All File Changes

v389_preview2 to v389_base (2019-10-07 to 2019-10-14) v389

• src/hg/cirm/cdw/cdwMakeFileTags/cdwMakeFileTags.c
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    10c9ea3293d43e8b5640bd7c07164d1a0d01d059 Fri Oct 11 16:27:24 2019 -0700
    fixes #22990. removing read_size column from faceted-field list as requested.
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 1, context: html, text, full: html, text
    10c9ea3293d43e8b5640bd7c07164d1a0d01d059 Fri Oct 11 16:27:24 2019 -0700
    fixes #22990. removing read_size column from faceted-field list as requested.
  • lines changed 1, context: html, text, full: html, text
    3639ec7fcb4926e92bc9da09c0a5dd81ab7b05b3 Fri Oct 11 23:02:28 2019 -0700
    Removing TabToSave from download page. More trouble to fix than it was worth. fixes RM#22202.
• src/hg/hgSession/hgSession.c
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    4a5ae434b97f4539c685b10c92813077361ea3f7 Mon Oct 14 10:15:46 2019 -0700
    database variable should be global no redmine
• src/hg/hgTracks/bedTrack.c
  • lines changed 6, context: html, text, full: html, text
    0440cfd6ef79932ae3d3d1934d9665b2848e8952 Mon Oct 7 14:54:50 2019 -0700
    Add filter activated notice to bigNarrowPeak. refs #24271
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    51d89ce7eda1b4b3a8669379230be74ec76e8150 Mon Oct 7 15:00:54 2019 -0700
    Fixes and flexibility for other track types, new filtering. refs #23365
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 6, context: html, text, full: html, text
    0440cfd6ef79932ae3d3d1934d9665b2848e8952 Mon Oct 7 14:54:50 2019 -0700
    Add filter activated notice to bigNarrowPeak. refs #24271
  • lines changed 1, context: html, text, full: html, text
    51d89ce7eda1b4b3a8669379230be74ec76e8150 Mon Oct 7 15:00:54 2019 -0700
    Fixes and flexibility for other track types, new filtering. refs #23365
• src/hg/hgTracks/encode.c
  • lines changed 2, context: html, text, full: html, text
    0440cfd6ef79932ae3d3d1934d9665b2848e8952 Mon Oct 7 14:54:50 2019 -0700
    Add filter activated notice to bigNarrowPeak. refs #24271
• src/hg/hgTracks/hgTracks.c
  • lines changed 6, context: html, text, full: html, text
    0440cfd6ef79932ae3d3d1934d9665b2848e8952 Mon Oct 7 14:54:50 2019 -0700
    Add filter activated notice to bigNarrowPeak. refs #24271
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    0440cfd6ef79932ae3d3d1934d9665b2848e8952 Mon Oct 7 14:54:50 2019 -0700
    Add filter activated notice to bigNarrowPeak. refs #24271
• src/hg/hgc/interactClick.c
  • lines changed 12, context: html, text, full: html, text
    ff9f567866c9c0e9e429e010fcdde9b6af5ea92e Mon Oct 14 10:07:49 2019 -0700
    Add collapsible panel for details of individual interactions in a cluster. Requested by QA. refs #24037
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 3, context: html, text, full: html, text
    318a5c110a86569bd4e4b8fd7263c684245e6049 Thu Oct 10 10:54:48 2019 -0700
    Changing JSON API to REST API and adding new entry to API help page refs #24282
• src/hg/htdocs/goldenPath/gbdDescriptions.html
  • lines changed 1, context: html, text, full: html, text
    318a5c110a86569bd4e4b8fd7263c684245e6049 Thu Oct 10 10:54:48 2019 -0700
    Changing JSON API to REST API and adding new entry to API help page refs #24282
• src/hg/htdocs/goldenPath/help/api.html
  • lines changed 16, context: html, text, full: html, text
    318a5c110a86569bd4e4b8fd7263c684245e6049 Thu Oct 10 10:54:48 2019 -0700
    Changing JSON API to REST API and adding new entry to API help page refs #24282
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 2, context: html, text, full: html, text
    318a5c110a86569bd4e4b8fd7263c684245e6049 Thu Oct 10 10:54:48 2019 -0700
    Changing JSON API to REST API and adding new entry to API help page refs #24282
• src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html
  • lines changed 3, context: html, text, full: html, text
    cc090f632344b7b43c2abad394ca9d4f4c62ed17 Thu Oct 10 15:44:43 2019 -0700
    Adding note about group auto-scale refs #3420
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html
  • lines changed 3, context: html, text, full: html, text
    6d5b5b9941f013a6cd0e8d7cb4d0df70b3f38e2c Tue Oct 8 11:31:28 2019 -0700
    Adding class new to new settings (forgot bout that).
