All File Changes

v416_preview2 to v416_base (2021-06-07 to 2021-06-14) v416

• confs/hgwdev.hg.conf
  • lines changed 3, context: html, text, full: html, text
    75fdae66dbbb87545f6685ecb864ae1e964a3f65 Sun Jun 13 01:11:51 2021 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgLiftOver/hgLiftOver.c
  • lines changed 4, context: html, text, full: html, text
    a58a77eaeb27e1725cafdb5b107525d7d3749041 Wed Jun 9 01:54:48 2021 -0700
    adding more details to liftOver text, refs #27657
• src/hg/hgTracks/hgTracks.c
  • lines changed 12, context: html, text, full: html, text
    36d5542588a99a3e44bf65d16aa3c4600b562b87 Tue Jun 8 10:10:30 2021 -0700
    changes in response to code review #27643
  • lines changed 2, context: html, text, full: html, text
    6566d72912b95b542d40d7d91302c21f83942320 Wed Jun 9 10:21:33 2021 -0700
    Remove Rec Track Set panel/button if hideTracks=1 in URL. refs #27682
  • lines changed 1, context: html, text, full: html, text
    c00e0481c53131d00bb175b9c3cf23037f47ebea Wed Jun 9 16:06:40 2021 -0700
    fix crash if track is in density mode and the bigDataUrl is not accessible #27661
  • lines changed 10, context: html, text, full: html, text
    f3495a72a10ae753d24daea0d0d3383e04aa124f Fri Jun 11 10:47:16 2021 -0700
    add a function to dump track names out for use with the image comparator
  • lines changed 1, context: html, text, full: html, text
    a5432eb58e2fbf55461c86d2faf02d54e592de93 Fri Jun 11 17:30:16 2021 -0700
    Removing unnecessary (and conflicting) pointer set for hic custom tracks, refs #27593
• src/hg/hgTracks/hicTrack.c
  • lines changed 11, context: html, text, full: html, text
    60aca91bcce6d4fa555e6c7c91d8ff8aa9e7bd2b Fri Jun 11 15:17:21 2021 -0700
    Updating hic support for files with large headers (over 100kb) and improving multi-region performance, refs #18842, #27593
• src/hg/hgTracks/recTrackSets.c
  • lines changed 2, context: html, text, full: html, text
    6e8ad2b034f0c2bbfba2fbcfc3e796d5b565dc59 Sun Jun 13 10:57:50 2021 -0700
    Rec track sets now preserve font type (though not yet style). refs #27688
• src/hg/hgTracks/renderMain.c
  • lines changed 1, context: html, text, full: html, text
    f3495a72a10ae753d24daea0d0d3383e04aa124f Fri Jun 11 10:47:16 2021 -0700
    add a function to dump track names out for use with the image comparator
• src/hg/hgTracks/simpleTracks.c
  • lines changed 9, context: html, text, full: html, text
    c00e0481c53131d00bb175b9c3cf23037f47ebea Wed Jun 9 16:06:40 2021 -0700
    fix crash if track is in density mode and the bigDataUrl is not accessible #27661
• src/hg/hgc/hgcData/gtexBoxplot.R
  • lines changed 5, context: html, text, full: html, text
    6eb046056d5151185fae6fdc18499be244ffd090 Thu Jun 10 14:53:14 2021 -0700
    Ensure the labels and colors of the GTEx boxplots match hgTracks, refs #26845
• src/hg/hgc/hgcData/gtexColorsV4.R
  • lines changed 57, context: html, text, full: html, text
    6eb046056d5151185fae6fdc18499be244ffd090 Thu Jun 10 14:53:14 2021 -0700
    Ensure the labels and colors of the GTEx boxplots match hgTracks, refs #26845
• src/hg/hgc/hgcData/gtexColorsV8.R
  • lines changed 4, context: html, text, full: html, text
    e2fc1496164bb7bee8f9766b46ede67ca375b809 Mon Jun 7 15:32:50 2021 -0700
    Fixing order of colors for gtex hgc boxplot, refs #26845
  • lines changed 62, context: html, text, full: html, text
    6eb046056d5151185fae6fdc18499be244ffd090 Thu Jun 10 14:53:14 2021 -0700
    Ensure the labels and colors of the GTEx boxplots match hgTracks, refs #26845
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 67, context: html, text, full: html, text
    96c750edb89fd5bde5eca4dbf167578f25bb00b4 Mon Jun 7 16:16:21 2021 -0700
    Updating CyVerse section and cleaning up some htmlValidate check paragraph items. refs #26511
  • lines changed 5, context: html, text, full: html, text
    8a1ad785c25e39aa796a0a074a5c4913680daeeb Thu Jun 10 11:59:40 2021 -0700
    Adding a note about refreshing the CyVerse cache if you replace a file refs #27543
