All File Changes

v462_base to v463_preview (2024-03-11 to 2024-03-18) v463

• confs/asia.hg.conf
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    3ee1c4d8b6b076d0c6548a145b4a8dcc6bca9e56 Sun Mar 17 01:11:22 2024 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 3, context: html, text, full: html, text
    3ee1c4d8b6b076d0c6548a145b4a8dcc6bca9e56 Sun Mar 17 01:11:22 2024 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 3, context: html, text, full: html, text
    3ee1c4d8b6b076d0c6548a145b4a8dcc6bca9e56 Sun Mar 17 01:11:22 2024 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgBlat/hgBlat.c
  • lines changed 6, context: html, text, full: html, text
    c73ce8bdfcc20de7da303476b3aeee1d2d3e313f Tue Mar 12 03:59:50 2024 -0700
    making blat dupl seq ID error message readable for human beings, no redmine, email from JM de sainte agathe
• src/hg/hgPhyloPlace/vcfFromFasta.c
  • lines changed 3, context: html, text, full: html, text
    6dfdf2e6277b1815d40117b0f1ff1508e6f92058 Fri Mar 15 13:41:09 2024 -0700
    Support for M. tuberculosis: at 4M bases, the genome is too large for arrays on the stack. Allocate & free instead.
• src/hg/hgPhyloPlace/writeCustomTracks.c
  • lines changed 6, context: html, text, full: html, text
    6dfdf2e6277b1815d40117b0f1ff1508e6f92058 Fri Mar 15 13:41:09 2024 -0700
    Support for M. tuberculosis: at 4M bases, the genome is too large for arrays on the stack. Allocate & free instead.
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 6, context: html, text, full: html, text
    8ccceea1c52492b6a869af8de3190a387d4b6550 Tue Mar 12 13:41:09 2024 -0700
    added exportedDataHubs dialog and code to deal with quickLifted hubs
• src/hg/hgTracks/chainTrack.c
  • lines changed 11, context: html, text, full: html, text
    a7dd4fa7826142ecfe082ad496d5019effa0c8e6 Wed Mar 13 13:27:35 2024 -0700
    if bigChain trackDb doesn't specify linkDataUrl then try adding .link.bb to the bigDataUrl
  • lines changed 54, context: html, text, full: html, text
    46a8a2fde9e17a401843959b8c0197c95d43ea45 Fri Mar 15 15:54:50 2024 -0700
    add quickLiftover chain to the list of tracks coming from an exported hub
• src/hg/hgTracks/exportedDataHubs.c
  • lines changed 52, context: html, text, full: html, text
    8ccceea1c52492b6a869af8de3190a387d4b6550 Tue Mar 12 13:41:09 2024 -0700
    added exportedDataHubs dialog and code to deal with quickLifted hubs
• src/hg/hgTracks/hgTracks.c
  • lines changed 3, context: html, text, full: html, text
    8ccceea1c52492b6a869af8de3190a387d4b6550 Tue Mar 12 13:41:09 2024 -0700
    added exportedDataHubs dialog and code to deal with quickLifted hubs
  • lines changed 2, context: html, text, full: html, text
    48c599cf257bef018784ab7262db9bc4011629df Tue Mar 12 14:50:16 2024 -0700
    fix pix auto-detection breaking rtracklayer, refs #33214
  • lines changed 7, context: html, text, full: html, text
    5bf315f014b13b0bfb51d268264297b06f370b37 Thu Mar 14 08:16:14 2024 -0700
    changing more info link such that it doesnt change the alignment anymore, refs #33065
  • lines changed 4, context: html, text, full: html, text
    71dd1c30ee6ab2807a14ef4f3beacb1b4c3ca21f Mon Mar 18 03:36:21 2024 -0700
    make move at least one bp, refs #23343
• src/hg/hgTracks/makefile
  • lines changed 1, context: html, text, full: html, text
    8ccceea1c52492b6a869af8de3190a387d4b6550 Tue Mar 12 13:41:09 2024 -0700
    added exportedDataHubs dialog and code to deal with quickLifted hubs
• src/hg/hgTracks/menu.c
