All File Changes

v488_preview2 to v488_base (2025-09-15 to 2025-09-22) v488

• confs/hgwdev.hg.conf
  • lines changed 3, context: html, text, full: html, text
    9b9f268d80b9614505e485d08652a617ddef84e0 Sun Sep 21 01:11:16 2025 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 5, context: html, text, full: html, text
    1031734c611c941fe2579426d90aa7e5db7c9cc8 Mon Sep 22 12:41:03 2025 -0700
    extending hub connect docs a little, refs #35667
• src/hg/hgTables/bam.c
  • lines changed 4, context: html, text, full: html, text
    c18ab1c5577b32368f3cf24abfe1664567a8420e Mon Sep 22 08:59:48 2025 -0700
    generate correct download link for BAMs in /gbdb #36390
• src/hg/hgTables/hic.c
  • lines changed 3, context: html, text, full: html, text
    03478e629ac21b1dc68b92ae7d993d1a7314cac2 Mon Sep 22 11:15:22 2025 -0700
    hgTables needed help finding trackDb for hic custom tracks, refs #36389
• src/hg/hgTables/mainPage.c
  • lines changed 10, context: html, text, full: html, text
    03478e629ac21b1dc68b92ae7d993d1a7314cac2 Mon Sep 22 11:15:22 2025 -0700
    hgTables needed help finding trackDb for hic custom tracks, refs #36389
• src/hg/hgTracks/hgTracks.c
  • lines changed 53, context: html, text, full: html, text
    0bf3abced28b96f2d93e811421130345c6549d9c Fri Sep 19 16:51:41 2025 -0700
    hgTracks cleanup suggested by Max, no rm for it.
  • lines changed 2, context: html, text, full: html, text
    583265155026a2b9b68d85daeb371147226ff990 Mon Sep 22 12:12:36 2025 -0700
    Adding new keyboard shortcut for quick hub connect, refs #35667
• src/hg/htdocs/admin/filePicker.html
  • lines changed 8, context: html, text, full: html, text
    7e32381bc2152e0bdf4e5be2f46fe033e80cb5d5 Mon Sep 15 17:41:54 2025 -0700
    (1) Broadcast a "filePickerReady" message on filePicker.html mode. (2) Make special input mode optional with a config parameter.
  • lines changed 6, context: html, text, full: html, text
    4eaf56ff3eb90ea8ebcf1697ac3830b8a7b5465f Tue Sep 16 09:32:52 2025 -0700
    Handle file picker edge case - picker is open but doesn't have handles for requested files. Also more comments and reformatting.
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 49, context: html, text, full: html, text
    157a2aba6a9a20bd1f995daf6b799f552a20c77c Fri Sep 19 12:56:24 2025 -0700
    Announcing the DDG2P track for hg38 and hg19, refs #35054
• src/hg/htdocs/images/newsArchImages/ddg2p.png
  • lines changed 0, context: html, text, full: html, text
    a9ecb97d353c65a2b0af67447a504a818dfd3252 Fri Sep 19 12:35:37 2025 -0700
    Adding the news image for the DDG2P track, refs #35054
• src/hg/htdocs/indexMeetings.html
  • lines changed 1, context: html, text, full: html, text
    d7a3005936e9074dbf36aa846bef00e8e143dd5e Thu Sep 18 14:06:21 2025 -0700
    Removing Poster Gallery link due to more work and updates to the Poster Gallery page, refs #36182
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    157a2aba6a9a20bd1f995daf6b799f552a20c77c Fri Sep 19 12:56:24 2025 -0700
    Announcing the DDG2P track for hg38 and hg19, refs #35054
• src/hg/htdocs/staff.html
  • lines changed 6, context: html, text, full: html, text
    9b6dede9f571a5ea40393b5e1399e978114b741b Fri Sep 19 13:14:24 2025 -0700
    Adding the summer 2025 student interns to the staff page, no Redmine
• src/hg/js/ajax.js
  • lines changed 1, context: html, text, full: html, text
    655bfafe866c38e0e881de53245836b6b5b340b9 Thu Sep 18 12:26:43 2025 -0700
    Revert "make sure AJAX called cartDump adds "db" to the URL" This reverts commit c04c97754729a8477bb1a57b2aaed75dcdb122b6.
