All File Changes

v447_preview to v447_preview2 (2023-04-10 to 2023-04-17) v447

• build/kent-core/makeKentCore
  • lines changed 5, context: html, text, full: html, text
    3c995f9bda5fd2e5ae2724cb2f293b593e01fe78 Tue Apr 11 08:18:16 2023 -0700
    small changes to kent-core, refs #12785
• build/kent-core/makeKentCore.rules
  • lines changed 1, context: html, text, full: html, text
    3c995f9bda5fd2e5ae2724cb2f293b593e01fe78 Tue Apr 11 08:18:16 2023 -0700
    small changes to kent-core, refs #12785
  • lines changed 45, context: html, text, full: html, text
    0cd3992c199170e8f903a7991560e0642361ab7a Thu Apr 13 03:37:40 2023 -0700
    more kent-core changes, after a bug report on Github, refs #12785
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    cc74633c9ffdfaabd6555b1895f19c8ac7f838d5 Mon Apr 17 05:09:38 2023 -0700
    removing webBlat, refs #2
• build/kent-core/makefile
  • lines changed 5, context: html, text, full: html, text
    3c995f9bda5fd2e5ae2724cb2f293b593e01fe78 Tue Apr 11 08:18:16 2023 -0700
    small changes to kent-core, refs #12785
  • lines changed 3, context: html, text, full: html, text
    0cd3992c199170e8f903a7991560e0642361ab7a Thu Apr 13 03:37:40 2023 -0700
    more kent-core changes, after a bug report on Github, refs #12785
• src/hg/hgTracks/config.c
  • lines changed 5, context: html, text, full: html, text
    af6898753ba6d5f3872957cd270872ce4c4e3dfc Tue Apr 11 08:19:27 2023 -0700
    tolerate if browser CSS theme files do not exist, cleaning up the resource link mess a little, refs #7867
• src/hg/hgTracks/hgTracks.c
  • lines changed 7, context: html, text, full: html, text
    49029c6209ad86693a552fd4dd8e7a4a55d8777f Thu Apr 13 09:48:13 2023 -0700
    fix problems with squishyPack track name and non-sticky squishyPackPoint refs #30225
• src/hg/hgTracks/wigCommon.h
  • lines changed 1, context: html, text, full: html, text
    141deaec9ba7a2912faedaf2a62fa189108b4c43 Thu Apr 13 12:15:01 2023 -0700
    some final clean-up on logoMaf: allow the user to turn it off, and scale by the amount of the data within the clipping rectangle
• src/hg/hgTracks/wigTrack.c
  • lines changed 17, context: html, text, full: html, text
    141deaec9ba7a2912faedaf2a62fa189108b4c43 Thu Apr 13 12:15:01 2023 -0700
    some final clean-up on logoMaf: allow the user to turn it off, and scale by the amount of the data within the clipping rectangle
  • lines changed 1, context: html, text, full: html, text
    c56860879bbbd543373aef1e6cc83bb647708459 Thu Apr 13 14:19:36 2023 -0700
    don't draw sequence logos in squish mode
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 13, context: html, text, full: html, text
    481dd77123df9a0bd00a6dedb595bbcf6546f3e7 Wed Apr 12 18:04:06 2023 -0700
    Adding FAQ for differences in conservation scores between download file and hgTracks/hgTables, refs #30734
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 7, context: html, text, full: html, text
    8f72a658697996ae65727d8583d0df20765b7b8b Mon Apr 17 06:43:13 2023 -0700
    changes after code review #31051, and after QA, refs #30904
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 40, context: html, text, full: html, text
    0ffa51e45bcc6d728797d7fb004c95b4387baef7 Tue Apr 11 09:42:09 2023 -0700
    Announcing the release of the cross tissue nuclei track for hg38, refs #29954
  • lines changed 1, context: html, text, full: html, text
    9ea337e7d1dabceebd7bc4ecbc2c3a11809116cf Tue Apr 11 09:59:55 2023 -0700
    Fixing a typo, refs #29954
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    0ffa51e45bcc6d728797d7fb004c95b4387baef7 Tue Apr 11 09:42:09 2023 -0700
    Announcing the release of the cross tissue nuclei track for hg38, refs #29954
• src/hg/htdocs/style/makefile
  • lines changed 2, context: html, text, full: html, text
    cedf33cf578d464709a4a816695bce36cf111ab6 Tue Apr 11 08:21:06 2023 -0700
    adding browser css themes, refs #7867
• src/hg/htdocs/style/theme-dark.css
  • lines changed 4, context: html, text, full: html, text
