All File Changes

v450_preview to v450_preview2 (2023-06-12 to 2023-06-20) v450

• src/hg/blastToPsl/pslBuild.c
  • lines changed 26, context: html, text, full: html, text
    b8d545da050a4050b3f0ae6af8fa93ac8ce6c6a3 Sun Jun 11 14:52:31 2023 -0700
    fixed incorrect calculation of indels causes by fix to pslTEnd() on protein/dna PSLs
• src/hg/cartReset/cartReset.c
  • lines changed 1, context: html, text, full: html, text
    5be810d6454c59c784482cbec0ec90e622abf317 Tue Jun 13 05:28:17 2023 -0700
    making localStorage reset global, refs #31503, idea by Braney and changed after code review, refs #31512
• src/hg/cirm/gateway/htdocs/inc/header.html
  • lines changed 1, context: html, text, full: html, text
    3598cb26fce53e10c3883a398215218452607cc3 Thu Jun 15 14:58:09 2023 -0700
    Added curly braces around the env variable as required by Rocky 9 on public cirm.
• src/hg/hgTracks/hgTracks.c
  • lines changed 4, context: html, text, full: html, text
    13a71608b50408e504d9c0e88526264e43e4be20 Fri Feb 17 12:28:47 2023 -0800
    Proof of concept tutorial overlay done
  • lines changed 6, context: html, text, full: html, text
    f77196f3a66db3bb1bce1913a2e7d6223db94c0b Mon May 22 15:58:42 2023 -0700
    Make tutorial login dependent, add a link to view the tutorial under Help
  • lines changed 2, context: html, text, full: html, text
    661ec62ccfe5864b48b9dbfd5e9f720a60e7c45e Thu Jun 15 11:06:30 2023 -0700
    Fix missing braces typo when deciding whether to include the hg.conf controlled tutorial on hgTracks, no refs
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 3, context: html, text, full: html, text
    b44df11903f0c8537dc9d716df324906bc89f92b Thu Jun 15 13:21:32 2023 -0700
    Adding documentation supporting snakes rearrangement display, refs #31241
• src/hg/htdocs/contacts.html
  • lines changed 8, context: html, text, full: html, text
    09397fdf2791a0407074e2088116ad14a77b7b6a Wed Jun 14 13:20:06 2023 -0700
    Clarifying the closure of the track hub developer list, and making some updates to the contact page in general such as removing the training URL. Refs #31340
• src/hg/htdocs/goldenPath/help/chain.html
  • lines changed 23, context: html, text, full: html, text
    b44df11903f0c8537dc9d716df324906bc89f92b Thu Jun 15 13:21:32 2023 -0700
    Adding documentation supporting snakes rearrangement display, refs #31241
  • lines changed 1, context: html, text, full: html, text
    a7f53180b993efb1a7484c732f9b8693e666fc76 Fri Jun 16 15:18:02 2023 -0700
    Removing a word since it can confuse and adds no value to the example, refs #31241
• src/hg/htdocs/goldenPath/help/hgUserPsl.html
  • lines changed 3, context: html, text, full: html, text
    f20b31ea40c4fd47327f892ebca33a3c63e8f5b4 Thu Jun 15 13:33:34 2023 -0700
    Adding a plug to rearrangement docs from the BLAT desc page, refs #31241
• src/hg/htdocs/goldenPath/help/trackDb/changes.html
  • lines changed 6, context: html, text, full: html, text
    3ddebd74b28ec0d0734a5fb8aaaa98d70f200376 Wed Jun 14 12:08:35 2023 -0700
    Adding one more setting to changes.html page, refs #31340
• src/hg/htdocs/images/rearrangementExample1.png
  • lines changed 0, context: html, text, full: html, text
    b44df11903f0c8537dc9d716df324906bc89f92b Thu Jun 15 13:21:32 2023 -0700
    Adding documentation supporting snakes rearrangement display, refs #31241
• src/hg/htdocs/images/rearrangementExample2.png
  • lines changed 0, context: html, text, full: html, text
    b44df11903f0c8537dc9d716df324906bc89f92b Thu Jun 15 13:21:32 2023 -0700
    Adding documentation supporting snakes rearrangement display, refs #31241
• src/hg/htdocs/style/HGStyle.css
  • lines changed 1, context: html, text, full: html, text
    752ca37b9f0031e59abc0dedef4752b7eb890946 Fri May 19 12:11:41 2023 -0700
    Generalize the notification box setups so we can have multiple of them. Starting on getting the tutorial to show up conditionally
• src/hg/js/hgTracks.js
  • lines changed 3, context: html, text, full: html, text
    e17ab1abdfd35d012ce831f46c24e972d52517db Thu Feb 16 16:20:49 2023 -0800
    Strip hub_id when making api requests for hub tracks/genomes, refs #30024
  • lines changed 5, context: html, text, full: html, text
    13a71608b50408e504d9c0e88526264e43e4be20 Fri Feb 17 12:28:47 2023 -0800
    Proof of concept tutorial overlay done
  • lines changed 15, context: html, text, full: html, text
    eb8483343ae0c285f9b74f7ebbc96d2abcb9816c Thu Mar 23 11:46:25 2023 -0700
    Merge branch 'master' into chmalee_hgTracksTutorial
  • lines changed 44, context: html, text, full: html, text
    7ea5ed7d0c917304cdf903d3acdc12d937e1d7cb Fri May 19 10:36:46 2023 -0700