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 21, context: html, text, full: html, text
    cde60ba0f1009a6bccbe1d0da148100dccd12468 Tue Oct 8 14:49:50 2019 -0700
    Releasing crisprAllTargets for hg38, refs #24172
  • lines changed 1, context: html, text, full: html, text
    3731d246a3536ab46a008dd6652656ebe14381c8 Tue Oct 8 16:30:05 2019 -0700
    Editing text for crisprAllTargets track, refs #24172
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    d9535c7a71dcab75772ae9e1bb900f1f32fbfd38 Thu Oct 10 16:10:09 2019 -0700
    Adding group auto-scale setting announcement refs #3420
  • lines changed 6, context: html, text, full: html, text
    7cbbd19f17a3044b489c37e460643e7826eb6022 Thu Oct 10 16:19:11 2019 -0700
    Adjusting image size auto-scale setting announcement refs #3420
• src/hg/htdocs/images/crisperAllTargetsHg38.png
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    cde60ba0f1009a6bccbe1d0da148100dccd12468 Tue Oct 8 14:49:50 2019 -0700
    Releasing crisprAllTargets for hg38, refs #24172
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    9a08d8d2fd4143cfa2d0877c201b16d5e963dcf4 Tue Oct 8 16:28:34 2019 -0700
    Editing image for crisprAllTargets track, refs #24172
• src/hg/htdocs/images/groupAutoScale.png
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    d9535c7a71dcab75772ae9e1bb900f1f32fbfd38 Thu Oct 10 16:10:09 2019 -0700
    Adding group auto-scale setting announcement refs #3420
• src/hg/htdocs/images/groupAutoSetting.png
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    d9535c7a71dcab75772ae9e1bb900f1f32fbfd38 Thu Oct 10 16:10:09 2019 -0700
    Adding group auto-scale setting announcement refs #3420
• src/hg/htdocs/images/hicDrawModes.png
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    0cb0b3c1c2b71b0fc116b1d1aeb5ad7f67e6f469 Wed Oct 9 15:24:42 2019 -0700
    Fixing external image reference to be internal, refs #24273
• src/hg/htdocs/inc/gbPageStartHardcoded.html
  • lines changed 1, context: html, text, full: html, text
    318a5c110a86569bd4e4b8fd7263c684245e6049 Thu Oct 10 10:54:48 2019 -0700
    Changing JSON API to REST API and adding new entry to API help page refs #24282
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 1, context: html, text, full: html, text
    318a5c110a86569bd4e4b8fd7263c684245e6049 Thu Oct 10 10:54:48 2019 -0700
    Changing JSON API to REST API and adding new entry to API help page refs #24282
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    8ccb4a6b98feda58e8ab1f383a5f4aee61a27830 Wed Oct 9 09:20:42 2019 -0700
    Updating indexNews for the hg38 cripsrAllTargets release, refs #24172
  • lines changed 7, context: html, text, full: html, text
    27de55159563a0f0efb200b962048e51dc475523 Fri Oct 11 11:07:29 2019 -0700
    Adding group auto-scale announcement on indexNews at request refs #3420
• src/hg/hubApi/apiUtils.c
  • lines changed 4, context: html, text, full: html, text
    8548a5903f6181e2912ce0e584a0f56240de1858 Thu Oct 10 10:58:23 2019 -0700
    extend supported types for schema display to bigBarChart bigInteract and bigLolly and correct indicate not supported VCF types refs #23589
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    20d72f662e55fd7c611413dbb471a3a2714b9684 Thu Oct 10 14:09:53 2019 -0700
    newly supported type wigMaf refs #23589
• src/hg/hubApi/dataApi.h
  • lines changed 3, context: html, text, full: html, text
    20d72f662e55fd7c611413dbb471a3a2714b9684 Thu Oct 10 14:09:53 2019 -0700
    newly supported type wigMaf refs #23589
• src/hg/hubApi/getData.c
  • lines changed 6, context: html, text, full: html, text
    20d72f662e55fd7c611413dbb471a3a2714b9684 Thu Oct 10 14:09:53 2019 -0700