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 24, context: html, text, full: html, text
    54332d10a159802c8310bc7d33bd66c85058426d Thu Jun 10 09:02:47 2021 -0700
    Updating news for the ncbiRefSeq track update, refs #27575
  • lines changed 120, context: html, text, full: html, text
    398507e945d474a1553f783d19d1c458ddbc064b Thu Jun 10 16:10:39 2021 -0700
    Announcing ensembl v104 annotations, refs #27616
• src/hg/htdocs/images/cyverseCreatePublicLink.png
  • lines changed 0, context: html, text, full: html, text
    96c750edb89fd5bde5eca4dbf167578f25bb00b4 Mon Jun 7 16:16:21 2021 -0700
    Updating CyVerse section and cleaning up some htmlValidate check paragraph items. refs #26511
• src/hg/htdocs/images/cyverseCreatePublicLink2.png
  • lines changed 0, context: html, text, full: html, text
    96c750edb89fd5bde5eca4dbf167578f25bb00b4 Mon Jun 7 16:16:21 2021 -0700
    Updating CyVerse section and cleaning up some htmlValidate check paragraph items. refs #26511
• src/hg/htdocs/images/cyverseUploadButton.png
  • lines changed 0, context: html, text, full: html, text
    96c750edb89fd5bde5eca4dbf167578f25bb00b4 Mon Jun 7 16:16:21 2021 -0700
    Updating CyVerse section and cleaning up some htmlValidate check paragraph items. refs #26511
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    54332d10a159802c8310bc7d33bd66c85058426d Thu Jun 10 09:02:47 2021 -0700
    Updating news for the ncbiRefSeq track update, refs #27575
  • lines changed 12, context: html, text, full: html, text
    398507e945d474a1553f783d19d1c458ddbc064b Thu Jun 10 16:10:39 2021 -0700
    Announcing ensembl v104 annotations, refs #27616
• src/hg/htdocs/indexStory.html
  • lines changed 2, context: html, text, full: html, text
    5357d4d4128e7457733d1b759ff706fc2154a226 Thu Jun 10 14:32:19 2021 -0700
    Adding to Our story in index.html a video link to overview about Browser ref #27560
• src/hg/inc/Cstraw.h
  • lines changed 26, context: html, text, full: html, text
    60aca91bcce6d4fa555e6c7c91d8ff8aa9e7bd2b Fri Jun 11 15:17:21 2021 -0700
    Updating hic support for files with large headers (over 100kb) and improving multi-region performance, refs #18842, #27593
• src/hg/inc/cStraw.h
  • lines changed 34, context: html, text, full: html, text
    60aca91bcce6d4fa555e6c7c91d8ff8aa9e7bd2b Fri Jun 11 15:17:21 2021 -0700
    Updating hic support for files with large headers (over 100kb) and improving multi-region performance, refs #18842, #27593
• src/hg/inc/hdb.h
  • lines changed 3, context: html, text, full: html, text
    36d5542588a99a3e44bf65d16aa3c4600b562b87 Tue Jun 8 10:10:30 2021 -0700
    changes in response to code review #27643
• src/hg/inc/hic.h
  • lines changed 2, context: html, text, full: html, text
    60aca91bcce6d4fa555e6c7c91d8ff8aa9e7bd2b Fri Jun 11 15:17:21 2021 -0700
    Updating hic support for files with large headers (over 100kb) and improving multi-region performance, refs #18842, #27593
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    ddaf486012f0411e815853fcfb7adfa73113411b Mon Jun 14 10:05:08 2021 -0700
    New version number v416
• src/hg/lib/cartRewrite.c
  • lines changed 9, context: html, text, full: html, text
    36d5542588a99a3e44bf65d16aa3c4600b562b87 Tue Jun 8 10:10:30 2021 -0700
    changes in response to code review #27643
  • lines changed 1, context: html, text, full: html, text
    62ee00276faee7fc54897ee27fe3bde616ec9f62 Wed Jun 9 10:33:58 2021 -0700
    cart rewrites are off by default
• src/hg/lib/hdb.c
  • lines changed 29, context: html, text, full: html, text
    36d5542588a99a3e44bf65d16aa3c4600b562b87 Tue Jun 8 10:10:30 2021 -0700
    changes in response to code review #27643
• src/hg/lib/hic.c
  • lines changed 5, context: html, text, full: html, text
    60aca91bcce6d4fa555e6c7c91d8ff8aa9e7bd2b Fri Jun 11 15:17:21 2021 -0700
    Updating hic support for files with large headers (over 100kb) and improving multi-region performance, refs #18842, #27593