    Merge branch 'master' into chmalee_hgTracksTutorial
  • lines changed 22, context: html, text, full: html, text
    cda1904f5a784ef6a94ee2ad8cfbcc3c0d0d4bef Fri May 19 11:23:11 2023 -0700
    Temporary commit generalizing the notification box
  • lines changed 11, context: html, text, full: html, text
    752ca37b9f0031e59abc0dedef4752b7eb890946 Fri May 19 12:11:41 2023 -0700
    Generalize the notification box setups so we can have multiple of them. Starting on getting the tutorial to show up conditionally
  • lines changed 7, context: html, text, full: html, text
    edb9731b4634655aba9aae9707a6aa8c9a1457cb Fri May 19 16:31:53 2023 -0700
    Don't show tutorial until a link is clicked, hide/show tutorial correctly. TODO: when tutorial is finished set the localStorage correctly
  • lines changed 14, context: html, text, full: html, text
    f77196f3a66db3bb1bce1913a2e7d6223db94c0b Mon May 22 15:58:42 2023 -0700
    Make tutorial login dependent, add a link to view the tutorial under Help
  • lines changed 1, context: html, text, full: html, text
    6c13a4db99ad6efef393ab837b3cbefacde6bd14 Mon May 22 16:02:29 2023 -0700
    Fix truthiness syntax after checking localStorage
  • lines changed 53, context: html, text, full: html, text
    78aafe96d19a48bef4bb7e4a1fc7401eb65a7daa Wed Jun 14 10:11:53 2023 -0700
    Fix merge conflict
• src/hg/js/makefile
  • lines changed 1, context: html, text, full: html, text
    13a71608b50408e504d9c0e88526264e43e4be20 Fri Feb 17 12:28:47 2023 -0800
    Proof of concept tutorial overlay done
• src/hg/js/tutorial.js
  • lines changed 69, context: html, text, full: html, text
    70b8a142600a4211810d41aa258b43cb2cea9e8c Thu Mar 2 11:22:03 2023 -0800
    Add file that controls the tutorial, refs #30670
  • lines changed 1, context: html, text, full: html, text
    f77196f3a66db3bb1bce1913a2e7d6223db94c0b Mon May 22 15:58:42 2023 -0700
    Make tutorial login dependent, add a link to view the tutorial under Help
• src/hg/js/utils.js
  • lines changed 20, context: html, text, full: html, text
    e17ab1abdfd35d012ce831f46c24e972d52517db Thu Feb 16 16:20:49 2023 -0800
    Strip hub_id when making api requests for hub tracks/genomes, refs #30024
  • lines changed 39, context: html, text, full: html, text
    cda1904f5a784ef6a94ee2ad8cfbcc3c0d0d4bef Fri May 19 11:23:11 2023 -0700
    Temporary commit generalizing the notification box
  • lines changed 11, context: html, text, full: html, text
    752ca37b9f0031e59abc0dedef4752b7eb890946 Fri May 19 12:11:41 2023 -0700
    Generalize the notification box setups so we can have multiple of them. Starting on getting the tutorial to show up conditionally
  • lines changed 2, context: html, text, full: html, text
    a415b46e764f69b880f0cb1220964c92c76e4914 Thu Jun 15 11:00:04 2023 -0700
    Don't show notification box on configure page of hgTracks, no refs
• src/hg/lib/hgHgvs.c
  • lines changed 1, context: html, text, full: html, text
    2b50ebde25b8ad6c5a43797ae0ceb85ae66fd0bc Sun Jun 11 13:58:19 2023 -0700
    fixed a couple of calls to pslTransMap to add new alignments
• src/hg/lib/hubConnect.c
  • lines changed 10, context: html, text, full: html, text
    8f399a09d7b39a87eadc3cc0a89c33598ddc5d2a Wed Apr 5 11:16:22 2023 -0700
    First attempt at surfacing up hub errors when the requested hub database doesn't exist, refs #30832
• src/hg/lib/trackHub.c
  • lines changed 6, context: html, text, full: html, text
    8f399a09d7b39a87eadc3cc0a89c33598ddc5d2a Wed Apr 5 11:16:22 2023 -0700
    First attempt at surfacing up hub errors when the requested hub database doesn't exist, refs #30832
  • lines changed 7, context: html, text, full: html, text
    966a8c19f18ac15df06580c18bb7515c6af258fd Tue Jun 13 12:23:26 2023 -0700
    Fixing merge conflict
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    3f9679e0fac12c4ed626a99c0503051635720e9f Wed Jun 14 10:23:43 2023 -0700
    adding brown house snake Boaedon fuliginosus per user request refs #29545
• src/hg/makeDb/doc/canFam3.txt
  • lines changed 21, context: html, text, full: html, text
    3fd174ec070cdd1cd53b276e135c76c869859a4b Mon Jun 12 00:19:18 2023 -0700
    Making FANTOM5 hub into native track, refs #21605
• src/hg/makeDb/doc/chm13v2.0userData/build.txt
  • lines changed 452, context: html, text, full: html, text
    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/doc/chm13v2.0_CytoBandMapping.readme.txt
  • lines changed 31, context: html, text, full: html, text
    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/doc/chm13v2.0_CytoBandMapping.tsv
  • lines changed 863, context: html, text, full: html, text