    newly supported type wigMaf refs #23589
• src/hg/hubApi/hubApi.c
  • lines changed 2, context: html, text, full: html, text
    20d72f662e55fd7c611413dbb471a3a2714b9684 Thu Oct 10 14:09:53 2019 -0700
    newly supported type wigMaf refs #23589
  • lines changed 2, context: html, text, full: html, text
    3b8b0dfa4a74833c50166b85257ebaf1affe5a06 Thu Oct 10 16:35:41 2019 -0700
    adding bigLolly type support
  • lines changed 7, context: html, text, full: html, text
    748c56e2d262310331911bee681b3608d7879051 Fri Oct 11 14:07:48 2019 -0700
    adding track types bigBarChart bigInteract clonePos refs #23589
• src/hg/hubApi/list.c
  • lines changed 25, context: html, text, full: html, text
    8548a5903f6181e2912ce0e584a0f56240de1858 Thu Oct 10 10:58:23 2019 -0700
    extend supported types for schema display to bigBarChart bigInteract and bigLolly and correct indicate not supported VCF types refs #23589
• src/hg/hubApi/tests/expected/list03.gz
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    5c53dedf24121412e28b539cdfba8f2891d60bee Thu Oct 10 11:31:59 2019 -0700
    up to date track list for ce11 refs #23589
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    7fea9ff255a6436de9e6095d69553d8b5bb75778 Thu Oct 10 12:58:47 2019 -0700
    only compare track name listings on the /list/tracks function to avoid the confusion of changing genbank tables messing up the comparison refs #23589
• src/hg/hubApi/tests/expected/list09.gz
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    5c53dedf24121412e28b539cdfba8f2891d60bee Thu Oct 10 11:31:59 2019 -0700
    up to date track list for ce11 refs #23589
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    7fea9ff255a6436de9e6095d69553d8b5bb75778 Thu Oct 10 12:58:47 2019 -0700
    only compare track name listings on the /list/tracks function to avoid the confusion of changing genbank tables messing up the comparison refs #23589
• src/hg/hubApi/tests/expected/list18.gz
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    25149d3a1dafdf85838536e178b5e66515f8736b Thu Oct 10 14:08:11 2019 -0700
    testing newly supported type wigMaf refs #23589
• src/hg/hubApi/tests/expected/notSup04.gz
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    e017e5e9d410b7f882fa5d9f343d7735b438a476 Fri Oct 11 15:27:26 2019 -0700
    remove obsolete test results refs #23589
• src/hg/hubApi/tests/expected/notSup05.gz
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    e017e5e9d410b7f882fa5d9f343d7735b438a476 Fri Oct 11 15:27:26 2019 -0700
    remove obsolete test results refs #23589
• src/hg/hubApi/tests/expected/notSup06.gz
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    e017e5e9d410b7f882fa5d9f343d7735b438a476 Fri Oct 11 15:27:26 2019 -0700
    remove obsolete test results refs #23589
• src/hg/hubApi/tests/expected/schema08.gz
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    25149d3a1dafdf85838536e178b5e66515f8736b Thu Oct 10 14:08:11 2019 -0700
    testing newly supported type wigMaf refs #23589
• src/hg/hubApi/tests/expected/schema09.gz
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    3b8b0dfa4a74833c50166b85257ebaf1affe5a06 Thu Oct 10 16:35:41 2019 -0700
    adding bigLolly type support
• src/hg/hubApi/tests/expected/schema10.gz
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    748c56e2d262310331911bee681b3608d7879051 Fri Oct 11 14:07:48 2019 -0700
    adding track types bigBarChart bigInteract clonePos refs #23589
• src/hg/hubApi/tests/expected/schema11.gz
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    748c56e2d262310331911bee681b3608d7879051 Fri Oct 11 14:07:48 2019 -0700
