All File Changes

v486_preview2 to v486_base (2025-08-04 to 2025-08-11) v486

• confs/hgwbeta.hg.conf
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    2b49261ee1bea8a6011bbd22d1413d72df8fdcc2 Sun Aug 10 01:11:15 2025 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/cdw/lib/cdwPageFooter.h
  • lines changed 5, context: html, text, full: html, text
    7985071d2ffc9f54f909048ccbd2f97cd735f299 Fri Aug 8 08:07:53 2025 -0700
    Fixing style class on links in CDW cdwPageFooter.h
• src/hg/cirm/gateway/htdocs/inc/footer.html
  • lines changed 2, context: html, text, full: html, text
    4a610cfcb2a33c8627aa0c5660a52bfaebf080c2 Thu Aug 7 13:39:36 2025 -0700
    Removing external link class on internal Timeline page on CDW inc/footer.html
• src/hg/hgConvert/hgConvert.c
  • lines changed 2, context: html, text, full: html, text
    b4c71eaaef3b428af083e5d6c3ced9392367c187 Fri Aug 8 10:18:50 2025 -0700
    setup chromAlias for use in hgConvert
• src/hg/hgLiftOver/hgLiftOver.c
  • lines changed 21, context: html, text, full: html, text
    1d4663b313f73cf69360c84c3c123821f15cee26 Sat Aug 9 11:49:49 2025 -0700
    some fixes for hgLiftOver using Genark hubs
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 4, context: html, text, full: html, text
    5f3f7a90d0801344279f4ac07091a35a2723b683 Mon Aug 4 15:41:27 2025 -0700
    Making changes from code review, CR #36198
  • lines changed 30, context: html, text, full: html, text
    9bc72b8d97e6fdd1f64881e08db9e9ac33d26bd3 Fri Aug 8 14:05:51 2025 -0700
    Releasing and announcing the PanelApp Australia track, refs #35758
  • lines changed 29, context: html, text, full: html, text
    705f2336e85d630113f716b97c66008df31584f2 Fri Aug 8 14:23:40 2025 -0700
    Staging news release for CLS long transcripts track, refs #35122
  • lines changed 1, context: html, text, full: html, text
    796c0f466262e4c4d9d56a8b75e394d9b66380e6 Fri Aug 8 16:41:27 2025 -0700
    Updating the image location for the PanelApp Australia track announcement, refs #35758
• src/hg/htdocs/images/clsLongTranscript.png
  • lines changed 0, context: html, text, full: html, text
    705f2336e85d630113f716b97c66008df31584f2 Fri Aug 8 14:23:40 2025 -0700
    Staging news release for CLS long transcripts track, refs #35122
• src/hg/htdocs/images/newsArchImages/panelAppAustralia.jpg
  • lines changed 0, context: html, text, full: html, text
    9bc72b8d97e6fdd1f64881e08db9e9ac33d26bd3 Fri Aug 8 14:05:51 2025 -0700
    Releasing and announcing the PanelApp Australia track, refs #35758
• src/hg/htdocs/images/panelAppAustralia.jpg
  • lines changed 0, context: html, text, full: html, text
    2393e9c3ee16112021d17b379ef63503ee5873c5 Fri Aug 8 16:38:14 2025 -0700
    Adding image for the PanelApp Australia track announcement, refs #35758
• src/hg/htdocs/inc/gbPageStartHardcoded.html
  • lines changed 4, context: html, text, full: html, text
    9ab37c22a7bd5ac747c9c8ce0271ecffd1d4862f Mon Aug 4 16:41:35 2025 -0700
    Adding the Donate button up to the blue nav bar, refs #36202
  • lines changed 4, context: html, text, full: html, text
    379665d3f5ff46d9c4ae126c7a6c870f5589762a Mon Aug 4 16:44:24 2025 -0700
    Revert "Adding the Donate button up to the blue nav bar, refs #36202" This reverts commit 9ab37c22a7bd5ac747c9c8ce0271ecffd1d4862f.