• src/hg/lib/hicUi.c
  • lines changed 1, context: html, text, full: html, text
    60aca91bcce6d4fa555e6c7c91d8ff8aa9e7bd2b Fri Jun 11 15:17:21 2021 -0700
    Updating hic support for files with large headers (over 100kb) and improving multi-region performance, refs #18842, #27593
• src/hg/lib/makefile
  • lines changed 3, context: html, text, full: html, text
    60aca91bcce6d4fa555e6c7c91d8ff8aa9e7bd2b Fri Jun 11 15:17:21 2021 -0700
    Updating hic support for files with large headers (over 100kb) and improving multi-region performance, refs #18842, #27593
• src/hg/lib/straw/cStraw.cpp
  • lines changed 169, context: html, text, full: html, text
    60aca91bcce6d4fa555e6c7c91d8ff8aa9e7bd2b Fri Jun 11 15:17:21 2021 -0700
    Updating hic support for files with large headers (over 100kb) and improving multi-region performance, refs #18842, #27593
• src/hg/lib/straw/makefile
  • lines changed 10, context: html, text, full: html, text
    60aca91bcce6d4fa555e6c7c91d8ff8aa9e7bd2b Fri Jun 11 15:17:21 2021 -0700
    Updating hic support for files with large headers (over 100kb) and improving multi-region performance, refs #18842, #27593
• src/hg/lib/straw/straw.cpp
  • lines changed 572, context: html, text, full: html, text
    60aca91bcce6d4fa555e6c7c91d8ff8aa9e7bd2b Fri Jun 11 15:17:21 2021 -0700
    Updating hic support for files with large headers (over 100kb) and improving multi-region performance, refs #18842, #27593
• src/hg/lib/straw/straw.h
  • lines changed 93, context: html, text, full: html, text
    60aca91bcce6d4fa555e6c7c91d8ff8aa9e7bd2b Fri Jun 11 15:17:21 2021 -0700
    Updating hic support for files with large headers (over 100kb) and improving multi-region performance, refs #18842, #27593
• src/hg/lib/straw/udcWrapper.h
  • lines changed 194, context: html, text, full: html, text
    60aca91bcce6d4fa555e6c7c91d8ff8aa9e7bd2b Fri Jun 11 15:17:21 2021 -0700
    Updating hic support for files with large headers (over 100kb) and improving multi-region performance, refs #18842, #27593
• src/hg/lib/trackDbCustom.c
  • lines changed 16, context: html, text, full: html, text
    36d5542588a99a3e44bf65d16aa3c4600b562b87 Tue Jun 8 10:10:30 2021 -0700
    changes in response to code review #27643
• src/hg/makeDb/doc/globalReference/genomes.txt
  • lines changed 110, context: html, text, full: html, text
    cc3e7eaf76475a948b97f4986a45e8e1c8f5077f Fri Jun 11 12:08:25 2021 -0700
    initial genomes.txt before dynamic blat server addition refs #24354
  • lines changed 30, context: html, text, full: html, text
    44b8755102648a288c1db8d9008b99ef88bbbaae Fri Jun 11 12:10:27 2021 -0700
    adding dynamic blat service refs #24354
• src/hg/makeDb/doc/hg38/cactus241way.txt
  • lines changed 16, context: html, text, full: html, text
    0b5b8713618f911dd69626d3e27df3f97918c28c Mon Jun 7 22:27:02 2021 -0700
    added notes on how 241-mammalian-2020v2.ucsc.bigMaf was built
• src/hg/makeDb/doc/mouseStrains/mouseStrains.genomes.txt
  • lines changed 78, context: html, text, full: html, text
    a2164e2ddb4e25ff50eec753a99e77d2fc58bd03 Wed Jun 9 11:44:17 2021 -0700
    convert to dynamic blat server refs #27553
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • lines changed 26, context: html, text, full: html, text
    36d5542588a99a3e44bf65d16aa3c4600b562b87 Tue Jun 8 10:10:30 2021 -0700
    changes in response to code review #27643
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 5, context: html, text, full: html, text
    f4fadf13df6633962b9065586302fe83927eb444 Mon Jun 14 09:14:46 2021 -0700
    Add searching and table browser identifiers search for gnomAD v3.1.1, refs #27256
• src/hg/makeDb/trackDb/human/hg38/liverMacParland.html
  • lines changed 12, context: html, text, full: html, text
    0f6ecc108fff71e3ac5a523c39127faf0b7b8ab3 Fri Jun 11 16:03:36 2021 -0700
    Made small formatting edits and added more detail to sections. refs #26970
• src/hg/makeDb/trackDb/human/hg38/liverMacParland.insert.html