• src/hg/js/hgGateway.js
  • lines changed 1, context: html, text, full: html, text
    38fb5103beda4b0f705574c541b290b8b253e670 Mon Sep 22 12:23:38 2025 -0700
    Remove 0-length characters from search strings, refs #36387
• src/hg/js/hgHubConnect.js
  • lines changed 19, context: html, text, full: html, text
    6f3696eafb4b9006227c1d5f42f8ccd6ecb5705e Thu Sep 18 10:32:02 2025 -0700
    Fix tab selection on hgHubConnect to update the url and make the page load the correct tab based on the url, refs Jonathan for the paper
• src/hg/js/hgSearch.js
  • lines changed 1, context: html, text, full: html, text
    38fb5103beda4b0f705574c541b290b8b253e670 Mon Sep 22 12:23:38 2025 -0700
    Remove 0-length characters from search strings, refs #36387
• src/hg/js/hgTracks.js
  • lines changed 1, context: html, text, full: html, text
    38fb5103beda4b0f705574c541b290b8b253e670 Mon Sep 22 12:23:38 2025 -0700
    Remove 0-length characters from search strings, refs #36387
• src/hg/js/igv.min.js
  • lines changed 2, context: html, text, full: html, text
    7e32381bc2152e0bdf4e5be2f46fe033e80cb5d5 Mon Sep 15 17:41:54 2025 -0700
    (1) Broadcast a "filePickerReady" message on filePicker.html mode. (2) Make special input mode optional with a config parameter.
  • lines changed 1, context: html, text, full: html, text
    1e82a3b6411cc32e625b36911f4949b552ffba3d Mon Sep 15 19:05:40 2025 -0700
    Add igv configuration menu to name panel. Also expose igv.js createIcon function
• src/hg/js/igvFileHelper.js
  • lines changed 17, context: html, text, full: html, text
    7e32381bc2152e0bdf4e5be2f46fe033e80cb5d5 Mon Sep 15 17:41:54 2025 -0700
    (1) Broadcast a "filePickerReady" message on filePicker.html mode. (2) Make special input mode optional with a config parameter.
  • lines changed 50, context: html, text, full: html, text
    1e82a3b6411cc32e625b36911f4949b552ffba3d Mon Sep 15 19:05:40 2025 -0700
    Add igv configuration menu to name panel. Also expose igv.js createIcon function
  • lines changed 40, context: html, text, full: html, text
    a83239e1585aac37a58288c933d2da9f3e4b8c9f Mon Sep 15 20:27:57 2025 -0700
    Bug fix -- igv local session was not cleared after removing last track (and consequently igvBrowser. Move igv configuration menu close to cog icon from where it's invoked
  • lines changed 243, context: html, text, full: html, text
    4eaf56ff3eb90ea8ebcf1697ac3830b8a7b5465f Tue Sep 16 09:32:52 2025 -0700
    Handle file picker edge case - picker is open but doesn't have handles for requested files. Also more comments and reformatting.
  • lines changed 3, context: html, text, full: html, text
    c2587413555c7cabd82b21c578d5a6f99599e7d7 Tue Sep 16 09:45:03 2025 -0700
    Bug -- missing await
• src/hg/js/parallelSegments.js
  • lines changed 446, context: html, text, full: html, text
    6ec3c94465c621547de374cef3c52db43b9f7bee Sun Sep 21 11:01:16 2025 -0700
    playing around with new display mode
• src/hg/lib/fakeCurl.c
  • lines changed 4, context: html, text, full: html, text
    336f121807d25e8762b218c6e00b03d3ab0aaef1 Mon Sep 22 09:34:47 2025 -0700
    Certain free() calls should be freeMem() to match the allocation routine, refs #36389
• src/hg/lib/hui.c
  • lines changed 5, context: html, text, full: html, text
    cec653ec536e9a536256b3ebddc39be5ef9701c8 Sun Sep 21 23:37:18 2025 -0700
    adding spliceAi wt track, refs #35100
• src/hg/lib/straw/cStraw.cpp
  • lines changed 12, context: html, text, full: html, text
    c2007dd0e1b2b6df27907f5d4678fa9458d0cbc9 Thu Sep 18 22:47:37 2025 -0700
    Fix to find normalization options for hic files that don't annotate the first chromosome, refs #36313