    adding track types bigBarChart bigInteract clonePos refs #23589
• src/hg/hubApi/tests/expected/schema12.gz
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    748c56e2d262310331911bee681b3608d7879051 Fri Oct 11 14:07:48 2019 -0700
    adding track types bigBarChart bigInteract clonePos refs #23589
• src/hg/hubApi/tests/expected/test26.gz
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    5c53dedf24121412e28b539cdfba8f2891d60bee Thu Oct 10 11:31:59 2019 -0700
    up to date track list for ce11 refs #23589
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    9ef5f7a93d3b60eeb501170a76be3e5b019bf6ae Thu Oct 10 12:51:22 2019 -0700
    eliminate dependency on genbank changing track to test genePred refs #23589
• src/hg/hubApi/tests/expected/test42.gz
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    25149d3a1dafdf85838536e178b5e66515f8736b Thu Oct 10 14:08:11 2019 -0700
    testing newly supported type wigMaf refs #23589
• src/hg/hubApi/tests/expected/test43.gz
  • lines changed 0, context: html, text, full: html, text
    25149d3a1dafdf85838536e178b5e66515f8736b Thu Oct 10 14:08:11 2019 -0700
    testing newly supported type wigMaf refs #23589
• src/hg/hubApi/tests/expected/test44.gz
  • lines changed 0, context: html, text, full: html, text
    25149d3a1dafdf85838536e178b5e66515f8736b Thu Oct 10 14:08:11 2019 -0700
    testing newly supported type wigMaf refs #23589
• src/hg/hubApi/tests/expected/test45.gz
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    3b8b0dfa4a74833c50166b85257ebaf1affe5a06 Thu Oct 10 16:35:41 2019 -0700
    adding bigLolly type support
• src/hg/hubApi/tests/expected/test46.gz
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    3b8b0dfa4a74833c50166b85257ebaf1affe5a06 Thu Oct 10 16:35:41 2019 -0700
    adding bigLolly type support
• src/hg/hubApi/tests/expected/test47.gz
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    3b8b0dfa4a74833c50166b85257ebaf1affe5a06 Thu Oct 10 16:35:41 2019 -0700
    adding bigLolly type support
• src/hg/hubApi/tests/expected/test48.gz
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    748c56e2d262310331911bee681b3608d7879051 Fri Oct 11 14:07:48 2019 -0700
    adding track types bigBarChart bigInteract clonePos refs #23589
• src/hg/hubApi/tests/expected/test49.gz
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    748c56e2d262310331911bee681b3608d7879051 Fri Oct 11 14:07:48 2019 -0700
    adding track types bigBarChart bigInteract clonePos refs #23589
• src/hg/hubApi/tests/expected/test50.gz
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    748c56e2d262310331911bee681b3608d7879051 Fri Oct 11 14:07:48 2019 -0700
    adding track types bigBarChart bigInteract clonePos refs #23589
• src/hg/hubApi/tests/expected/test51.gz
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    748c56e2d262310331911bee681b3608d7879051 Fri Oct 11 14:07:48 2019 -0700
    adding track types bigBarChart bigInteract clonePos refs #23589
• src/hg/hubApi/tests/expected/test52.gz
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    748c56e2d262310331911bee681b3608d7879051 Fri Oct 11 14:07:48 2019 -0700
    adding track types bigBarChart bigInteract clonePos refs #23589
• src/hg/hubApi/tests/expected/test53.gz
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    748c56e2d262310331911bee681b3608d7879051 Fri Oct 11 14:07:48 2019 -0700
    adding track types bigBarChart bigInteract clonePos refs #23589
• src/hg/hubApi/tests/expected/test54.gz
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    748c56e2d262310331911bee681b3608d7879051 Fri Oct 11 14:07:48 2019 -0700
    adding track types bigBarChart bigInteract clonePos refs #23589