  • lines changed 11, context: html, text, full: html, text
    8ccceea1c52492b6a869af8de3190a387d4b6550 Tue Mar 12 13:41:09 2024 -0700
    added exportedDataHubs dialog and code to deal with quickLifted hubs
• src/hg/hgTracks/simpleTracks.c
  • lines changed 10, context: html, text, full: html, text
    7b475d1ee80e5e8725e2caf2b227e81abb413021 Fri Mar 15 13:54:33 2024 -0700
    make maxItemsPossible an hg.conf variable
• src/hg/hgc/bigBedClick.c
  • lines changed 6, context: html, text, full: html, text
    8ccceea1c52492b6a869af8de3190a387d4b6550 Tue Mar 12 13:41:09 2024 -0700
    added exportedDataHubs dialog and code to deal with quickLifted hubs
• src/hg/hgc/hgc.c
  • lines changed 12, context: html, text, full: html, text
    12cb5e1c3222732f385e0509c646b5cd14c53f5c Wed Mar 13 13:29:21 2024 -0700
    another place where we try to find a linkDataUrl if the trackDb doesn't specify it
• src/hg/htdocs/goldenPath/help/cram.html
  • lines changed 10, context: html, text, full: html, text
    45bd9a6393500fbd7565c85875ccf2e3d82f07ac Tue Mar 12 09:49:51 2024 -0700
    Edits to Mark Diekhans recent changes for the CRAM refUrl setting, refs #33061
• src/hg/htdocs/goldenPath/help/hic.html
  • lines changed 8, context: html, text, full: html, text
    5551b0fccd8b90a7bf3f19ff7273ac5329691bb4 Mon Mar 11 14:22:15 2024 -0700
    Clarifying that only hic versions 6-8 are supported, not 9. Refs #33054
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 3, context: html, text, full: html, text
    45bd9a6393500fbd7565c85875ccf2e3d82f07ac Tue Mar 12 09:49:51 2024 -0700
    Edits to Mark Diekhans recent changes for the CRAM refUrl setting, refs #33061
  • lines changed 11, context: html, text, full: html, text
    12bb23814fdb530c7ec548ca00d9b7f06c81ec77 Thu Mar 14 07:50:08 2024 -0700
    adding a note about bigBedMaxItems to tdb docs, refs #33023
  • lines changed 1, context: html, text, full: html, text
    8132683ea01b86501483bef1faed10cc0a77419e Thu Mar 14 07:56:11 2024 -0700
    adding a note about maxItems limit, refs #33023
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 1, context: html, text, full: html, text
    8ccceea1c52492b6a869af8de3190a387d4b6550 Tue Mar 12 13:41:09 2024 -0700
    added exportedDataHubs dialog and code to deal with quickLifted hubs
• src/hg/inc/exportedDataHubs.h
  • lines changed 7, context: html, text, full: html, text
    8ccceea1c52492b6a869af8de3190a387d4b6550 Tue Mar 12 13:41:09 2024 -0700
    added exportedDataHubs dialog and code to deal with quickLifted hubs
  • lines changed 11, context: html, text, full: html, text
    9c3e6d832e0b4b881dadc9ad039483f9193d970b Tue Mar 12 13:47:25 2024 -0700
    full definition of exportedDataHubs structure
  • lines changed 5, context: html, text, full: html, text
    72d39449db0b514146be085cd8620740f32b8a5a Tue Mar 12 13:52:10 2024 -0700
    try this again
• src/hg/inc/hubConnect.h
  • lines changed 4, context: html, text, full: html, text
    8ccceea1c52492b6a869af8de3190a387d4b6550 Tue Mar 12 13:41:09 2024 -0700
    added exportedDataHubs dialog and code to deal with quickLifted hubs
• src/hg/inc/instaPort.h
  • lines changed 18, context: html, text, full: html, text
    8ccceea1c52492b6a869af8de3190a387d4b6550 Tue Mar 12 13:41:09 2024 -0700
    added exportedDataHubs dialog and code to deal with quickLifted hubs
• src/hg/inc/quickLift.h
  • lines changed 19, context: html, text, full: html, text
    8ccceea1c52492b6a869af8de3190a387d4b6550 Tue Mar 12 13:41:09 2024 -0700
    added exportedDataHubs dialog and code to deal with quickLifted hubs
