All File Changes

v403_preview to v403_preview2 (2020-08-10 to 2020-08-17) v403

• confs/hgwdev.hg.conf
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    e858179673c346776dfc9d95293d9f84638d1653 Sun Aug 16 01:11:30 2020 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 6, context: html, text, full: html, text
    42f1dc531b4d7d739a1c28b552c4c7dd21823390 Wed Aug 12 10:04:30 2020 -0700
    Move printing of hub search results div to after we've made sure we got a search result, refs #26013
• src/hg/hgSession/hgSession.c
  • lines changed 3, context: html, text, full: html, text
    bd6e3996c720821a29a4eaf6b8e9972e4c98a028 Wed Aug 12 16:50:17 2020 -0700
    Add hg.conf var to enable Recommended Track Sets. Remove hgSession URL mod, in favor of hgTracks detecting non-Track-Set session load. Build patch. refs #25601
• src/hg/hgTracks/hgTracks.c
  • lines changed 5, context: html, text, full: html, text
    bd6e3996c720821a29a4eaf6b8e9972e4c98a028 Wed Aug 12 16:50:17 2020 -0700
    Add hg.conf var to enable Recommended Track Sets. Remove hgSession URL mod, in favor of hgTracks detecting non-Track-Set session load. Build patch. refs #25601
• src/hg/hgTracks/hgTracks.h
  • lines changed 4, context: html, text, full: html, text
    bd6e3996c720821a29a4eaf6b8e9972e4c98a028 Wed Aug 12 16:50:17 2020 -0700
    Add hg.conf var to enable Recommended Track Sets. Remove hgSession URL mod, in favor of hgTracks detecting non-Track-Set session load. Build patch. refs #25601
• src/hg/hgTracks/recTrackSets.c
  • lines changed 25, context: html, text, full: html, text
    bd6e3996c720821a29a4eaf6b8e9972e4c98a028 Wed Aug 12 16:50:17 2020 -0700
    Add hg.conf var to enable Recommended Track Sets. Remove hgSession URL mod, in favor of hgTracks detecting non-Track-Set session load. Build patch. refs #25601
• src/hg/hgc/vcfClick.c
  • lines changed 21, context: html, text, full: html, text
    8ea61fe719baa254eb7411b93cdd3de71c9cc7f3 Thu Aug 13 13:32:18 2020 -0700
    Suppress diploid-specific descriptions when species is not diploid. refs #25409
• src/hg/js/ajax.js
  • lines changed 15, context: html, text, full: html, text
    c8eef4a1e85bcfd8b41e87e287cbf15f09fc357a Sun Aug 16 22:19:22 2020 -0700
    Replacing beforeUnload synchronous updates (blocked by Chrome) with async updates. Also fixing the suggestion box, so following a suggestion turns on the track and highlights the item. refs #25017, #25703
• src/hg/js/autocomplete.js
  • lines changed 2, context: html, text, full: html, text
    c8eef4a1e85bcfd8b41e87e287cbf15f09fc357a Sun Aug 16 22:19:22 2020 -0700
    Replacing beforeUnload synchronous updates (blocked by Chrome) with async updates. Also fixing the suggestion box, so following a suggestion turns on the track and highlights the item. refs #25017, #25703
• src/hg/js/hgTracks.js
  • lines changed 2, context: html, text, full: html, text
    de4b38dd0aff87ec136ba422f09cda5c284e0e21 Fri Aug 14 13:50:43 2020 -0700
    Fixing overly ambitious hgTrackUi link selector which broke track search metadata dropdowns and pagination, fixes #25969 and #25968
  • lines changed 40, context: html, text, full: html, text
    c8eef4a1e85bcfd8b41e87e287cbf15f09fc357a Sun Aug 16 22:19:22 2020 -0700
    Replacing beforeUnload synchronous updates (blocked by Chrome) with async updates. Also fixing the suggestion box, so following a suggestion turns on the track and highlights the item. refs #25017, #25703
• src/hg/lib/liftOver.c
  • lines changed 4, context: html, text, full: html, text
    da79c37696a46e9978a93218407e6afcdc71326c Fri Aug 14 17:45:37 2020 -0700
    Fixed bug in hgLiftOver CGI and liftOver utility reported by user. Also tested liftability of knwonGene on Chr1 to panTro6. All remining cases of Boundary error are real and not due to a bug. Added test cases, especially for BED12 which had been oddly missing. refs #26057.