• src/hg/hubApi/tests/expected/test55.gz
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    748c56e2d262310331911bee681b3608d7879051 Fri Oct 11 14:07:48 2019 -0700
    adding track types bigBarChart bigInteract clonePos refs #23589
• src/hg/hubApi/tests/expected/test56.gz
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    748c56e2d262310331911bee681b3608d7879051 Fri Oct 11 14:07:48 2019 -0700
    adding track types bigBarChart bigInteract clonePos refs #23589
• src/hg/hubApi/tests/makefile
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    9c835eff071e0d0439042a30012634119712bc27 Thu Oct 10 11:34:10 2019 -0700
    updated error testing refs #23589
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    9ef5f7a93d3b60eeb501170a76be3e5b019bf6ae Thu Oct 10 12:51:22 2019 -0700
    eliminate dependency on genbank changing track to test genePred refs #23589
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    7fea9ff255a6436de9e6095d69553d8b5bb75778 Thu Oct 10 12:58:47 2019 -0700
    only compare track name listings on the /list/tracks function to avoid the confusion of changing genbank tables messing up the comparison refs #23589
  • lines changed 36, context: html, text, full: html, text
    25149d3a1dafdf85838536e178b5e66515f8736b Thu Oct 10 14:08:11 2019 -0700
    testing newly supported type wigMaf refs #23589
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    3b8b0dfa4a74833c50166b85257ebaf1affe5a06 Thu Oct 10 16:35:41 2019 -0700
    adding bigLolly type support
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    748c56e2d262310331911bee681b3608d7879051 Fri Oct 11 14:07:48 2019 -0700
    adding track types bigBarChart bigInteract clonePos refs #23589
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    360e462570bd06a078eaea70efdc84d5498db76a Fri Oct 11 15:24:42 2019 -0700
    eliminate tests for not supported as they are now supported refs #23589
• src/hg/inc/hui.h
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    0440cfd6ef79932ae3d3d1934d9665b2848e8952 Mon Oct 7 14:54:50 2019 -0700
    Add filter activated notice to bigNarrowPeak. refs #24271
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    51d89ce7eda1b4b3a8669379230be74ec76e8150 Mon Oct 7 15:00:54 2019 -0700
    Fixes and flexibility for other track types, new filtering. refs #23365
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    c1f5ad256c535d3dcf03c897a8728a4dbc30ae86 Mon Oct 14 10:36:34 2019 -0700
    New version number v389
• src/hg/lib/bigBedFind.c
  • lines changed 27, context: html, text, full: html, text
    e25660cfe3e40f77688852171a4868c0784afa69 Fri Oct 11 12:56:01 2019 -0700
    Fixing error in assembly hub composite track search; also, don't default to bigBed name index unless a searchSpec (hfs) is given. refs #24238
• src/hg/lib/hui.c
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    32d3adcbf1d7b6d589e7213beac07291d2369fa7 Mon Oct 7 11:02:29 2019 -0700
    require that FilterValues have a value in trackDb
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    0440cfd6ef79932ae3d3d1934d9665b2848e8952 Mon Oct 7 14:54:50 2019 -0700
    Add filter activated notice to bigNarrowPeak. refs #24271
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    51d89ce7eda1b4b3a8669379230be74ec76e8150 Mon Oct 7 15:00:54 2019 -0700
    Fixes and flexibility for other track types, new filtering. refs #23365
  • lines changed 151, context: html, text, full: html, text
    a66704e3ade50461e9be68288199903410f4f31e Fri Oct 11 12:36:01 2019 -0700
    remove EXTRA_FIELDS support which was a failed experiment, support "." syntax with FILTER_TEXT, suppress automatic filter if text filter is set.