  • lines changed 3, context: html, text, full: html, text
    336f121807d25e8762b218c6e00b03d3ab0aaef1 Mon Sep 22 09:34:47 2025 -0700
    Certain free() calls should be freeMem() to match the allocation routine, refs #36389
• src/hg/lib/straw/hReplaceGbdb.h
  • lines changed 3, context: html, text, full: html, text
    336f121807d25e8762b218c6e00b03d3ab0aaef1 Mon Sep 22 09:34:47 2025 -0700
    Certain free() calls should be freeMem() to match the allocation routine, refs #36389
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    fb1e22b084def517ed20cc226a7e2e1fd4806abc Fri Sep 19 16:06:08 2025 -0700
    RefSeq update adding a couple of new ones refs #29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    fb1e22b084def517ed20cc226a7e2e1fd4806abc Fri Sep 19 16:06:08 2025 -0700
    RefSeq update adding a couple of new ones refs #29545
• src/hg/makeDb/doc/hg38/colorsDb.txt
  • lines changed 231, context: html, text, full: html, text
    7695dddf01704294850c170907fe7c4607576dc3 Fri Sep 19 15:27:25 2025 -0700
    Adding the makedoc for ColorsDb, refs #34120
• src/hg/makeDb/doc/hg38/ddg2p.txt
  • lines changed 191, context: html, text, full: html, text
    84e874dbd850363c0e7169978dcffc031d8f75f6 Fri Sep 19 12:07:03 2025 -0700
    Adding the DDG2P make doc, refs #35054
• src/hg/makeDb/doc/hg38/spliceAI.txt
  • lines changed 1, context: html, text, full: html, text
    cec653ec536e9a536256b3ebddc39be5ef9701c8 Sun Sep 21 23:37:18 2025 -0700
    adding spliceAi wt track, refs #35100
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 13, context: html, text, full: html, text
    5e3d6a4c37c01514443d2bf6c1632b14cbadf7dd Fri Sep 19 16:28:49 2025 -0700
    RefSeq update adding a couple of new ones refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    fb1e22b084def517ed20cc226a7e2e1fd4806abc Fri Sep 19 16:06:08 2025 -0700
    RefSeq update adding a couple of new ones refs #29545
• src/hg/makeDb/doc/ucscGenes/mm39.gencodeVM38.sh
  • lines changed 52, context: html, text, full: html, text
    eae5b1c7579021039d592b5d7f4ce27a166caa89 Wed Sep 17 13:08:05 2025 -0700
    Makedoc for VM38 knownGene, refs #36165
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 6, context: html, text, full: html, text
    44c4479a850baccdca9e6b239f2899c20d30d941 Fri Sep 19 16:25:14 2025 -0700
    RefSeq update adding a couple of new ones refs #29545
• src/hg/makeDb/trackDb/human/decipher.ra
  • lines changed 1, context: html, text, full: html, text
    696c4a434f69146ba5729acb48572fa193887e9c Fri Sep 19 11:04:56 2025 -0700
    Updating the searching for the population CNV file Yesenia wrangled, no Redmine
  • lines changed 9, context: html, text, full: html, text
    8aae31876e1061cfdae882f5d5e4f7ae9b5534df Fri Sep 19 11:19:50 2025 -0700
    Staging the DDG2P track for release, refs #35054
  • lines changed 2, context: html, text, full: html, text
    a6b27a9e2934c7d1454209d20ff0eddeb4069d47 Fri Sep 19 12:55:49 2025 -0700
    Adding pennantIcons for the DDG2P track, refs #35054
• src/hg/makeDb/trackDb/human/decipherContainer.html
  • lines changed 63, context: html, text, full: html, text
    8aae31876e1061cfdae882f5d5e4f7ae9b5534df Fri Sep 19 11:19:50 2025 -0700
    Staging the DDG2P track for release, refs #35054
  • lines changed 30, context: html, text, full: html, text
    1dee540669a2ac51afa2ebdff3b53e7f3abc7cc2 Fri Sep 19 12:24:43 2025 -0700
    Updating the descripiton to match the styling of the other tracks in the composite, refs #35054
• src/hg/makeDb/trackDb/human/hg38/problematic.ra
  • lines changed 1, context: html, text, full: html, text
