All File Changes

v458_preview2 to v458_base (2023-12-04 to 2023-12-11) v458

• src/hg/gar/gar.cgi.pl
  • lines changed 41, context: html, text, full: html, text
    20b2b8064f87457847fd5b20ac7fb4f66b986edc Fri Dec 8 07:37:07 2023 -0800
    send email to a google group mail list refs #28930
• src/hg/gar/garTable.pl
  • lines changed 1, context: html, text, full: html, text
    303cc7fe3c22a430303783b284c830846f535eaf Fri Dec 8 07:41:09 2023 -0800
    make the table header sticky so it will stay at the top of the page when scrolled refs #28930
• src/hg/gar/mkAlias.pl
  • lines changed 8, context: html, text, full: html, text
    9909807c4830a971e6493793a4d48b3ff42e3a1e Fri Dec 8 07:39:14 2023 -0800
    do not make any alias for UCSC db names refs #28930
• src/hg/hgGeneGraph/hgGeneGraph
  • lines changed 1, context: html, text, full: html, text
    917c0dcd5623fc858c2871418993dedc2745bb0f Tue Dec 5 04:28:27 2023 -0800
    fixing dumbest possible bug thanks to code review, and thanks to chmalee, refs #32714
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 47, context: html, text, full: html, text
    f00ee8d8e407da35c50e5d61815250a49960dabe Tue Dec 5 13:52:12 2023 -0800
    More refinements for displaying RSV results. Still need to make it more config-driven.
• src/hg/hgPhyloPlace/phyloPlace.h
  • lines changed 2, context: html, text, full: html, text
    ff94dc36ad4584d7ccdeeb545b2b92825735d225 Fri Dec 8 09:55:19 2023 -0800
    If an auspiceMeta.json file is specified in config.ra then use it for organism-specific tree colors & filters. Also use CDS coords when writing genome annotations in Auspice output; not all viral genes are CDS-only.
• src/hg/hgPhyloPlace/phyloPlaceMain.c
  • lines changed 8, context: html, text, full: html, text
    0114df80d5034a730eeb50f04fca0afe73af3dce Tue Dec 5 13:51:41 2023 -0800
    When db is really a db/hub, use it as db not just refName.
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
  • lines changed 8, context: html, text, full: html, text
    f00ee8d8e407da35c50e5d61815250a49960dabe Tue Dec 5 13:52:12 2023 -0800
    More refinements for displaying RSV results. Still need to make it more config-driven.
  • lines changed 114, context: html, text, full: html, text
    ff94dc36ad4584d7ccdeeb545b2b92825735d225 Fri Dec 8 09:55:19 2023 -0800
    If an auspiceMeta.json file is specified in config.ra then use it for organism-specific tree colors & filters. Also use CDS coords when writing genome annotations in Auspice output; not all viral genes are CDS-only.
• src/hg/hgTables/bigBed.c
  • lines changed 8, context: html, text, full: html, text
    fe3f52d294f42461f732844e254e8f0caa8990ab Fri Dec 8 08:56:32 2023 -0800
    Adding a NULL check, HT braney in code review #32706
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    e36fcacb6d63cca2f344e5929b4cae77c12f1e9b Tue Dec 5 17:34:21 2023 -0800
    add the ability to simulate a custom track load error that calls errAbort. This used to delete the ctfile, but now just puts out a message.
• src/hg/htdocs/goldenPath/help/mirrorManual.html
  • lines changed 27, context: html, text, full: html, text
    b9693e22a8071944d6438facd0dea2b33ce38d18 Wed Dec 6 08:52:22 2023 -0800
    adding docs how to add public hubs to mirrors, refs #23428
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    debba9d1a4a931d8433a25ff3f3bc375cc1bc765 Mon Dec 11 08:53:36 2023 -0800
    New version number v458
• src/hg/js/hgTracks.js
  • lines changed 7, context: html, text, full: html, text
    05bbbe65e099bbf8e717ce9da12c608b2849bd7b Wed Dec 6 14:38:46 2023 -0800
    Make input boxes in hgTracks dialogs submit on pressing the enter key, refs #32684
• src/hg/js/jquery.contextmenu.js
  • lines changed 15, context: html, text, full: html, text
    ffea7ccf62ba088c64b5f5c3a8e3d56865e4b297 Fri Dec 8 09:33:52 2023 -0800
    More tooltip fixups, hide/show the tooltip when leaving/re-entering the window, hide them upon opening a dropdown, fix hiding/showing them on right clicks and when entering the search bar, refs #32697
• src/hg/js/utils.js
  • lines changed 67, context: html, text, full: html, text
    ffea7ccf62ba088c64b5f5c3a8e3d56865e4b297 Fri Dec 8 09:33:52 2023 -0800
    More tooltip fixups, hide/show the tooltip when leaving/re-entering the window, hide them upon opening a dropdown, fix hiding/showing them on right clicks and when entering the search bar, refs #32697
• src/hg/lib/customTrack.c
  • lines changed 2, context: html, text, full: html, text
    e36fcacb6d63cca2f344e5929b4cae77c12f1e9b Tue Dec 5 17:34:21 2023 -0800
    add the ability to simulate a custom track load error that calls errAbort. This used to delete the ctfile, but now just puts out a message.