  • lines changed 3, context: html, text, full: html, text
    0f6ecc108fff71e3ac5a523c39127faf0b7b8ab3 Fri Jun 11 16:03:36 2021 -0700
    Made small formatting edits and added more detail to sections. refs #26970
• src/hg/makeDb/trackDb/human/hg38/liverMacParlandCellType.insert.html
  • lines changed 9, context: html, text, full: html, text
    0f6ecc108fff71e3ac5a523c39127faf0b7b8ab3 Fri Jun 11 16:03:36 2021 -0700
    Made small formatting edits and added more detail to sections. refs #26970
• src/hg/makeDb/trackDb/human/hg38/liverMacParlandDonor.insert.html
  • lines changed 16, context: html, text, full: html, text
    0f6ecc108fff71e3ac5a523c39127faf0b7b8ab3 Fri Jun 11 16:03:36 2021 -0700
    Made small formatting edits and added more detail to sections. refs #26970
• src/hg/makeDb/trackDb/human/hg38/muscleDeMicheli.html
  • lines changed 2, context: html, text, full: html, text
    0ea907a116be0e213b936f4eeff7aba5ca053bc8 Fri Jun 11 16:04:39 2021 -0700
    Made small formatting edits and added more detail to sections. refs #26968
• src/hg/makeDb/trackDb/human/hg38/muscleDeMicheli.insert.html
  • lines changed 3, context: html, text, full: html, text
    59de07380c17527acfab1ff05cb7c0df555dc86e Fri Jun 11 16:05:49 2021 -0700
    Adding insert page so that there is no error. refs #26968
• src/hg/makeDb/trackDb/human/hg38/muscleDeMicheli.ra
  • lines changed 3, context: html, text, full: html, text
    e56b9bc8eec6e7a06f0a040d13aeeadcc320a780 Fri Jun 11 16:00:56 2021 -0700
    Added release alpha tags to parent and children stanzas. refs #26968
• src/hg/makeDb/trackDb/human/hg38/muscleDeMicheliCellType.insert.html
  • lines changed 6, context: html, text, full: html, text
    0ea907a116be0e213b936f4eeff7aba5ca053bc8 Fri Jun 11 16:04:39 2021 -0700
    Made small formatting edits and added more detail to sections. refs #26968
  • lines changed 1, context: html, text, full: html, text
    a8bbcdf9e173b50f5e9cffc2f929187e05a50ce9 Fri Jun 11 16:12:56 2021 -0700
    Removed extra / from copyright citation per Kate's request. refs #26968
• src/hg/makeDb/trackDb/human/hg38/muscleDeMicheliSample.insert.html
  • lines changed 19, context: html, text, full: html, text
    0ea907a116be0e213b936f4eeff7aba5ca053bc8 Fri Jun 11 16:04:39 2021 -0700
    Made small formatting edits and added more detail to sections. refs #26968
  • lines changed 2, context: html, text, full: html, text
    a8bbcdf9e173b50f5e9cffc2f929187e05a50ce9 Fri Jun 11 16:12:56 2021 -0700
    Removed extra / from copyright citation per Kate's request. refs #26968
• src/hg/makeDb/trackDb/human/revel.ra
  • lines changed 1, context: html, text, full: html, text
    7c11687d53cd01dd6dd6e17b258aa7f32a214961 Tue Jun 8 04:40:53 2021 -0700
    fixing tdb error in revel, refs #27142
• src/hg/makeDb/trackDb/refSeqFuncElems.html
  • lines changed 11, context: html, text, full: html, text
    9c2c393cc048d73c20ef64cd54dde1ad559f1135 Wed Jun 9 10:51:14 2021 -0700
    Adding a data access section to the refSeqFuncElems track, refs #27662
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    01c18821ef1d55f347fa9f82f790e34f47d5a00d Thu Jun 10 16:13:44 2021 -0700
    Adding pennantIcon for ensemble v104 refs #27616
• src/hg/utils/hgTracksDelta/hgTracksDelta.c
  • lines changed 116, context: html, text, full: html, text
    1ecb9661f16d03762b2353a9d3a7f5602dbeecbc Fri Jun 11 11:24:51 2021 -0700
    first cut of C based hgTracks image comparator
• src/hg/utils/hgTracksDelta/makefile
  • lines changed 3, context: html, text, full: html, text
    1ecb9661f16d03762b2353a9d3a7f5602dbeecbc Fri Jun 11 11:24:51 2021 -0700
    first cut of C based hgTracks image comparator
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    ddaf486012f0411e815853fcfb7adfa73113411b Mon Jun 14 10:05:08 2021 -0700
    New version number v416
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    162e587b63ce79ff85f062cefcae061dd7046c08 Mon Jun 14 10:04:24 2021 -0700
    v416 final build, refs #27655

• lines changed: 2071
• files changed: 66