    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/html/catLiftOffGenesV1.html
  • lines changed 104, context: html, text, full: html, text
    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/html/censat.html
  • lines changed 34, context: html, text, full: html, text
    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/html/clinVar20220313.html
  • lines changed 14, context: html, text, full: html, text
    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/html/dbSNP155.html
  • lines changed 14, context: html, text, full: html, text
    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/html/encode.html
  • lines changed 41, context: html, text, full: html, text
    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/html/gwasSNPs2022-03-08.html
  • lines changed 14, context: html, text, full: html, text
    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/html/hgCactus.html
  • lines changed 44, context: html, text, full: html, text
    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/html/hgLiftOver.html
  • lines changed 251, context: html, text, full: html, text
    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/html/hgUnique.html
  • lines changed 45, context: html, text, full: html, text
    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/html/microsatellites.html
  • lines changed 31, context: html, text, full: html, text
    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/html/proseq.html
  • lines changed 57, context: html, text, full: html, text
    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/html/rdnaModel.html
  • lines changed 10, context: html, text, full: html, text
    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/html/rnaseq.html
  • lines changed 68, context: html, text, full: html, text
    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/html/sedefSegDups.html
  • lines changed 43, context: html, text, full: html, text
    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/html/sgdpCopyNumber.html
  • lines changed 33, context: html, text, full: html, text
    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/html/t2tRepeatMasker.bigRmsk.html
  • lines changed 488, context: html, text, full: html, text
    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/html/t2tRepeatMasker.html
  • lines changed 153, context: html, text, full: html, text
    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/makefile
  • lines changed 80, context: html, text, full: html, text
    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/schema/cenSat.as
  • lines changed 14, context: html, text, full: html, text
    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/schema/sedefSegDups.as
  • lines changed 48, context: html, text, full: html, text
    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/trackDb/catLiftOffGenesV1.trackDb.txt
  • lines changed 16, context: html, text, full: html, text
    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/trackDb/censat.trackDb.txt
  • lines changed 11, context: html, text, full: html, text
    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/trackDb/clinVar20220313.trackDb.txt
  • lines changed 9, context: html, text, full: html, text
    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/trackDb/cytoBandMapped.trackDb.txt
  • lines changed 8, context: html, text, full: html, text
    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/trackDb/dbSNP155.trackDb.txt
  • lines changed 9, context: html, text, full: html, text
    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/trackDb/encode.trackDb.txt
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    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/trackDb/gwasSNPs2022-03-08.trackDb.txt
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    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/trackDb/hgCactus.trackDb.txt
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    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/trackDb/hgLiftOver.trackDb.txt
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    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/trackDb/hgUnique.trackDb.txt
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    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/trackDb/microsatellites.trackDb.txt
  • lines changed 48, context: html, text, full: html, text
    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/trackDb/proseq.trackDb.txt
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    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/trackDb/rdnaModel.trackDb.txt