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 6, context: html, text, full: html, text
    9ab37c22a7bd5ac747c9c8ce0271ecffd1d4862f Mon Aug 4 16:41:35 2025 -0700
    Adding the Donate button up to the blue nav bar, refs #36202
  • lines changed 6, context: html, text, full: html, text
    379665d3f5ff46d9c4ae126c7a6c870f5589762a Mon Aug 4 16:44:24 2025 -0700
    Revert "Adding the Donate button up to the blue nav bar, refs #36202" This reverts commit 9ab37c22a7bd5ac747c9c8ce0271ecffd1d4862f.
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    9bc72b8d97e6fdd1f64881e08db9e9ac33d26bd3 Fri Aug 8 14:05:51 2025 -0700
    Releasing and announcing the PanelApp Australia track, refs #35758
  • lines changed 12, context: html, text, full: html, text
    705f2336e85d630113f716b97c66008df31584f2 Fri Aug 8 14:23:40 2025 -0700
    Staging news release for CLS long transcripts track, refs #35122
• src/hg/htdocs/makefile
  • lines changed 1, context: html, text, full: html, text
    fceca77094f54cf65d73d7cef5db47a0c074195a Mon Aug 4 15:58:05 2025 -0700
    Fixing the makefile which was complaining Error 23 because the file was not owned by qateam.
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    95b2b325bf5a1fe48ee74a56408275edaf61049d Mon Aug 11 15:26:20 2025 -0700
    New version number v486
• src/hg/js/ajax.js
  • lines changed 1, context: html, text, full: html, text
    c04c97754729a8477bb1a57b2aaed75dcdb122b6 Wed Aug 6 11:54:07 2025 -0700
    make sure AJAX called cartDump adds "db" to the URL
  • lines changed 1, context: html, text, full: html, text
    3f33aec6742f933956af5ea084f97f4cbb2ff8aa Wed Aug 6 14:52:44 2025 -0700
    oops... add missing &
• src/hg/js/hgTracks.js
  • lines changed 5, context: html, text, full: html, text
    1579f2c7a1412b6c9073d995bd29d2ca325157d9 Wed Aug 6 13:58:13 2025 -0700
    pass db into imgTrackOnly callbacks
  • lines changed 5, context: html, text, full: html, text
    e207bd65b41b5536965ff6b62286350152ec50ec Wed Aug 6 14:47:31 2025 -0700
    Revert "pass db into imgTrackOnly callbacks" This reverts commit 1579f2c7a1412b6c9073d995bd29d2ca325157d9.
  • lines changed 5, context: html, text, full: html, text
    bccf5bd09a77a1158d14d23716c56b185386b5b0 Wed Aug 6 15:00:50 2025 -0700
    Reapply "pass db into imgTrackOnly callbacks" This reverts commit e207bd65b41b5536965ff6b62286350152ec50ec.
