- rtracklayer
- Graph
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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;
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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;
-
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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;
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-
-
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;
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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;
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-
b5d2e0f9
one more tweak suggested by Sanchit Saini by
Hervé Pagès <hpages.on.github@gmail.com>
2023-10-19 23:13:55 -0700;
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8f85d70f
Address more potential annoying messages from readGFF() by
Hervé Pagès <hpages.on.github@gmail.com>
2023-10-19 21:41:28 -0700;
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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;
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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;
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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;
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-
b9533db9
Update to handle UCSC genome names for hs1 & mpxvRivers by
Sanchit Saini <sanchitsaini14@gmail.com>
2023-09-28 17:59:48 +0530;
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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;
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d38270a6
Update url to prevent redirection for ucscTables by
Sanchit Saini <sanchitsaini14@gmail.com>
2023-09-12 18:15:42 +0530;
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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;
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ab6876b8
Sanchit Saini's fix for #88. by
Michael Lawrence <michafla@gene.com>
2023-08-14 15:18:38 -0700;
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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;
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4ee55033
Add code to handle edge case while parsing JSON by
Sanchit Saini <sanchitsaini14@gmail.com>
2022-12-13 17:32:29 +0530;
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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;
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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;
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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;
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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;
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fc647bac
Fix udcFileMayOpen and udcFilesCacheFiles to handle basename with query parameters by
Sanchit Saini <sanchitsaini14@gmail.com>
2022-05-25 17:09:26 +0530;
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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;
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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;
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41013d06
doc fixes by
Michael Lawrence <michafla@gene.com>
2021-12-07 13:33:00 -0800;
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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;
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09f1bfa6
Pass serialized S4 instances thru updateObject() by
Hervé Pagès <hpages.on.github@gmail.com>
2021-11-21 00:50:52 -0500;
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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;
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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;
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d9e4d166
oops by
Hervé Pagès <hpages.on.github@gmail.com>
2021-08-12 12:39:31 -0700;
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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;
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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;
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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;
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245e6cc9
Update code according to updated .parseURI() implementation by
Sanchit Saini <sanchitsaini14@gmail.com>
2021-05-11 09:11:37 +0530;
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72f981da
Remove duplicate code already present in BiocIO by
Sanchit Saini <sanchitsaini14@gmail.com>
2021-05-10 22:34:30 +0530;
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-
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;
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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;
-
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6062183a
Update bed tests remove file scheme uri by
Sanchit Saini <sanchitsaini14@gmail.com>
2021-05-04 19:51:19 +0530;
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0ef8b82a
Update ucsc tests to avoid check on windows by
Sanchit Saini <sanchitsaini14@gmail.com>
2021-05-04 19:49:52 +0530;
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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;
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-
-
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67b9a46e
Move ret & udcCacheEnabled() out of #ifndef WIN32 by
Sanchit Saini <sanchitsaini14@gmail.com>
2021-04-12 06:24:07 +0530;
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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;
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22bac8e7
version bump by
Michael Lawrence <michafla@gene.com>
2021-03-02 13:58:09 -0800;
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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;
-
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0d8250af
Update '=' to '<-' for consistency in track method by
Sanchit Saini <sanchitsaini14@gmail.com>
2021-02-02 00:08:58 +0530;
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98a61577
Update JSON response parsing approach by
Sanchit Saini <sanchitsaini14@gmail.com>
2021-01-29 06:27:41 +0530;
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1851134d
Update tableNames() of UCSCTableQuery class to make it backward compatible by
Sanchit Saini <sanchitsaini14@gmail.com>
2021-01-29 05:19:48 +0530;
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f99d9fb5
Fix tableNames() of UCSCTableQuery class to list correct table names by
Sanchit Saini <sanchitsaini14@gmail.com>
2021-01-29 04:57:01 +0530;
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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;
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456b44a4
Update function call from parseURI() to .parseURI() by
Sanchit Saini <sanchitsaini14@gmail.com>
2021-01-21 00:45:31 +0530;
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410167a3
Clean Up track() of TrackHubGenome class by
Sanchit Saini <sanchitsaini14@gmail.com>
2021-01-21 00:42:08 +0530;
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-
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;
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63b7fa75
Rename parseBwDf() and parseBbDf() to parseBigWigDf(),parseBigBedDf() by
Sanchit Saini <sanchitsaini14@gmail.com>
2021-01-13 06:33:02 +0530;
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8f4023aa
Clean handleResponseForOutputTypes() to make it more modular by
Sanchit Saini <sanchitsaini14@gmail.com>
2021-01-13 05:25:21 +0530;
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60a02700
Update seqlengths() of UCSCSession to avoid call stackoverflow by
Sanchit Saini <sanchitsaini14@gmail.com>
2021-01-13 05:15:42 +0530;
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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;
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6dff5694
Add support for genePred format for ucscTableQuery by
Sanchit Saini <sanchitsaini14@gmail.com>
2021-01-07 03:36:11 +0530;
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3d6ce983
Update deprecation warning of ucscTableQuery() for 'track' parameter by
Sanchit Saini <sanchitsaini14@gmail.com>
2021-01-07 03:32:46 +0530;
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ab6ee70a
Fix track to table conversion logic by
Sanchit Saini <sanchitsaini14@gmail.com>
2021-01-07 03:27:11 +0530;
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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;
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6362beec
path() is a method (on RTLFile) again by
Michael Lawrence <michafla@gene.com>
2021-01-04 14:07:12 -0800;
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b81097a4
Move scraper logic into a separate function by
Sanchit Saini <sanchitsaini14@gmail.com>
2021-01-03 20:13:15 +0530;
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c381ad69
Issue a deprecation warning when a track parameter is used by
Sanchit Saini <sanchitsaini14@gmail.com>
2021-01-03 20:09:38 +0530;
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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;
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e68d6d16
move restfulr to imports by
Michael Lawrence <michafla@gene.com>
2020-12-23 18:03:07 -0800;
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7b794d0f
fix browseGenome() by
Michael Lawrence <michafla@gene.com>
2020-12-23 18:02:42 -0800;
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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;
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5c72eb26
Add accessor method for UCSCTableQuery class by
Sanchit Saini <sanchitsaini14@gmail.com>
2020-12-14 21:15:21 +0530;
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5cbccaf2
Remove unnecessary check from ucscTableQuery character constructor by
Sanchit Saini <sanchitsaini14@gmail.com>
2020-12-14 21:11:49 +0530;
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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;
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3aff923d
Add unit tests for UCSCTableQuery class by
Sanchit Saini <sanchitsaini14@gmail.com>
2020-12-07 15:05:50 +0530;
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ab971217
Update getTable() of UCSCTableQuery class for better name filtering support by
Sanchit Saini <sanchitsaini14@gmail.com>
2020-12-07 14:58:27 +0530;
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d835c817
Update bigDataUrl of trackhub test data and testcase by
Sanchit Saini <sanchitsaini14@gmail.com>
2020-12-07 12:22:48 +0530;
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172ad956
Update test data of a TrackHub by
Sanchit Saini <sanchitsaini14@gmail.com>
2020-12-07 12:09:44 +0530;
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8d3da659
Add genome() accessor for UCSCTableQuery class by
Sanchit Saini <sanchitsaini14@gmail.com>
2020-12-07 12:06:41 +0530;