• src/hg/makeDb/doc/hg19.txt
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    68330303d5124f562b963ace7e4e808e7c8981d9 Mon Oct 7 16:38:44 2019 -0700
    Initial commit of Hi-C native tracks on hg19 and hg38, refs #18842
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    fbd7a94213923088270a2bc3da63d0b8139451f0 Thu Oct 10 14:33:52 2019 -0700
    LRG now distinguishes between fix_patch and novel_patch in their XML, so we can include mappings to fix & alt patch sequences. Overdue for an update anyway. refs #24285
• src/hg/makeDb/doc/hg38/gnomad.txt
  • lines changed 52, context: html, text, full: html, text
    d88101b2f5f3804786bcd15ee7e75fb8270bdc32 Tue Oct 8 11:09:51 2019 -0700
    gnomAD variants track for hg38. Quick track load for SAB. refs #21782
  • lines changed 9, context: html, text, full: html, text
    c9e2acd282cda244daf6e9ecb4feaea2b1994df7 Tue Oct 8 11:25:31 2019 -0700
    Adding download times to build doc. refs #21782
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 26, context: html, text, full: html, text
    68330303d5124f562b963ace7e4e808e7c8981d9 Mon Oct 7 16:38:44 2019 -0700
    Initial commit of Hi-C native tracks on hg19 and hg38, refs #18842
  • lines changed 11, context: html, text, full: html, text
    fbd7a94213923088270a2bc3da63d0b8139451f0 Thu Oct 10 14:33:52 2019 -0700
    LRG now distinguishes between fix_patch and novel_patch in their XML, so we can include mappings to fix & alt patch sequences. Overdue for an update anyway. refs #24285
• src/hg/makeDb/doc/mm10.txt
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    c528cca108442ed73954b1ab87e64088c7c7c7d1 Mon Oct 7 14:23:18 2019 -0700
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    68330303d5124f562b963ace7e4e808e7c8981d9 Mon Oct 7 16:38:44 2019 -0700
    Initial commit of Hi-C native tracks on hg19 and hg38, refs #18842
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    6c8913cd8543363f45ca3123d99ac374dff31e95 Mon Oct 7 17:18:46 2019 -0700
    Slight documentation change for Hi-C native track on hg38, refs #18842
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    8071f305cf8ac1840edc31419e18de85f320d0da Wed Oct 9 12:01:07 2019 -0700
    Adding Data Access section to track docs, refs #18842
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    0cb0b3c1c2b71b0fc116b1d1aeb5ad7f67e6f469 Wed Oct 9 15:24:42 2019 -0700
    Fixing external image reference to be internal, refs #24273
• src/hg/makeDb/trackDb/human/hg38/knownGene.back
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    7f892f8fa5f41b18d489cfdbb0255c05b1b3e3f3 Mon Oct 7 10:55:15 2019 -0700
    Updating http to https for hg19, uiLinks cronjob.
