All File Changes

v487_preview2 to v487_base (2025-08-25 to 2025-09-01) v487

• src/hg/hgGene/hgGene.c
  • lines changed 2, context: html, text, full: html, text
    a75cfac22803c312074299aa0dcf286ca336ce89 Wed Aug 27 13:28:08 2025 -0700
    ongoing work on quickLift hgc page plus a fix for genepreds that don't successfully quickLift
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 1, context: html, text, full: html, text
    9cf83b9d3400d0b2b15989e5b0d7583291c3cc57 Thu Aug 28 18:58:20 2025 -0700
    eliminate hub prefixe from hOrganism() output refs #36263
• src/hg/hgTracks/chainTrack.c
  • lines changed 56, context: html, text, full: html, text
    485724bcdce8810dcf1b65755c97dbb3c39fa02a Mon Aug 25 15:37:25 2025 -0700
    give quickLiftChains there own methods in hgTracks and a special hgc page
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    485724bcdce8810dcf1b65755c97dbb3c39fa02a Mon Aug 25 15:37:25 2025 -0700
    give quickLiftChains there own methods in hgTracks and a special hgc page
• src/hg/hgTracks/hgTracks.h
  • lines changed 4, context: html, text, full: html, text
    485724bcdce8810dcf1b65755c97dbb3c39fa02a Mon Aug 25 15:37:25 2025 -0700
    give quickLiftChains there own methods in hgTracks and a special hgc page
• src/hg/hgTracks/lollyTrack.c
  • lines changed 4, context: html, text, full: html, text
    a75cfac22803c312074299aa0dcf286ca336ce89 Wed Aug 27 13:28:08 2025 -0700
    ongoing work on quickLift hgc page plus a fix for genepreds that don't successfully quickLift
• src/hg/hgTracks/quickLift.c
  • lines changed 34, context: html, text, full: html, text
    485724bcdce8810dcf1b65755c97dbb3c39fa02a Mon Aug 25 15:37:25 2025 -0700
    give quickLiftChains there own methods in hgTracks and a special hgc page
  • lines changed 39, context: html, text, full: html, text
    a75cfac22803c312074299aa0dcf286ca336ce89 Wed Aug 27 13:28:08 2025 -0700
    ongoing work on quickLift hgc page plus a fix for genepreds that don't successfully quickLift
  • lines changed 2, context: html, text, full: html, text
    795662304c0ac18f4fc1e466e75f3ae14021896b Wed Aug 27 13:37:33 2025 -0700
    oops, wasn't checking type correctly in quickLiftChain.c
• src/hg/hgTracks/quickLiftPull.c
  • lines changed 60, context: html, text, full: html, text
    a75cfac22803c312074299aa0dcf286ca336ce89 Wed Aug 27 13:28:08 2025 -0700
    ongoing work on quickLift hgc page plus a fix for genepreds that don't successfully quickLift
• src/hg/hgTracks/simpleTracks.c
  • lines changed 4, context: html, text, full: html, text
    485724bcdce8810dcf1b65755c97dbb3c39fa02a Mon Aug 25 15:37:25 2025 -0700
    give quickLiftChains there own methods in hgTracks and a special hgc page
  • lines changed 6, context: html, text, full: html, text
    a75cfac22803c312074299aa0dcf286ca336ce89 Wed Aug 27 13:28:08 2025 -0700
    ongoing work on quickLift hgc page plus a fix for genepreds that don't successfully quickLift
• src/hg/hgTracks/variation.c
  • lines changed 2, context: html, text, full: html, text
    0ead52725effa01825a6fcfac7935eaa4979f76e Wed Aug 27 09:56:02 2025 -0700
    Incorporating Lou's feedback ragarding the bigDbSnp mouseOver, refs #36249
• src/hg/hgc/facetedBar.c
  • lines changed 25, context: html, text, full: html, text
    eb9441d7f6347f6b9ed58aeae694c75ec7b3eb61 Thu Aug 28 17:03:18 2025 -0700
    Improve the column names for single cell output using combined facets and matrix, changed column count to cell count, column val to read count. Also updated the 4 html files with improved notations about those columns, and corrected note about expCount field. Added a new tag for trackDb singleCellColumnNames off to support old default column names. fixes #34628
• src/hg/hgc/hgc.c
  • lines changed 198, context: html, text, full: html, text
    485724bcdce8810dcf1b65755c97dbb3c39fa02a Mon Aug 25 15:37:25 2025 -0700
    give quickLiftChains there own methods in hgTracks and a special hgc page
  • lines changed 33, context: html, text, full: html, text
    a75cfac22803c312074299aa0dcf286ca336ce89 Wed Aug 27 13:28:08 2025 -0700