    6595f9ed43f871cb9b544432e711591a9ff4b68b Tue Apr 11 01:33:36 2023 -0700
    tiny fix to dark theme, refs 7867
• src/hg/htdocs/style/theme-default.css
  • lines changed 0, context: html, text, full: html, text
    cedf33cf578d464709a4a816695bce36cf111ab6 Tue Apr 11 08:21:06 2023 -0700
    adding browser css themes, refs #7867
• src/hg/hubApi/list.c
  • lines changed 1, context: html, text, full: html, text
    edbba2de34acf9063eed1399e6c28bbe8f91ec88 Mon Apr 10 11:52:32 2023 -0700
    do not need the pipelineFree after the pipelineClose already done refs #23589
• src/hg/inc/web.h
  • lines changed 8, context: html, text, full: html, text
    af6898753ba6d5f3872957cd270872ce4c4e3dfc Tue Apr 11 08:19:27 2023 -0700
    tolerate if browser CSS theme files do not exist, cleaning up the resource link mess a little, refs #7867
• src/hg/inc/wiggle.h
  • lines changed 7, context: html, text, full: html, text
    141deaec9ba7a2912faedaf2a62fa189108b4c43 Thu Apr 13 12:15:01 2023 -0700
    some final clean-up on logoMaf: allow the user to turn it off, and scale by the amount of the data within the clipping rectangle
• src/hg/lib/cart.c
  • lines changed 2, context: html, text, full: html, text
    af6898753ba6d5f3872957cd270872ce4c4e3dfc Tue Apr 11 08:19:27 2023 -0700
    tolerate if browser CSS theme files do not exist, cleaning up the resource link mess a little, refs #7867
• src/hg/lib/hui.c
  • lines changed 4, context: html, text, full: html, text
    49029c6209ad86693a552fd4dd8e7a4a55d8777f Thu Apr 13 09:48:13 2023 -0700
    fix problems with squishyPack track name and non-sticky squishyPackPoint refs #30225
  • lines changed 11, context: html, text, full: html, text
    141deaec9ba7a2912faedaf2a62fa189108b4c43 Thu Apr 13 12:15:01 2023 -0700
    some final clean-up on logoMaf: allow the user to turn it off, and scale by the amount of the data within the clipping rectangle
  • lines changed 11, context: html, text, full: html, text
    8f72a658697996ae65727d8583d0df20765b7b8b Mon Apr 17 06:43:13 2023 -0700
    changes after code review #31051, and after QA, refs #30904
• src/hg/lib/web.c
  • lines changed 46, context: html, text, full: html, text
    af6898753ba6d5f3872957cd270872ce4c4e3dfc Tue Apr 11 08:19:27 2023 -0700
    tolerate if browser CSS theme files do not exist, cleaning up the resource link mess a little, refs #7867
• src/hg/lib/wiggleCart.c
  • lines changed 16, context: html, text, full: html, text
    141deaec9ba7a2912faedaf2a62fa189108b4c43 Thu Apr 13 12:15:01 2023 -0700
    some final clean-up on logoMaf: allow the user to turn it off, and scale by the amount of the data within the clipping rectangle
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    137792ebd8921e7f933dfba90966d5c1d7cd3ea4 Mon Apr 10 10:48:25 2023 -0700
    per user request GCA_921998555.2_129S1_SvImJ_v3 for a liftOver refs #31040
• src/hg/makeDb/doc/hg38/hprcCoverage.txt
  • lines changed 196, context: html, text, full: html, text
    39b70f7f9425b87eb06dc521f2579abf86d877b6 Wed Apr 12 09:13:06 2023 -0700
    calculating coverage on hg38 of HPRC lift.over chains refs #30508
• src/hg/makeDb/doc/hg38/problematic.txt
  • lines changed 6, context: html, text, full: html, text
    481aac4c5d50c29d04226490eb99913927250981 Tue Apr 11 02:13:10 2023 -0700
    small addition to problematic regions track, email from Markd, refs #30801
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    a7290f420163ec189215bb563368993282050de7 Mon Apr 10 10:50:10 2023 -0700
    per user request GCA_921998555.2_129S1_SvImJ_v3 for a liftOver refs #31040
• src/hg/makeDb/trackDb/human/chainNetHuman.ra
  • lines changed 6432, context: html, text, full: html, text
    d3a29443ea8bdc441a131bfd1b8390da40a3a2b1 Mon Apr 10 17:09:21 2023 -0700
    trying out the display of all 96 HPRC genomes + T2T refs #30508
  • lines changed 1758, context: html, text, full: html, text
    f32eaf0fbacb8a8c500dc002f68d73166067143e Tue Apr 11 10:44:37 2023 -0700
    all liftOver tracks now available for HPRC on hg38 refs #30508
