- rtracklayer
- Graph
- 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;