• src/hg/lib/hdb.c
  • lines changed 2, context: html, text, full: html, text
    7b6f3754b360c658474379263645fd8e91d6f46d Wed Dec 6 16:49:47 2023 -0800
    add fixTrackDb program that will prune a trackDb table of tracks that have no data
• src/hg/lib/hgFind.c
  • lines changed 3, context: html, text, full: html, text
    10f2c49311106872cac183406d9eb3d875906257 Mon Dec 4 14:39:48 2023 -0800
    Making the refseq historical track open when doing an hgvs search on an outdated transcript, refs #32639
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 4, context: html, text, full: html, text
    a656f1cfedd95d0399c15f6969196e0e8ae23b3c Fri Dec 8 10:16:09 2023 -0800
    adding 4 per user request refs #29545
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    a656f1cfedd95d0399c15f6969196e0e8ae23b3c Fri Dec 8 10:16:09 2023 -0800
    adding 4 per user request refs #29545
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • lines changed 1, context: html, text, full: html, text
    7b6f3754b360c658474379263645fd8e91d6f46d Wed Dec 6 16:49:47 2023 -0800
    add fixTrackDb program that will prune a trackDb table of tracks that have no data
• src/hg/makeDb/trackDb/chicken/galGal5/fantom5.ra
  • lines changed 1, context: html, text, full: html, text
    df3fa676945f8d8c3765ca2f0393d3fcd0fe55c8 Wed Dec 6 15:29:37 2023 -0800
    Squashing old pennantIcons, no RM.
• src/hg/makeDb/trackDb/dog/canFam3/fantom5.ra
  • lines changed 1, context: html, text, full: html, text
    df3fa676945f8d8c3765ca2f0393d3fcd0fe55c8 Wed Dec 6 15:29:37 2023 -0800
    Squashing old pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    df3fa676945f8d8c3765ca2f0393d3fcd0fe55c8 Wed Dec 6 15:29:37 2023 -0800
    Squashing old pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 21, context: html, text, full: html, text
    ee07d5a59eb7fb9bf1062741f44c77388e16c40a Mon Dec 4 15:11:41 2023 -0800
    Restructuring the RefSeqComposite track to be at the mouse and human level so that we can add an override at the hg38/hg19/mm10/mm39 level. The motivation is to have the RefSeq all track on my default for non human and mouse assemblies, but keep only curated for human and mouse. Refs #32716
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV44lift37.ra
  • lines changed 1, context: html, text, full: html, text
    df3fa676945f8d8c3765ca2f0393d3fcd0fe55c8 Wed Dec 6 15:29:37 2023 -0800
    Squashing old pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/hg38/hprcArr.ra
  • lines changed 2, context: html, text, full: html, text
    3e0eca97aa424f446aad5650b7caf3c9b84b48ce Fri Dec 8 15:52:52 2023 -0800
    some clean-up on the HPRC tracks
• src/hg/makeDb/trackDb/human/hg38/hprcArrV1.html
  • lines changed 17, context: html, text, full: html, text
    3e0eca97aa424f446aad5650b7caf3c9b84b48ce Fri Dec 8 15:52:52 2023 -0800
    some clean-up on the HPRC tracks
• src/hg/makeDb/trackDb/human/hg38/hprcChainNet.ra
  • lines changed 2, context: html, text, full: html, text
    3e0eca97aa424f446aad5650b7caf3c9b84b48ce Fri Dec 8 15:52:52 2023 -0800
    some clean-up on the HPRC tracks
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra
  • lines changed 1, context: html, text, full: html, text
    df3fa676945f8d8c3765ca2f0393d3fcd0fe55c8 Wed Dec 6 15:29:37 2023 -0800
    Squashing old pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/hg38/mane.ra
  • lines changed 1, context: html, text, full: html, text
    845fb03943703bf640cb4f32fdced4c06cf81359 Mon Dec 4 15:08:32 2023 -0800
    Forgot to commit my change for the MANE mouseOver improvement, refs #32459
• src/hg/makeDb/trackDb/human/hg38/problematic.ra
  • lines changed 2, context: html, text, full: html, text
    df3fa676945f8d8c3765ca2f0393d3fcd0fe55c8 Wed Dec 6 15:29:37 2023 -0800
    Squashing old pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    df3fa676945f8d8c3765ca2f0393d3fcd0fe55c8 Wed Dec 6 15:29:37 2023 -0800
    Squashing old pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/hg38/trackDb.hprc90way.ra
  • lines changed 8, context: html, text, full: html, text
    3e0eca97aa424f446aad5650b7caf3c9b84b48ce Fri Dec 8 15:52:52 2023 -0800
    some clean-up on the HPRC tracks
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 38, context: html, text, full: html, text