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    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/trackDb/rnaseq.trackDb.txt
  • lines changed 46, context: html, text, full: html, text
    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/trackDb/sedefSegDups.trackDb.txt
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    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/trackDb/sgdpCopyNumber.trackDb.txt
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    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/chm13v2.0userData/trackDb/t2tRepeatMasker.trackDb.txt
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    4492d656288371cb1802c3a38217acb11bde6368 Thu Jun 15 11:45:05 2023 -0700
    removed obsolete attempt to integrate CHM13 with GenArk
• src/hg/makeDb/doc/galGal5/fantom5.txt
  • lines changed 21, context: html, text, full: html, text
    3fd174ec070cdd1cd53b276e135c76c869859a4b Mon Jun 12 00:19:18 2023 -0700
    Making FANTOM5 hub into native track, refs #21605
• src/hg/makeDb/doc/hg19.txt
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    3fd174ec070cdd1cd53b276e135c76c869859a4b Mon Jun 12 00:19:18 2023 -0700
    Making FANTOM5 hub into native track, refs #21605
• src/hg/makeDb/doc/hg38/fantom5.txt
  • lines changed 21, context: html, text, full: html, text
    3fd174ec070cdd1cd53b276e135c76c869859a4b Mon Jun 12 00:19:18 2023 -0700
    Making FANTOM5 hub into native track, refs #21605
• src/hg/makeDb/doc/hg38/problematic.txt
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    13d78f3b0149c4d9216fb78f28fbd9f91c088237 Tue Jun 13 15:50:10 2023 -0700
    Remove sample level high repro region beds and replace with a single overlapped item bed, refs #31122
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    2bdb4c4bf6c6b3525de22edaf18815061acd800b Wed Jun 14 13:43:45 2023 -0700
    Change highRepro bed track to a bigBed 9 so filters can work, refs #31122
• src/hg/makeDb/doc/mm10.txt
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    3fd174ec070cdd1cd53b276e135c76c869859a4b Mon Jun 12 00:19:18 2023 -0700
    Making FANTOM5 hub into native track, refs #21605
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    7c371e97e282fccecaf3cc8e0109c69a36a9caf3 Mon Jun 12 12:57:28 2023 -0700
    completed liftOver to GCA_001624675.1 no redmine
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• src/hg/makeDb/trackDb/chicken/galGal5/fantom5.ra
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    3765ac407abd18d240ad41ee087e39fd5ef3d3d4 Tue Jun 13 16:36:29 2023 -0700
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    3765ac407abd18d240ad41ee087e39fd5ef3d3d4 Tue Jun 13 16:36:29 2023 -0700
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    3765ac407abd18d240ad41ee087e39fd5ef3d3d4 Tue Jun 13 16:36:29 2023 -0700
    Add a description of the highly reproducible regions tracks to the problematic regions track, get release tags working so description doesn't go out until the track is ready, refs #31122
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    c116020240a724bf9ee3501da8e5cdcd1dc79847 Mon Jun 19 15:12:27 2023 -0700
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• src/hg/makeDb/trackDb/human/hg38/trackDb.447way.ra
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    0475bf97636771eb7aaeebf032de1a647c87c0dc Mon Jun 12 12:52:59 2023 -0700
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    Making FANTOM5 hub into native track, refs #21605
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    0475bf97636771eb7aaeebf032de1a647c87c0dc Mon Jun 12 12:52:59 2023 -0700
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    3765ac407abd18d240ad41ee087e39fd5ef3d3d4 Tue Jun 13 16:36:29 2023 -0700
    Add a description of the highly reproducible regions tracks to the problematic regions track, get release tags working so description doesn't go out until the track is ready, refs #31122
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV43.ra
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• src/hg/makeDb/trackDb/mouse/mm10/fantom5.ra
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    Making FANTOM5 hub into native track, refs #21605
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
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    3fd174ec070cdd1cd53b276e135c76c869859a4b Mon Jun 12 00:19:18 2023 -0700
    Making FANTOM5 hub into native track, refs #21605
• src/hg/makeDb/trackDb/mouse/mm39/knownGene.ra
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• src/hg/makeDb/trackDb/rat/rn6/fantom5.ra
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    Making FANTOM5 hub into native track, refs #21605