    ongoing work on quickLift hgc page plus a fix for genepreds that don't successfully quickLift
• src/hg/hgc/makefile
  • lines changed 1, context: html, text, full: html, text
    485724bcdce8810dcf1b65755c97dbb3c39fa02a Mon Aug 25 15:37:25 2025 -0700
    give quickLiftChains there own methods in hgTracks and a special hgc page
• src/hg/hgc/quickLift.c
  • lines changed 24, context: html, text, full: html, text
    485724bcdce8810dcf1b65755c97dbb3c39fa02a Mon Aug 25 15:37:25 2025 -0700
    give quickLiftChains there own methods in hgTracks and a special hgc page
• src/hg/htdocs/goldenPath/help/mirrorManual.html
  • lines changed 41, context: html, text, full: html, text
    1954c1095a389ec259e7754dfe9dc5bf98cfba41 Tue Aug 26 05:43:37 2025 -0700
    adding api redirect rules to mirror docs, refs #36269
• src/hg/htdocs/style/HGStyle.css
  • lines changed 5, context: html, text, full: html, text
    7b0c89608f69abda761354d7148a3a79ba2ca604 Fri Aug 29 09:19:32 2025 -0700
    Add line break settings to the tooltip CSS to allow web browsers to break at any character but in practice usually puncuation. This does not affect if we manually stick line breaks in, only wrapping long text lines, refs #36287
• src/hg/inc/quickLift.h
  • lines changed 1, context: html, text, full: html, text
    a75cfac22803c312074299aa0dcf286ca336ce89 Wed Aug 27 13:28:08 2025 -0700
    ongoing work on quickLift hgc page plus a fix for genepreds that don't successfully quickLift
• src/hg/js/utils.js
  • lines changed 8, context: html, text, full: html, text
    96cb9cb21c8b1640c00d14ffba72545d8eab3522 Wed Aug 27 15:19:30 2025 -0700
    Make gear icon tooltip same as grey bars, refs #34420
  • lines changed 1, context: html, text, full: html, text
    f0c40470463316d47375e75b4ca14feb9abf47d5 Wed Aug 27 16:43:46 2025 -0700
    Updating the tooltip for the gear icon to be consistent with the grey bar button, refs #34420
• src/hg/lib/barChartUi.c
  • lines changed 10, context: html, text, full: html, text
    eb9441d7f6347f6b9ed58aeae694c75ec7b3eb61 Thu Aug 28 17:03:18 2025 -0700
    Improve the column names for single cell output using combined facets and matrix, changed column count to cell count, column val to read count. Also updated the 4 html files with improved notations about those columns, and corrected note about expCount field. Added a new tag for trackDb singleCellColumnNames off to support old default column names. fixes #34628
• src/hg/lib/hubConnect.c
  • lines changed 1, context: html, text, full: html, text
    485724bcdce8810dcf1b65755c97dbb3c39fa02a Mon Aug 25 15:37:25 2025 -0700
    give quickLiftChains there own methods in hgTracks and a special hgc page
• src/hg/lib/liftOver.c
  • lines changed 1, context: html, text, full: html, text
    a75cfac22803c312074299aa0dcf286ca336ce89 Wed Aug 27 13:28:08 2025 -0700
    ongoing work on quickLift hgc page plus a fix for genepreds that don't successfully quickLift
• src/hg/lib/quickLift.c
  • lines changed 3, context: html, text, full: html, text
    485724bcdce8810dcf1b65755c97dbb3c39fa02a Mon Aug 25 15:37:25 2025 -0700
    give quickLiftChains there own methods in hgTracks and a special hgc page
  • lines changed 24, context: html, text, full: html, text
    a75cfac22803c312074299aa0dcf286ca336ce89 Wed Aug 27 13:28:08 2025 -0700
    ongoing work on quickLift hgc page plus a fix for genepreds that don't successfully quickLift
• src/hg/makeDb/doc/hg38/problematic.txt
  • lines changed 6, context: html, text, full: html, text
    e05b985e2e81191b8e46da0afd336382afc66e12 Fri Aug 29 00:58:40 2025 -0700
    adding panmask track, refs #36293
• src/hg/makeDb/trackDb/human/hg38/crossTissueMaps.html
  • lines changed 16, context: html, text, full: html, text
    eb9441d7f6347f6b9ed58aeae694c75ec7b3eb61 Thu Aug 28 17:03:18 2025 -0700
    Improve the column names for single cell output using combined facets and matrix, changed column count to cell count, column val to read count. Also updated the 4 html files with improved notations about those columns, and corrected note about expCount field. Added a new tag for trackDb singleCellColumnNames off to support old default column names. fixes #34628