• src/hg/liftOver/tests/expected/bed12.bed
  • lines changed 2, context: html, text, full: html, text
    da79c37696a46e9978a93218407e6afcdc71326c Fri Aug 14 17:45:37 2020 -0700
    Fixed bug in hgLiftOver CGI and liftOver utility reported by user. Also tested liftability of knwonGene on Chr1 to panTro6. All remining cases of Boundary error are real and not due to a bug. Added test cases, especially for BED12 which had been oddly missing. refs #26057.
• src/hg/liftOver/tests/input/bed12.bed
  • lines changed 2, context: html, text, full: html, text
    da79c37696a46e9978a93218407e6afcdc71326c Fri Aug 14 17:45:37 2020 -0700
    Fixed bug in hgLiftOver CGI and liftOver utility reported by user. Also tested liftability of knwonGene on Chr1 to panTro6. All remining cases of Boundary error are real and not due to a bug. Added test cases, especially for BED12 which had been oddly missing. refs #26057.
• src/hg/liftOver/tests/makefile
  • lines changed 3, context: html, text, full: html, text
    da79c37696a46e9978a93218407e6afcdc71326c Fri Aug 14 17:45:37 2020 -0700
    Fixed bug in hgLiftOver CGI and liftOver utility reported by user. Also tested liftability of knwonGene on Chr1 to panTro6. All remining cases of Boundary error are real and not due to a bug. Added test cases, especially for BED12 which had been oddly missing. refs #26057.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 31, context: html, text, full: html, text
    2fd288fe28c984b85b1c51fff4ea5ce46caad329 Thu Aug 13 19:17:29 2020 -0700
    adding ncbiRefSeqGenomicDiff track to hg19 refs #20215
• src/hg/makeDb/trackDb/cow/bosTau4/multiz5way.html
  • lines changed 1, context: html, text, full: html, text
    d459290c3875e48bf31b9ceb19ac4bf20100daf6 Wed Jul 22 09:30:17 2020 -0700
    Updating redirectd links found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/cow/bosTau4/nscanGene.html
  • lines changed 1, context: html, text, full: html, text
    d459290c3875e48bf31b9ceb19ac4bf20100daf6 Wed Jul 22 09:30:17 2020 -0700
    Updating redirectd links found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/human/giab.html
  • lines changed 81, context: html, text, full: html, text
    733a78c585ca10d21d9f7f580eac56d8f9b52584 Wed Aug 12 13:47:08 2020 -0700
    made new track description page refs #24349
• src/hg/makeDb/trackDb/human/hg38/tgpTrios.html
  • lines changed 1, context: html, text, full: html, text
    3fe1549c4eee6b24918300d6858ee67d6cd24405 Fri Aug 14 14:39:07 2020 -0700
    Minor fixups after code review, refs #26021
  • lines changed 1, context: html, text, full: html, text
    194d40e45c50e8559c44abbb3cf055979fd72092 Fri Aug 14 14:41:17 2020 -0700
    Forgot a missing quot, refs #26021
  • lines changed 1, context: html, text, full: html, text
    b45cb7f34c5a1c788ed935621a35a35ce9c040d5 Mon Aug 17 09:55:19 2020 -0700
    Fix up some grammar errors after code review, refs #26021
• src/hg/makeDb/trackDb/human/lovdComp.html
  • lines changed 0, context: html, text, full: html, text
    fc3f5edfa98344ad222a3e598cc3ec149401dec7 Mon Aug 10 13:57:34 2020 -0700
    add space between 50 and bp refs #25993
• src/hg/makeDb/trackDb/human/trackDb.clinvarTest.ra
  • lines changed 13, context: html, text, full: html, text
    6220b9f75319ff66c8e033505bad4b0d0e7c98cd Thu Aug 13 06:23:42 2020 -0700
    compositing the clinvar tracks again, refs #24850
• src/hg/makeDb/trackDb/human/trackDb.giab.ra
  • lines changed 1, context: html, text, full: html, text
    733a78c585ca10d21d9f7f580eac56d8f9b52584 Wed Aug 12 13:47:08 2020 -0700
    made new track description page refs #24349