    ee07d5a59eb7fb9bf1062741f44c77388e16c40a Mon Dec 4 15:11:41 2023 -0800
    Restructuring the RefSeqComposite track to be at the mouse and human level so that we can add an override at the hg38/hg19/mm10/mm39 level. The motivation is to have the RefSeq all track on my default for non human and mouse assemblies, but keep only curated for human and mouse. Refs #32716
  • lines changed 1, context: html, text, full: html, text
    df3fa676945f8d8c3765ca2f0393d3fcd0fe55c8 Wed Dec 6 15:29:37 2023 -0800
    Squashing old pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV44.ra
  • lines changed 1, context: html, text, full: html, text
    df3fa676945f8d8c3765ca2f0393d3fcd0fe55c8 Wed Dec 6 15:29:37 2023 -0800
    Squashing old pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 31, context: html, text, full: html, text
    ee07d5a59eb7fb9bf1062741f44c77388e16c40a Mon Dec 4 15:11:41 2023 -0800
    Restructuring the RefSeqComposite track to be at the mouse and human level so that we can add an override at the hg38/hg19/mm10/mm39 level. The motivation is to have the RefSeq all track on my default for non human and mouse assemblies, but keep only curated for human and mouse. Refs #32716
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 17, context: html, text, full: html, text
    ee07d5a59eb7fb9bf1062741f44c77388e16c40a Mon Dec 4 15:11:41 2023 -0800
    Restructuring the RefSeqComposite track to be at the mouse and human level so that we can add an override at the hg38/hg19/mm10/mm39 level. The motivation is to have the RefSeq all track on my default for non human and mouse assemblies, but keep only curated for human and mouse. Refs #32716
• src/hg/makeDb/trackDb/mouse/mm39/knownGene.ra
  • lines changed 1, context: html, text, full: html, text
    df3fa676945f8d8c3765ca2f0393d3fcd0fe55c8 Wed Dec 6 15:29:37 2023 -0800
    Squashing old pennantIcons, no RM.
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    df3fa676945f8d8c3765ca2f0393d3fcd0fe55c8 Wed Dec 6 15:29:37 2023 -0800
    Squashing old pennantIcons, no RM.
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
  • lines changed 15, context: html, text, full: html, text
    ee07d5a59eb7fb9bf1062741f44c77388e16c40a Mon Dec 4 15:11:41 2023 -0800
    Restructuring the RefSeqComposite track to be at the mouse and human level so that we can add an override at the hg38/hg19/mm10/mm39 level. The motivation is to have the RefSeq all track on my default for non human and mouse assemblies, but keep only curated for human and mouse. Refs #32716
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM33.ra
  • lines changed 1, context: html, text, full: html, text
    df3fa676945f8d8c3765ca2f0393d3fcd0fe55c8 Wed Dec 6 15:29:37 2023 -0800
    Squashing old pennantIcons, no RM.
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • lines changed 12, context: html, text, full: html, text
    ee07d5a59eb7fb9bf1062741f44c77388e16c40a Mon Dec 4 15:11:41 2023 -0800
    Restructuring the RefSeqComposite track to be at the mouse and human level so that we can add an override at the hg38/hg19/mm10/mm39 level. The motivation is to have the RefSeq all track on my default for non human and mouse assemblies, but keep only curated for human and mouse. Refs #32716
• src/hg/makeDb/trackDb/rat/rn6/fantom5.ra
  • lines changed 1, context: html, text, full: html, text
    df3fa676945f8d8c3765ca2f0393d3fcd0fe55c8 Wed Dec 6 15:29:37 2023 -0800
    Squashing old pennantIcons, no RM.
• src/hg/makeDb/trackDb/refSeqComposite.ra
  • lines changed 1, context: html, text, full: html, text
    160c7d0da174bb21094fb458577ed945b70dd9fe Mon Dec 4 12:56:20 2023 -0800
    Fixing some broken outlinks, refs #32668
  • lines changed 1, context: html, text, full: html, text
    ee07d5a59eb7fb9bf1062741f44c77388e16c40a Mon Dec 4 15:11:41 2023 -0800
    Restructuring the RefSeqComposite track to be at the mouse and human level so that we can add an override at the hg38/hg19/mm10/mm39 level. The motivation is to have the RefSeq all track on my default for non human and mouse assemblies, but keep only curated for human and mouse. Refs #32716
• src/hg/makeDb/trackDb/rhesus/rheMac8/fantom5.ra
  • lines changed 1, context: html, text, full: html, text
    df3fa676945f8d8c3765ca2f0393d3fcd0fe55c8 Wed Dec 6 15:29:37 2023 -0800
    Squashing old pennantIcons, no RM.