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    Making FANTOM5 hub into native track, refs #21605
• src/hg/makeDb/trackDb/rhesus/rheMac8/fantom5.ra
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    3fd174ec070cdd1cd53b276e135c76c869859a4b Mon Jun 12 00:19:18 2023 -0700
    Making FANTOM5 hub into native track, refs #21605
• src/hg/makeDb/trackDb/rhesus/rheMac8/trackDb.ra
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    3fd174ec070cdd1cd53b276e135c76c869859a4b Mon Jun 12 00:19:18 2023 -0700
    Making FANTOM5 hub into native track, refs #21605
• src/hg/makeDb/trackDb/tagTypes.tab
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    0475bf97636771eb7aaeebf032de1a647c87c0dc Mon Jun 12 12:52:59 2023 -0700
    adding Cactus 447-way no redmine
• src/hg/makeDb/trackDb/trackDb.ra
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• src/hg/pslCDnaFilter/hapRegions.c
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    fixed a couple of calls to pslTransMap to add new alignments
• src/hg/utils/hubCheck/tests/input/badType.txt
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    f697b7634598c60ac8ccef17e988867512d1d94a Wed Jun 14 09:47:16 2023 -0700
    Change test hub genome to a real one so as not to bring up spurious errors, refs build email
• src/inc/psl.h
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    0919ab12c7fff4d83613273cad9d7a13b1af668c Mon Jun 12 19:29:34 2023 -0700
    allow pslMapPostChain handle protein/NA alignments
• src/inc/pslTransMap.h
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    a97f8a0fffb31a2b3521e573a03f454fb60275d3 Tue May 30 21:30:12 2023 -0700
    Add mechnaism to fix problem with mapping prot-prot via prot-na alignment by explictly specifying the type of alignments
• src/lib/htmshell.c
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    Proof of concept tutorial overlay done
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• src/lib/pslTransMap.c
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    195a08fae15bd2ca55f2f2ed11d0c359521efcc4 Wed May 17 09:13:21 2023 -0700
    added program to convert protein/protein or protein NA PSLs to NA/NA PSLs. The multiplies coordinates by three; trimming any overlapping blocks that might be creates. This is intended to use with pslMap
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    a97f8a0fffb31a2b3521e573a03f454fb60275d3 Tue May 30 21:30:12 2023 -0700
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    a4887527b333527019132f93bfcebab37e594b5a Sat Jun 10 12:17:57 2023 -0700
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• src/utils/makefile
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    195a08fae15bd2ca55f2f2ed11d0c359521efcc4 Wed May 17 09:13:21 2023 -0700
    added program to convert protein/protein or protein NA PSLs to NA/NA PSLs. The multiplies coordinates by three; trimming any overlapping blocks that might be creates. This is intended to use with pslMap
• src/utils/pslMap/pslMap.c
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    a97f8a0fffb31a2b3521e573a03f454fb60275d3 Tue May 30 21:30:12 2023 -0700
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• src/utils/pslMap/tests/expected/testProtNa_NaNa.psl
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• src/utils/pslMap/tests/expected/testProtPort_ProtNa.mapinfo
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• src/utils/pslMap/tests/expected/testProtPort_ProtNa.psl
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• src/utils/pslMap/tests/expected/testProtPort_ProtProt.psl
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• src/utils/pslMap/tests/expected/testProtProt_NaNa.psl
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    a97f8a0fffb31a2b3521e573a03f454fb60275d3 Tue May 30 21:30:12 2023 -0700
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    a97f8a0fffb31a2b3521e573a03f454fb60275d3 Tue May 30 21:30:12 2023 -0700
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    a97f8a0fffb31a2b3521e573a03f454fb60275d3 Tue May 30 21:30:12 2023 -0700
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• src/utils/pslMap/usage.txt
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• src/utils/pslMapPostChain/pslMapPostChain.c
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    0919ab12c7fff4d83613273cad9d7a13b1af668c Mon Jun 12 19:29:34 2023 -0700
    allow pslMapPostChain handle protein/NA alignments
• src/utils/pslMapPostChain/tests/expected/blastProtRnaTest.psl
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    0919ab12c7fff4d83613273cad9d7a13b1af668c Mon Jun 12 19:29:34 2023 -0700
    allow pslMapPostChain handle protein/NA alignments