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    05fe2aa1f5c3f2730cdc72669b9cda4bd74d455f Mon Oct 7 12:01:25 2019 -0700
    Staging the v32 GENCODE track for hg38. Copying the contents from knownGene.alpha.html to the live HTML file. Removing an accidentally added file, knownGene.back (backup of knownGene.ra) from my uiLinks commit. refs #24032
• src/hg/makeDb/trackDb/human/hg38/knownGene.html
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    05fe2aa1f5c3f2730cdc72669b9cda4bd74d455f Mon Oct 7 12:01:25 2019 -0700
    Staging the v32 GENCODE track for hg38. Copying the contents from knownGene.alpha.html to the live HTML file. Removing an accidentally added file, knownGene.back (backup of knownGene.ra) from my uiLinks commit. refs #24032
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra
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    7f892f8fa5f41b18d489cfdbb0255c05b1b3e3f3 Mon Oct 7 10:55:15 2019 -0700
    Updating http to https for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg38/knownGeneOld11.html
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    668414388523c2effa3f4f0948900dd4dd30852d Mon Oct 7 14:19:18 2019 -0700
    Clarifying the previous version in the Old UCSC Genes track description page for hg38, refs #24032
• src/hg/makeDb/trackDb/human/hg38/platinumGenomes.html
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    8d536c01c2c1830957ab16863aaedbf45ecd5c75 Mon Oct 7 15:43:04 2019 -0700
    adding platinum VCF file tracks to hg38 and hg19 refs #21784
• src/hg/makeDb/trackDb/human/hg38/platinumGenomes.ra
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    8d536c01c2c1830957ab16863aaedbf45ecd5c75 Mon Oct 7 15:43:04 2019 -0700
    adding platinum VCF file tracks to hg38 and hg19 refs #21784
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    a33c17e011949877036dce77048b220274dc1feb Mon Oct 7 15:47:58 2019 -0700
    correct symlinks refs #21784
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    a8e19c9657462c53e955bb58de7ef4093fda6d9c Wed Oct 9 11:43:23 2019 -0700
    adding data access section and correct reference refs #21784
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    05fe2aa1f5c3f2730cdc72669b9cda4bd74d455f Mon Oct 7 12:01:25 2019 -0700
    Staging the v32 GENCODE track for hg38. Copying the contents from knownGene.alpha.html to the live HTML file. Removing an accidentally added file, knownGene.back (backup of knownGene.ra) from my uiLinks commit. refs #24032
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    8d536c01c2c1830957ab16863aaedbf45ecd5c75 Mon Oct 7 15:43:04 2019 -0700
    adding platinum VCF file tracks to hg38 and hg19 refs #21784
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    68330303d5124f562b963ace7e4e808e7c8981d9 Mon Oct 7 16:38:44 2019 -0700
    Initial commit of Hi-C native tracks on hg19 and hg38, refs #18842
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    d88101b2f5f3804786bcd15ee7e75fb8270bdc32 Tue Oct 8 11:09:51 2019 -0700
    gnomAD variants track for hg38. Quick track load for SAB. refs #21782
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    898e87ad94321521bcf2330139673df6bfe1cfe5 Tue Oct 8 11:11:16 2019 -0700
    Merge
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    dc3d5f6897654577d4349c40f62ef8f139f2117a Tue Oct 8 13:09:25 2019 -0700
    Add info and pennantIcon about lift, as per AH suggestion. refs #21782
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    9db135f92c1f1ca5445f23101f7617f655827fe7 Wed Oct 9 10:24:45 2019 -0700
    adding platinum VCF tracks refs #21784
• src/hg/makeDb/trackDb/human/hgIkmc.html
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    7f892f8fa5f41b18d489cfdbb0255c05b1b3e3f3 Mon Oct 7 10:55:15 2019 -0700
    Updating http to https for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hiSeqDepth.html
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    7f892f8fa5f41b18d489cfdbb0255c05b1b3e3f3 Mon Oct 7 10:55:15 2019 -0700
    Updating http to https for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/lovd.html
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    7f892f8fa5f41b18d489cfdbb0255c05b1b3e3f3 Mon Oct 7 10:55:15 2019 -0700
    Updating http to https for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/omimAvSnp.html
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    7f892f8fa5f41b18d489cfdbb0255c05b1b3e3f3 Mon Oct 7 10:55:15 2019 -0700
    Updating http to https for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/placentalChainNet.html