• src/hg/makeDb/trackDb/human/hg38/fetalGeneAtlas.html
  • lines changed 16, context: html, text, full: html, text
    eb9441d7f6347f6b9ed58aeae694c75ec7b3eb61 Thu Aug 28 17:03:18 2025 -0700
    Improve the column names for single cell output using combined facets and matrix, changed column count to cell count, column val to read count. Also updated the 4 html files with improved notations about those columns, and corrected note about expCount field. Added a new tag for trackDb singleCellColumnNames off to support old default column names. fixes #34628
• src/hg/makeDb/trackDb/human/hg38/problematic.html
  • lines changed 22, context: html, text, full: html, text
    e05b985e2e81191b8e46da0afd336382afc66e12 Fri Aug 29 00:58:40 2025 -0700
    adding panmask track, refs #36293
  • lines changed 3, context: html, text, full: html, text
    d3d7a608470d51e11d838ef30db3af88d6be0667 Fri Aug 29 01:04:51 2025 -0700
    tiny typo
  • lines changed 5, context: html, text, full: html, text
    fb1dd95190e117c536c04e4915736b7c672c08ec Fri Aug 29 01:26:12 2025 -0700
    changing wording of track docs page a little, now that GIAB data does exist for hg38, refs #31062
• src/hg/makeDb/trackDb/human/hg38/problematic.ra
  • lines changed 10, context: html, text, full: html, text
    e05b985e2e81191b8e46da0afd336382afc66e12 Fri Aug 29 00:58:40 2025 -0700
    adding panmask track, refs #36293
• src/hg/makeDb/trackDb/human/hg38/singleCellMerged.html
  • lines changed 6, context: html, text, full: html, text
    eb9441d7f6347f6b9ed58aeae694c75ec7b3eb61 Thu Aug 28 17:03:18 2025 -0700
    Improve the column names for single cell output using combined facets and matrix, changed column count to cell count, column val to read count. Also updated the 4 html files with improved notations about those columns, and corrected note about expCount field. Added a new tag for trackDb singleCellColumnNames off to support old default column names. fixes #34628
• src/hg/makeDb/trackDb/human/hg38/tabulaSapiens.html
  • lines changed 13, context: html, text, full: html, text
    eb9441d7f6347f6b9ed58aeae694c75ec7b3eb61 Thu Aug 28 17:03:18 2025 -0700
    Improve the column names for single cell output using combined facets and matrix, changed column count to cell count, column val to read count. Also updated the 4 html files with improved notations about those columns, and corrected note about expCount field. Added a new tag for trackDb singleCellColumnNames off to support old default column names. fixes #34628
• src/hg/makeDb/trackDb/human/panelApp.html
  • lines changed 1, context: html, text, full: html, text
    ebccdd48004d96aa3d5dce2d4bd4f493e86b0e4f Fri Aug 29 19:06:39 2025 -0700
    Updating panelApp Aus to include all gene panels but display only the two curated ones by default, refs #36219
• src/hg/makeDb/trackDb/human/panelApp.ra
  • lines changed 4, context: html, text, full: html, text
    ebccdd48004d96aa3d5dce2d4bd4f493e86b0e4f Fri Aug 29 19:06:39 2025 -0700
    Updating panelApp Aus to include all gene panels but display only the two curated ones by default, refs #36219
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    eb9441d7f6347f6b9ed58aeae694c75ec7b3eb61 Thu Aug 28 17:03:18 2025 -0700
    Improve the column names for single cell output using combined facets and matrix, changed column count to cell count, column val to read count. Also updated the 4 html files with improved notations about those columns, and corrected note about expCount field. Added a new tag for trackDb singleCellColumnNames off to support old default column names. fixes #34628
• src/product/mirrorManual.txt
  • lines changed 36, context: html, text, full: html, text
    1954c1095a389ec259e7754dfe9dc5bf98cfba41 Tue Aug 26 05:43:37 2025 -0700
    adding api redirect rules to mirror docs, refs #36269
• src/utils/qa/qaTestScript.py
  • lines changed 10, context: html, text, full: html, text
    70221396ca9c73d88b5e4e8dd25ae5287111805d Thu Aug 28 11:34:04 2025 -0700
    Updating the hgBlat tests due to the change of the hgBlat display, which now has two buttons, No RM

• lines changed: 740
• files changed: 42