• src/utils/pslMapPostChain/tests/input/blastProtRna.psl
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    0919ab12c7fff4d83613273cad9d7a13b1af668c Mon Jun 12 19:29:34 2023 -0700
    allow pslMapPostChain handle protein/NA alignments
• src/utils/pslMapPostChain/tests/makefile
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    0919ab12c7fff4d83613273cad9d7a13b1af668c Mon Jun 12 19:29:34 2023 -0700
    allow pslMapPostChain handle protein/NA alignments
• src/utils/pslProtToRnaCoords/makefile
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    195a08fae15bd2ca55f2f2ed11d0c359521efcc4 Wed May 17 09:13:21 2023 -0700
    added program to convert protein/protein or protein NA PSLs to NA/NA PSLs. The multiplies coordinates by three; trimming any overlapping blocks that might be creates. This is intended to use with pslMap
• src/utils/pslProtToRnaCoords/pslProtToRnaCoords.c
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    195a08fae15bd2ca55f2f2ed11d0c359521efcc4 Wed May 17 09:13:21 2023 -0700
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• src/utils/pslProtToRnaCoords/tests/expected/kgProtTest.psl
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    195a08fae15bd2ca55f2f2ed11d0c359521efcc4 Wed May 17 09:13:21 2023 -0700
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    updated test results based on fixes elsewhere
• src/utils/pslProtToRnaCoords/tests/expected/spAnnotTest.psl
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    195a08fae15bd2ca55f2f2ed11d0c359521efcc4 Wed May 17 09:13:21 2023 -0700
    added program to convert protein/protein or protein NA PSLs to NA/NA PSLs. The multiplies coordinates by three; trimming any overlapping blocks that might be creates. This is intended to use with pslMap
• src/utils/pslProtToRnaCoords/tests/expected/spGencodeTest.psl
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    195a08fae15bd2ca55f2f2ed11d0c359521efcc4 Wed May 17 09:13:21 2023 -0700
    added program to convert protein/protein or protein NA PSLs to NA/NA PSLs. The multiplies coordinates by three; trimming any overlapping blocks that might be creates. This is intended to use with pslMap
• src/utils/pslProtToRnaCoords/tests/expected/spIsoCanonTest.psl
  • lines changed 1, context: html, text, full: html, text
    195a08fae15bd2ca55f2f2ed11d0c359521efcc4 Wed May 17 09:13:21 2023 -0700
    added program to convert protein/protein or protein NA PSLs to NA/NA PSLs. The multiplies coordinates by three; trimming any overlapping blocks that might be creates. This is intended to use with pslMap
• src/utils/pslProtToRnaCoords/tests/input/swissprotAnnotsToProt.psl
  • lines changed 1, context: html, text, full: html, text
    195a08fae15bd2ca55f2f2ed11d0c359521efcc4 Wed May 17 09:13:21 2023 -0700
    added program to convert protein/protein or protein NA PSLs to NA/NA PSLs. The multiplies coordinates by three; trimming any overlapping blocks that might be creates. This is intended to use with pslMap
• src/utils/pslProtToRnaCoords/tests/input/swissprotGencode.psl
  • lines changed 88, context: html, text, full: html, text
    195a08fae15bd2ca55f2f2ed11d0c359521efcc4 Wed May 17 09:13:21 2023 -0700
    added program to convert protein/protein or protein NA PSLs to NA/NA PSLs. The multiplies coordinates by three; trimming any overlapping blocks that might be creates. This is intended to use with pslMap
• src/utils/pslProtToRnaCoords/tests/input/swissprotIsoCanon.psl
  • lines changed 1, context: html, text, full: html, text
    195a08fae15bd2ca55f2f2ed11d0c359521efcc4 Wed May 17 09:13:21 2023 -0700
    added program to convert protein/protein or protein NA PSLs to NA/NA PSLs. The multiplies coordinates by three; trimming any overlapping blocks that might be creates. This is intended to use with pslMap
• src/utils/pslProtToRnaCoords/tests/makefile
  • lines changed 42, context: html, text, full: html, text
    195a08fae15bd2ca55f2f2ed11d0c359521efcc4 Wed May 17 09:13:21 2023 -0700
    added program to convert protein/protein or protein NA PSLs to NA/NA PSLs. The multiplies coordinates by three; trimming any overlapping blocks that might be creates. This is intended to use with pslMap
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    39360281905f83bf6c258d77a3b78382ef372178 Tue Jun 20 09:54:09 2023 -0700
    v450 preview2, refs #31506
• src/utils/userApps/fetchChromSizes
  • lines changed 1, context: html, text, full: html, text
    0b612ae13030153b427d971498a9a31be06e1fa6 Mon Jun 12 14:33:45 2023 -0700
    Changing code syntax from == to = reported by a user, refs #31377

• lines changed: 261376
• files changed: 177