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    7f892f8fa5f41b18d489cfdbb0255c05b1b3e3f3 Mon Oct 7 10:55:15 2019 -0700
    Updating http to https for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/platinumGenomes.html
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    a8e19c9657462c53e955bb58de7ef4093fda6d9c Wed Oct 9 11:43:23 2019 -0700
    adding data access section and correct reference refs #21784
• src/hg/makeDb/trackDb/human/primateChainNet.html
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    7f892f8fa5f41b18d489cfdbb0255c05b1b3e3f3 Mon Oct 7 10:55:15 2019 -0700
    Updating http to https for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/snp150Common.html
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    7f892f8fa5f41b18d489cfdbb0255c05b1b3e3f3 Mon Oct 7 10:55:15 2019 -0700
    Updating http to https for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/snp151Common.html
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    7f892f8fa5f41b18d489cfdbb0255c05b1b3e3f3 Mon Oct 7 10:55:15 2019 -0700
    Updating http to https for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/stsMap.html
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    7f892f8fa5f41b18d489cfdbb0255c05b1b3e3f3 Mon Oct 7 10:55:15 2019 -0700
    Updating http to https for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/vertebrateChainNet.html
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    7f892f8fa5f41b18d489cfdbb0255c05b1b3e3f3 Mon Oct 7 10:55:15 2019 -0700
    Updating http to https for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
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    10402810ce85c7070e134f42b13196ffc846c122 Fri Oct 11 08:35:52 2019 -0700
    updating release tags to display gencode vm23 on beta, refs #24087
• src/hg/makeDb/trackDb/recombRate.html
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    7f892f8fa5f41b18d489cfdbb0255c05b1b3e3f3 Mon Oct 7 10:55:15 2019 -0700
    Updating http to https for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/sacCer/multizYeast.html
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    5cf0c242b31fa4d3929d19b485b5c5f5cdf1824e Wed Oct 9 09:46:35 2019 -0700
    Updating http to https for sacCer1, uiLinks cronjob.
• src/hg/makeDb/trackDb/xenTro/xenTro1/multiz5way.html
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    6ca88a128e05455bc0a55b9b40d26779140ba12e Mon Oct 14 09:47:30 2019 -0700
    Updating http to https for xenTro1, uiLinks cronjob.
• src/hg/pslCheck/pslCheck.c
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    89dc43c1ed51a5f783b2e84485864aa5d17d57c5 Thu Oct 10 09:33:07 2019 -0700
    Capture PSL parse errors and report them instead of failing. Add option to act as a filter and not error exit
• src/hg/utils/automation/parseLrgXml.pl
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    fbd7a94213923088270a2bc3da63d0b8139451f0 Thu Oct 10 14:33:52 2019 -0700
    LRG now distinguishes between fix_patch and novel_patch in their XML, so we can include mappings to fix & alt patch sequences. Overdue for an update anyway. refs #24285
• src/hg/utils/hubCheck/hubCheck.c
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    23f8d773ae8d7d57314f9d57692c96a8194f0019 Fri Oct 11 10:02:55 2019 -0700
    Fixing bug where hubCheck thought composites with only one child were multiWigs with only one child, refs #18870#note-61
• src/hg/utils/otto/clinvar/clinVarToBed
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    d8159489a9a2b570997cbc8b198e193d850c65da Tue Oct 8 02:27:29 2019 -0700
    adding a success message to clinvar otto job, no redmine
• src/hg/utils/otto/mastermind/buildMastermind.sh
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    1fc6cdebe7cf85faeebd56f8040a5ff691f5979f Tue Oct 8 08:17:02 2019 -0700
    adding OK message to mastermind otto, no redmine
• src/inc/srcVersion.h
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    c1f5ad256c535d3dcf03c897a8728a4dbc30ae86 Mon Oct 14 10:36:34 2019 -0700
    New version number v389
• src/utils/qa/weeklybld/buildEnv.csh
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    70cfe46bcc68fb2f7167180b944cdb59d7558168 Mon Oct 14 10:32:15 2019 -0700
    v389 final build, refs #NNNNN
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    06eaf5abb2e92a9650777ba4a367f0acceba98f6 Mon Oct 14 10:35:29 2019 -0700
    v389 final build, refs #24238

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