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    df3fa676945f8d8c3765ca2f0393d3fcd0fe55c8 Wed Dec 6 15:29:37 2023 -0800
    Squashing old pennantIcons, no RM.
• src/hg/near/hgNear/knownGene.c
  • lines changed 3, context: html, text, full: html, text
    c5da1c6a2532482e2f990c4a23c80f03654b5324 Tue Dec 5 13:31:44 2023 -0800
    make sure we put the geneTable name on the link from the description lines
• src/hg/utils/automation/doRepeatModeler.pl
  • lines changed 1, context: html, text, full: html, text
    63ecd290dc939b85a1c4cfe01384925076ac0c73 Wed Dec 6 18:32:11 2023 -0800
    correct reference to RepeatModeler binary to record modelerVersion.txt refs #29545
• src/hg/utils/fixTrackDb/fixTrackDb.c
  • lines changed 145, context: html, text, full: html, text
    7b6f3754b360c658474379263645fd8e91d6f46d Wed Dec 6 16:49:47 2023 -0800
    add fixTrackDb program that will prune a trackDb table of tracks that have no data
• src/hg/utils/fixTrackDb/makefile
  • lines changed 3, context: html, text, full: html, text
    7b6f3754b360c658474379263645fd8e91d6f46d Wed Dec 6 16:49:47 2023 -0800
    add fixTrackDb program that will prune a trackDb table of tracks that have no data
• src/hg/utils/makefile
  • lines changed 2, context: html, text, full: html, text
    a8c308afb80bda0d8bcafcaff9f0920afc622e86 Thu Dec 7 00:45:53 2023 -0800
    adding fixTrackDb to userapps, refs #32741
• src/hg/utils/tdbQuery/tdbQuery.c
  • lines changed 2, context: html, text, full: html, text
    208a148e1625db67b80fa3e38a21aba532394810 Tue Dec 5 11:59:25 2023 -0800
    ignore overrides when looking for parents
• src/inc/bigBedCmdSupport.h
  • lines changed 4, context: html, text, full: html, text
    0130f6314dc5ec61189863dc025aad9fbd91c717 Thu Dec 7 15:07:19 2023 -0800
    Add -tsv option to bigBedToBed to create a TSV-style header that can be used with tools that work with TSVs, such as python CVS/TSV reader and Pandas
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    debba9d1a4a931d8433a25ff3f3bc375cc1bc765 Mon Dec 11 08:53:36 2023 -0800
    New version number v458
• src/lib/bigBedCmdSupport.c
  • lines changed 16, context: html, text, full: html, text
    0130f6314dc5ec61189863dc025aad9fbd91c717 Thu Dec 7 15:07:19 2023 -0800
    Add -tsv option to bigBedToBed to create a TSV-style header that can be used with tools that work with TSVs, such as python CVS/TSV reader and Pandas
• src/product/installer/browserSetup.sh
  • lines changed 1, context: html, text, full: html, text
    c04b09f87f28de8fecd79e27fea27e2bfcf28c1f Tue Dec 5 01:34:25 2023 -0800
    fixing proteome bug found by refs #32665
• src/product/mirrorManual.txt
  • lines changed 16, context: html, text, full: html, text
    b9693e22a8071944d6438facd0dea2b33ce38d18 Wed Dec 6 08:52:22 2023 -0800
    adding docs how to add public hubs to mirrors, refs #23428
• src/utils/bigBedToBed/bigBedToBed.c
  • lines changed 8, context: html, text, full: html, text
    0130f6314dc5ec61189863dc025aad9fbd91c717 Thu Dec 7 15:07:19 2023 -0800
    Add -tsv option to bigBedToBed to create a TSV-style header that can be used with tools that work with TSVs, such as python CVS/TSV reader and Pandas
• src/utils/newPythonProg/newPythonProg.c
  • lines changed 1, context: html, text, full: html, text
    e196e2966a9c192db0ae18a94623487dc2d73175 Thu Dec 7 13:34:30 2023 -0800
    chmod 775 instead of 755 so group members can update the /cluster/bin/scripts installation.
• src/utils/qa/weeklybld/buildEnv.csh
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    e8fda12ee8aaa2e6204c1b851aca3a3045ba803d Mon Dec 11 08:52:21 2023 -0800
    v458 final build, refs #32676

• lines changed: 760
• files changed: 64