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 0, context: html, text, full: html, text
    fc3f5edfa98344ad222a3e598cc3ec149401dec7 Mon Aug 10 13:57:34 2020 -0700
    add space between 50 and bp refs #25993
  • lines changed 25, context: html, text, full: html, text
    e6a1df7168dd6c375eb74716d8083611b9373b7c Thu Aug 13 17:05:34 2020 -0700
    Turn DECIPHER into a bigBed so we can have filters and merge spanned items, refs #25841
• src/hg/makeDb/trackDb/refSeqFuncElems.html
  • lines changed 8, context: html, text, full: html, text
    c5ad86284bb8e2ae9012c00dc1d5a2ddf4573c82 Wed Aug 12 14:33:24 2020 -0700
    Adding New Version section to refSeqFuncElems.hmtl to share Public Hub until new track made refs #26048
• src/hg/makeDb/trackDb/uniprot.html
  • lines changed 7, context: html, text, full: html, text
    93d687b27a8bc7761d5f60b1ed11a943dcf6f199 Fri Aug 14 15:34:53 2020 -0700
    Bolding the uniprot track colors so they are clearer refs #25784
• src/hg/makefile
  • lines changed 2, context: html, text, full: html, text
    da79c37696a46e9978a93218407e6afcdc71326c Fri Aug 14 17:45:37 2020 -0700
    Fixed bug in hgLiftOver CGI and liftOver utility reported by user. Also tested liftability of knwonGene on Chr1 to panTro6. All remining cases of Boundary error are real and not due to a bug. Added test cases, especially for BED12 which had been oddly missing. refs #26057.
• src/hg/utils/otto/clinGen/processClinGenDosage.py
  • lines changed 9, context: html, text, full: html, text
    14d5ef6dec5cf726ae7e59384352ae1188b0ef6b Fri Aug 14 14:45:56 2020 -0700
    Updating clinGenDosage build script after feedback from clingen
• src/hg/utils/otto/dbVar/processNstd175.py
  • lines changed 2, context: html, text, full: html, text
    3fe1549c4eee6b24918300d6858ee67d6cd24405 Fri Aug 14 14:39:07 2020 -0700
    Minor fixups after code review, refs #26021
• src/hg/utils/otto/lovd/checkAndLoad.sh
  • lines changed 10, context: html, text, full: html, text
    12e803e0ba9fd1b68163960b8b8e2bc876558b28 Fri Aug 14 14:29:20 2020 -0700
    When switching LOVD to bigBed, I overwrote the message to check chrMT instead of chrM for annotations, good find by Angie, refs #26021
• src/utils/qa/weeklybld/buildCgi32.csh
  • lines changed 1, context: html, text, full: html, text
    08dbac9faf64656dc2119a28d1e971367c517636 Thu Aug 13 15:32:00 2020 -0700
    removing references to download-sd.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    cb39c32273edacfc2888ea50381e0071f03463b9 Mon Aug 17 10:00:53 2020 -0700
    v403 preview2
• src/utils/qa/weeklybld/buildHgCentralSql.csh
  • lines changed 3, context: html, text, full: html, text
    08dbac9faf64656dc2119a28d1e971367c517636 Thu Aug 13 15:32:00 2020 -0700
    removing references to download-sd.
• src/utils/qa/weeklybld/doHgDownloadUtils.csh
  • lines changed 1, context: html, text, full: html, text
    08dbac9faf64656dc2119a28d1e971367c517636 Thu Aug 13 15:32:00 2020 -0700
    removing references to download-sd.
• src/utils/qa/weeklybld/doZip.csh
  • lines changed 4, context: html, text, full: html, text
    08dbac9faf64656dc2119a28d1e971367c517636 Thu Aug 13 15:32:00 2020 -0700
    removing references to download-sd.
• src/utils/qa/weeklybld/makeUserApps.csh
  • lines changed 6, context: html, text, full: html, text
    08dbac9faf64656dc2119a28d1e971367c517636 Thu Aug 13 15:32:00 2020 -0700
    removing references to download-sd.
• src/utils/qa/weeklybld/userApps.sh
  • lines changed 7, context: html, text, full: html, text
    08dbac9faf64656dc2119a28d1e971367c517636 Thu Aug 13 15:32:00 2020 -0700
    removing references to download-sd.

• lines changed: 355
• files changed: 40