  • lines changed 93, context: html, text, full: html, text
    cc5e3c90e84384bb7afc43f35cfa1177e8e5975e Thu Apr 13 13:47:45 2023 -0700
    add in the T2T-CHM13v2.0 chains nets refs #30508
• src/hg/makeDb/trackDb/human/hg17/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    564d25350e37e5c43606291ec3378e03155c1de1 Sat Apr 15 04:12:13 2023 -0700
    fix cartVersion problem on hg17
• src/hg/makeDb/trackDb/human/hg38/crossTissueMaps.html
  • lines changed 6, context: html, text, full: html, text
    7341a62a0e97a3b1cd8a56efc6741d3fd6aefea0 Mon Apr 10 16:03:18 2023 -0700
    Fixing typos for the track description page , refs #29954
  • lines changed 2, context: html, text, full: html, text
    d40aaa6d7633f5d2bafd3f57635dde74ea0f6571 Tue Apr 11 09:35:54 2023 -0700
    Fixing comma placement on track description page, refs #29954
• src/hg/makeDb/trackDb/human/hg38/crossTissueMaps.ra
  • lines changed 2, context: html, text, full: html, text
    0ffa51e45bcc6d728797d7fb004c95b4387baef7 Tue Apr 11 09:42:09 2023 -0700
    Announcing the release of the cross tissue nuclei track for hg38, refs #29954
• src/hg/makeDb/trackDb/human/hg38/hprcCoverage.ra
  • lines changed 65, context: html, text, full: html, text
    2cad1d6b9819c8a3e4e1913dcddc5de72b338f58 Wed Apr 12 21:12:22 2023 -0700
    5 different tracks for coverage to indicate the five different coverage brackets refs #30508
• src/hg/makeDb/trackDb/human/hg38/problematic.ra
  • lines changed 11, context: html, text, full: html, text
    481aac4c5d50c29d04226490eb99913927250981 Tue Apr 11 02:13:10 2023 -0700
    small addition to problematic regions track, email from Markd, refs #30801
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    c3ceb018e7b3873d1e34745fb63f13f0da28df83 Mon Apr 10 16:28:19 2023 -0700
    Removing release tag, refs #29954
  • lines changed 1, context: html, text, full: html, text
    88acb2c4456b3246f76cf33f4a1d1591edc045ba Wed Apr 12 21:15:54 2023 -0700
    5 different tracks for coverage to indicate the five different coverage brackets refs #30508
• src/hg/makeDb/trackDb/relatedTracks.ra
  • lines changed 2, context: html, text, full: html, text
    0458a53c1240f4f1d45b721469aaaa4769c369a1 Tue Apr 11 13:57:06 2023 -0700
    linking incidents and problematic, refs #30801
• src/hg/makefile
  • lines changed 12, context: html, text, full: html, text
    0cd3992c199170e8f903a7991560e0642361ab7a Thu Apr 13 03:37:40 2023 -0700
    more kent-core changes, after a bug report on Github, refs #12785
  • lines changed 1, context: html, text, full: html, text
    5cefa4d0b6762f089c82a3483d34554e2711a416 Thu Apr 13 03:48:04 2023 -0700
    small kent-core fix for make clean, refs #12785
• src/lib/https.c
  • lines changed 12, context: html, text, full: html, text
    1867b83f43011496f85ba9a8f68fd3d7f36897b0 Sun Apr 16 12:05:19 2023 -0700
    adding some final domains to https whitelist
• src/makefile
  • lines changed 2, context: html, text, full: html, text
    6184aa9c294043e6b3ca1e52b036c9ea8cbcb5bc Thu Apr 13 05:51:50 2023 -0700
    and another kent-core bug, refs #12785
• src/product/ex.hg.conf
  • lines changed 10, context: html, text, full: html, text
    3fc21a3255e765cf252e59c97ee8c2fba6b228c5 Tue Apr 11 10:03:01 2023 -0700
    docing browser themes, refs #7867
• src/utils/qa/buildPublicSessionThumbnailsIndexPage.py
  • lines changed 1, context: html, text, full: html, text
    19d69d9d2db3a4c42bfbf28086c0db04b284cfaf Tue Apr 11 18:33:50 2023 -0700
    Fixing the path to be relative in the thumbNail links page as the page and the images are always placed together.
• src/utils/qa/checkHTTPS
  • lines changed 1, context: html, text, full: html, text
    39c0acbf8d099b4bda66c885b91e4eab4467ba2a Fri Apr 14 12:10:19 2023 -0700
    Adding download-euro to the certificate check script.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    9482bff8fb8625e73276b80ed4cb3d266b3f3796 Mon Apr 17 10:06:28 2023 -0700
    v447 preview2, refs #31044

• lines changed: 8900
• files changed: 52