• src/hg/lib/hdb.c
  • lines changed 13, context: html, text, full: html, text
    1d4663b313f73cf69360c84c3c123821f15cee26 Sat Aug 9 11:49:49 2025 -0700
    some fixes for hgLiftOver using Genark hubs
• src/hg/lib/recount3.as
  • lines changed 2, context: html, text, full: html, text
    003337bf766f61f102c61cb924af98ad09372ad0 Tue Aug 5 12:41:24 2025 -0700
    added size and splice junction filters to recount3
• src/hg/liftOver/makefile
  • lines changed 1, context: html, text, full: html, text
    76c80e8a2d474b39149845cc226bdfad4332a2cf Tue Aug 5 12:45:53 2025 -0700
    typo fix in makefile from user hartzell at github
• src/hg/makeDb/doc/asmHubs/groups.txt
  • lines changed 1, context: html, text, full: html, text
    241bc6b486d5da90860df83aec006e30363e43e7 Wed Aug 6 10:53:04 2025 -0700
    Updating the RNA track group label for GenArk, refs #36093
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 148, context: html, text, full: html, text
    69912c49d43ebd244c03a5defaee9575b7082d4a Mon Aug 4 22:06:06 2025 -0700
    BRC update refs #34337
• src/hg/makeDb/doc/genarkOrg.txt
  • lines changed 34, context: html, text, full: html, text
    9e79e16956fd1400cda121b2ac69aaa27a88ab8a Mon Aug 11 14:39:59 2025 -0700
    add new method of calculating genarkOrg table
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 88, context: html, text, full: html, text
    1894735f9c73d4188ec8f613dfc73fa99e13c8bc Wed Aug 6 10:38:56 2025 -0700
    MaveDB track revision to include sequence alignments, refs #31812
• src/hg/makeDb/doc/hg38/recount3.txt
  • lines changed 31, context: html, text, full: html, text
    003337bf766f61f102c61cb924af98ad09372ad0 Tue Aug 5 12:41:24 2025 -0700
    added size and splice junction filters to recount3
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 205, context: html, text, full: html, text
    69912c49d43ebd244c03a5defaee9575b7082d4a Mon Aug 4 22:06:06 2025 -0700
    BRC update refs #34337
• src/hg/makeDb/doc/mm10.txt
  • lines changed 33, context: html, text, full: html, text
    003337bf766f61f102c61cb924af98ad09372ad0 Tue Aug 5 12:41:24 2025 -0700
    added size and splice junction filters to recount3
• src/hg/makeDb/outside/clsLongReadRna/clsTrackTool
  • lines changed 4, context: html, text, full: html, text
    b41c642953ac393117aa27489d92279a50887e6f Wed Aug 6 12:05:42 2025 -0700
    set two more views to non-hide and their tracks to hide to try to work around selection issues. However, this does not work. Checkin to get help from others
  • lines changed 6, context: html, text, full: html, text
    74a92d6585c2ce31334ab80849982caea1ccca60 Wed Aug 6 13:17:30 2025 -0700
    hopefully fixed composite control issues on clsLongReadRna
  • lines changed 1, context: html, text, full: html, text
    ca87c570c3f3d00af004d9dc296740372c1f2c1c Wed Aug 6 14:42:52 2025 -0700
    fixed on more CLS composite track issue
• src/hg/makeDb/outside/recount3/junctionsToBed.py
  • lines changed 6, context: html, text, full: html, text
    003337bf766f61f102c61cb924af98ad09372ad0 Tue Aug 5 12:41:24 2025 -0700
    added size and splice junction filters to recount3
• src/hg/makeDb/trackDb/human/hg38/clsLongReadRna.ra
  • lines changed 98, context: html, text, full: html, text
    b41c642953ac393117aa27489d92279a50887e6f Wed Aug 6 12:05:42 2025 -0700
    set two more views to non-hide and their tracks to hide to try to work around selection issues. However, this does not work. Checkin to get help from others
  • lines changed 111, context: html, text, full: html, text
    74a92d6585c2ce31334ab80849982caea1ccca60 Wed Aug 6 13:17:30 2025 -0700
    hopefully fixed composite control issues on clsLongReadRna
  • lines changed 1, context: html, text, full: html, text
    ca87c570c3f3d00af004d9dc296740372c1f2c1c Wed Aug 6 14:42:52 2025 -0700