    50df9e24774f4e418396a23a107d1cdf8191f880 Fri Sep 19 09:11:15 2025 -0700
    Staging the Panmask track on hgwbeta, refs #36293
• src/hg/makeDb/trackDb/human/hg38/spliceAi.ra
  • lines changed 38, context: html, text, full: html, text
    cec653ec536e9a536256b3ebddc39be5ef9701c8 Sun Sep 21 23:37:18 2025 -0700
    adding spliceAi wt track, refs #35100
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    cec653ec536e9a536256b3ebddc39be5ef9701c8 Sun Sep 21 23:37:18 2025 -0700
    adding spliceAi wt track, refs #35100
• src/hg/makeDb/trackDb/human/hg38/varFreqs.html
  • lines changed 56, context: html, text, full: html, text
    9980a96c9edc6ebe150c32d7857a1c5466de8e05 Tue Sep 16 05:15:38 2025 -0700
    docs page for mexico biobank, refs #36259
  • lines changed 1, context: html, text, full: html, text
    c01c8fdded5d12a949f0b97684685aecb9b4cbaf Tue Sep 16 14:14:22 2025 -0700
    small change to docs page, as per submitter
• src/hg/makeDb/trackDb/human/spliceAI.html
  • lines changed 26, context: html, text, full: html, text
    cec653ec536e9a536256b3ebddc39be5ef9701c8 Sun Sep 21 23:37:18 2025 -0700
    adding spliceAi wt track, refs #35100
• src/hg/makeDb/trackDb/human/spliceAI.ra
  • lines changed 10, context: html, text, full: html, text
    cec653ec536e9a536256b3ebddc39be5ef9701c8 Sun Sep 21 23:37:18 2025 -0700
    adding spliceAi wt track, refs #35100
• src/hg/makeDb/trackDb/human/spliceAIWt.ra
  • lines changed 45, context: html, text, full: html, text
    cec653ec536e9a536256b3ebddc39be5ef9701c8 Sun Sep 21 23:37:18 2025 -0700
    adding spliceAi wt track, refs #35100
• src/hg/makeDb/trackDb/human/spliceImpactSuper.ra
  • lines changed 5, context: html, text, full: html, text
    cec653ec536e9a536256b3ebddc39be5ef9701c8 Sun Sep 21 23:37:18 2025 -0700
    adding spliceAi wt track, refs #35100
• src/hg/makeDb/trackDb/mouse/mm39/knownGene.alpha.ra
  • lines changed 6, context: html, text, full: html, text
    476fb549a27985605163e8c58fdfd61ab8ad0abf Wed Sep 17 13:07:10 2025 -0700
    VM38 knownGene trackDb
• src/hg/makeDb/trackDb/mouse/mm39/knownGeneArchive.ra
  • lines changed 24, context: html, text, full: html, text
    0b82b501aff92020f3e79021baaa80bd22e2cc5f Wed Sep 17 13:34:01 2025 -0700
    Adding knownGene VM37 to knownGene archive, refs #36165
• src/hg/makeDb/trackDb/mouse/mm39/knownGeneVM38.html
  • lines changed 124, context: html, text, full: html, text
    476fb549a27985605163e8c58fdfd61ab8ad0abf Wed Sep 17 13:07:10 2025 -0700
    VM38 knownGene trackDb
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    476fb549a27985605163e8c58fdfd61ab8ad0abf Wed Sep 17 13:07:10 2025 -0700
    VM38 knownGene trackDb
• src/hg/utils/automation/asmHubRepeatMasker.sh
  • lines changed 9, context: html, text, full: html, text
    e1874141e3c52a43cbdd32bcceff60f2a4232807 Mon Sep 15 12:57:55 2025 -0700
    fixed rmToTrackHub.pl script from Robert
• src/hg/utils/automation/doBlastzChainNet.pl
  • lines changed 17, context: html, text, full: html, text
    d82bb72f23414b783c5f3a7158a36002f27270d8 Mon Sep 15 15:24:56 2025 -0700
    adding quickLift file creation refs #35575
  • lines changed 6, context: html, text, full: html, text
    6ddbb235ad633ecb2f7958329710b79fb07ff1c5 Tue Sep 16 11:51:08 2025 -0700
    adding the quickLift symlinks to /gbdb/ when database assembly refs #35575
• src/hg/utils/automation/doRepeatMasker.pl
  • lines changed 1, context: html, text, full: html, text
    67eb161b05397c50dcfb3c7ec1b60654b15d66d2 Mon Sep 15 13:00:04 2025 -0700
    fixed rmToTrackHub.pl script from Robert

• lines changed: 1994
• files changed: 63