit-saini/ucscTables_url_fix by Michael Lawrence <michafla@gene.com> 2023-09-19 08:19:43 -0700;
d38270a6 Update url to prevent redirection for ucscTables by Sanchit Saini <sanchitsaini14@gmail.com> 2023-09-12 18:15:42 +0530;
55c0c7a4 (origin/RELEASE_3_17, RELEASE_3_17) Sanchit Saini's fix for #88. by Michael Lawrence <michafla@gene.com> 2023-08-14 15:18:38 -0700;
ab6876b8 Sanchit Saini's fix for #88. by Michael Lawrence <michafla@gene.com> 2023-08-14 15:18:38 -0700;
24dbcb05 bump x.y.z version to odd y following creation of RELEASE_3_17 branch by J Wokaty <jwokaty@users.noreply.github.com> 2023-04-25 09:46:41 -0400;
de35bc03 bump x.y.z version to even y prior to creation of RELEASE_3_17 branch by J Wokaty <jwokaty@users.noreply.github.com> 2023-04-25 09:46:41 -0400;
861e3d81 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;
82216503 Explicitly use 'BiocGenerics::connection' to prevent warning message 'Found more than one class "connection" in cache' by Sven Gato Redsun <svengato@svengato.com> 2022-11-27 11:17:33 -0700;
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;