    fixed on more CLS composite track issue
• src/hg/makeDb/trackDb/human/hg38/long_read_transcripts.ra
  • lines changed 2, context: html, text, full: html, text
    e0c0d49c409e33e0997922ecf4dfec2924fd4191 Fri Aug 8 12:01:35 2025 -0700
    Silent release of long read transcripts track, refs #35122
• src/hg/makeDb/trackDb/human/hg38/mavedb.html
  • lines changed 25, context: html, text, full: html, text
    1894735f9c73d4188ec8f613dfc73fa99e13c8bc Wed Aug 6 10:38:56 2025 -0700
    MaveDB track revision to include sequence alignments, refs #31812
• src/hg/makeDb/trackDb/human/hg38/mavedb.ra
  • lines changed 38, context: html, text, full: html, text
    1894735f9c73d4188ec8f613dfc73fa99e13c8bc Wed Aug 6 10:38:56 2025 -0700
    MaveDB track revision to include sequence alignments, refs #31812
  • lines changed 2, context: html, text, full: html, text
    74c55818c9e08569f24b52bb77ff039bfb04c992 Wed Aug 6 10:52:40 2025 -0700
    Moving MaveDB sequence alignments above the heatmaps by default, refs #31812
• src/hg/makeDb/trackDb/human/hg38/mavedb_align.html
  • lines changed 43, context: html, text, full: html, text
    1894735f9c73d4188ec8f613dfc73fa99e13c8bc Wed Aug 6 10:38:56 2025 -0700
    MaveDB track revision to include sequence alignments, refs #31812
• src/hg/makeDb/trackDb/human/hg38/mavedb_maps.html
  • lines changed 16, context: html, text, full: html, text
    1894735f9c73d4188ec8f613dfc73fa99e13c8bc Wed Aug 6 10:38:56 2025 -0700
    MaveDB track revision to include sequence alignments, refs #31812
• src/hg/makeDb/trackDb/human/hg38/recount3.ra
  • lines changed 35, context: html, text, full: html, text
    003337bf766f61f102c61cb924af98ad09372ad0 Tue Aug 5 12:41:24 2025 -0700
    added size and splice junction filters to recount3
  • lines changed 70, context: html, text, full: html, text
    baaa3bf6a68b611cca4ae2e70408aad376b99284 Wed Aug 6 21:45:23 2025 -0700
    can not get split junction filter to work in composite
  • lines changed 14, context: html, text, full: html, text
    171b29f18a5037d3d19fe6c11049824e462fd497 Wed Aug 6 23:34:22 2025 -0700
    moved filters to individual tracks
  • lines changed 1, context: html, text, full: html, text
    e4e3a81fd04f0a799894b069d1977092d60f5bba Thu Aug 7 15:43:08 2025 -0700
    Updating the track description page. Moving the Methods section before the Data Access, restructuring the Display Conventions section, adding a link to the recount3 website... Removing .html from the html line in trackDb, refs #34886
• src/hg/makeDb/trackDb/human/hs1/cytoBandMapped.trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    14973a6843effe29ee6aeabfb35190cecf54cd62 Thu Aug 7 13:44:45 2025 -0700
    Adding the searchIndex line and stanza for searching the chromosome ideogram, refs #32541
  • lines changed 11, context: html, text, full: html, text
    b5a756529b8ac3b9051d8a6f6bdcaf672c434e58 Fri Aug 8 16:43:08 2025 -0700
    Adding a stanza for the CytoBand track, refs #32541
• src/hg/makeDb/trackDb/human/panelApp.alpha.ra
  • lines changed 2, context: html, text, full: html, text
    e5b6fab7e4e0f80843313e3b7a143265249527e8 Wed Aug 6 16:21:54 2025 -0700
    Updating the PanelApp Genes track description and fixing the hgncID urls, refs #35758
  • lines changed 120, context: html, text, full: html, text
    9bc72b8d97e6fdd1f64881e08db9e9ac33d26bd3 Fri Aug 8 14:05:51 2025 -0700
    Releasing and announcing the PanelApp Australia track, refs #35758
• src/hg/makeDb/trackDb/human/panelApp.html
  • lines changed 6, context: html, text, full: html, text
    e5b6fab7e4e0f80843313e3b7a143265249527e8 Wed Aug 6 16:21:54 2025 -0700
    Updating the PanelApp Genes track description and fixing the hgncID urls, refs #35758
  • lines changed 10, context: html, text, full: html, text
    dc8dfaf0aa08855d2f8351b872797527f03480a5 Wed Aug 6 17:27:19 2025 -0700
    Updating the panelApp description page, refs #35758
• src/hg/makeDb/trackDb/human/panelApp.ra
  • lines changed 80, context: html, text, full: html, text
    9bc72b8d97e6fdd1f64881e08db9e9ac33d26bd3 Fri Aug 8 14:05:51 2025 -0700
    Releasing and announcing the PanelApp Australia track, refs #35758
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    84be64b22a9a57b3263b0040ffa62915c0a20f9d Wed Aug 6 17:38:23 2025 -0700
    Staging the PanelApp Australia track on hgwbeta, refs #35758
  • lines changed 2, context: html, text, full: html, text
    9bc72b8d97e6fdd1f64881e08db9e9ac33d26bd3 Fri Aug 8 14:05:51 2025 -0700
    Releasing and announcing the PanelApp Australia track, refs #35758
• src/hg/makeDb/trackDb/mouse/mm10/clsLongReadRna.ra
  • lines changed 82, context: html, text, full: html, text
    b41c642953ac393117aa27489d92279a50887e6f Wed Aug 6 12:05:42 2025 -0700
    set two more views to non-hide and their tracks to hide to try to work around selection issues. However, this does not work. Checkin to get help from others
  • lines changed 93, context: html, text, full: html, text
    74a92d6585c2ce31334ab80849982caea1ccca60 Wed Aug 6 13:17:30 2025 -0700
    hopefully fixed composite control issues on clsLongReadRna
  • lines changed 1, context: html, text, full: html, text
    ca87c570c3f3d00af004d9dc296740372c1f2c1c Wed Aug 6 14:42:52 2025 -0700
    fixed on more CLS composite track issue
• src/hg/makeDb/trackDb/mouse/mm10/encode4LongRnaTranscripts.ra
  • lines changed 1, context: html, text, full: html, text
    b62a4110a52330ab68ad1a2a2a05f5dfbd22f28c Sun Aug 10 10:25:21 2025 -0700
    forgot to change track line before release, refs #31368
• src/hg/makeDb/trackDb/mouse/mm10/long_read_transcripts.ra
  • lines changed 3, context: html, text, full: html, text
    e0c0d49c409e33e0997922ecf4dfec2924fd4191 Fri Aug 8 12:01:35 2025 -0700
    Silent release of long read transcripts track, refs #35122
• src/hg/makeDb/trackDb/mouse/mm10/recount3.ra
  • lines changed 16, context: html, text, full: html, text
    003337bf766f61f102c61cb924af98ad09372ad0 Tue Aug 5 12:41:24 2025 -0700
    added size and splice junction filters to recount3
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    32eb33d095c68da0fa54075d94e4e927b6cb4d99 Fri Aug 8 13:27:51 2025 -0700
    Silent release of long read transcripts track, refs #35122
  • lines changed 1, context: html, text, full: html, text
    5ec76992b1578c2cc3fd87f4604d3611fd8cbc0d Sun Aug 10 10:17:13 2025 -0700
    removing release tag for mouse long read track
• src/hg/makeDb/trackDb/recount3.html
  • lines changed 31, context: html, text, full: html, text
    e4e3a81fd04f0a799894b069d1977092d60f5bba Thu Aug 7 15:43:08 2025 -0700
    Updating the track description page. Moving the Methods section before the Data Access, restructuring the Display Conventions section, adding a link to the recount3 website... Removing .html from the html line in trackDb, refs #34886
• src/hg/utils/otto/panelApp/doPanelApp.py
  • lines changed 3, context: html, text, full: html, text
    2b19cd11a40b973defb2f4c00b9002634bd6c9bd Thu Aug 7 15:11:10 2025 -0700
    Flipping the file names because the item count check was comparing the new count as the old count and vice versa. This did not change the check at all, since it was looking for 10% absolute difference, but led to a confusing output. No RM.
• src/inc/srcVersion.h
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    95b2b325bf5a1fe48ee74a56408275edaf61049d Mon Aug 11 15:26:20 2025 -0700
    New version number v486
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    2b9cf6c7a13d53d5801c1c5018885ee26fc5c3b1 Mon Aug 11 15:26:01 2025 -0700
    v486 final build, refs #36171

• lines changed: 1664
• files changed: 73