• src/hg/inc/trackHub.h
  • lines changed 1, context: html, text, full: html, text
    8ccceea1c52492b6a869af8de3190a387d4b6550 Tue Mar 12 13:41:09 2024 -0700
    added exportedDataHubs dialog and code to deal with quickLifted hubs
  • lines changed 1, context: html, text, full: html, text
    46a8a2fde9e17a401843959b8c0197c95d43ea45 Fri Mar 15 15:54:50 2024 -0700
    add quickLiftover chain to the list of tracks coming from an exported hub
• src/hg/js/hgSearch.js
  • lines changed 4, context: html, text, full: html, text
    9302f32f52e5aa823884f7e0b07339b9459fd582 Thu Mar 14 14:26:47 2024 -0700
    Only add match description to autocomplete results when it is defined, refs #29611
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    fb23bce308b7ce29749b4f6a0347bada22e8c885 Thu Mar 14 15:56:53 2024 -0700
    Set the value and label for the autocomplete data to the correct variables so the bolded item stays in the drop down list but then when you select the item the bold tags go away in the input box, refs #29611
• src/hg/js/hgTracks.js
  • lines changed 8, context: html, text, full: html, text
    8ccceea1c52492b6a869af8de3190a387d4b6550 Tue Mar 12 13:41:09 2024 -0700
    added exportedDataHubs dialog and code to deal with quickLifted hubs
• src/hg/lib/exportedDataHubs.as
  • lines changed 3, context: html, text, full: html, text
    8ccceea1c52492b6a869af8de3190a387d4b6550 Tue Mar 12 13:41:09 2024 -0700
    added exportedDataHubs dialog and code to deal with quickLifted hubs
• src/hg/lib/exportedDataHubs.c
  • lines changed 29, context: html, text, full: html, text
    8ccceea1c52492b6a869af8de3190a387d4b6550 Tue Mar 12 13:41:09 2024 -0700
    added exportedDataHubs dialog and code to deal with quickLifted hubs
• src/hg/lib/exportedDataHubs.sql
  • lines changed 3, context: html, text, full: html, text
    8ccceea1c52492b6a869af8de3190a387d4b6550 Tue Mar 12 13:41:09 2024 -0700
    added exportedDataHubs dialog and code to deal with quickLifted hubs
• src/hg/lib/hubConnect.c
  • lines changed 91, context: html, text, full: html, text
    8ccceea1c52492b6a869af8de3190a387d4b6550 Tue Mar 12 13:41:09 2024 -0700
    added exportedDataHubs dialog and code to deal with quickLifted hubs
  • lines changed 46, context: html, text, full: html, text
    46a8a2fde9e17a401843959b8c0197c95d43ea45 Fri Mar 15 15:54:50 2024 -0700
    add quickLiftover chain to the list of tracks coming from an exported hub
• src/hg/lib/hui.c
  • lines changed 7, context: html, text, full: html, text
    eaa6da7f826e935dba8cdf70e52b556964017b54 Tue Mar 12 03:02:59 2024 -0700
    adding clear button to text filters, refs #24752
• src/hg/lib/instaPort.c
  • lines changed 111, context: html, text, full: html, text
    8ccceea1c52492b6a869af8de3190a387d4b6550 Tue Mar 12 13:41:09 2024 -0700
    added exportedDataHubs dialog and code to deal with quickLifted hubs
• src/hg/lib/makefile
  • lines changed 2, context: html, text, full: html, text
    8ccceea1c52492b6a869af8de3190a387d4b6550 Tue Mar 12 13:41:09 2024 -0700
    added exportedDataHubs dialog and code to deal with quickLifted hubs
• src/hg/lib/quickLift.c
  • lines changed 111, context: html, text, full: html, text
    8ccceea1c52492b6a869af8de3190a387d4b6550 Tue Mar 12 13:41:09 2024 -0700
    added exportedDataHubs dialog and code to deal with quickLifted hubs
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    067fb83d75952110057ca62ab59c231e46ddc6e8 Fri Mar 15 14:36:33 2024 -0700
    adding GCA_004007595.1_JHU_CGRice_1.0 Asian cultivated rice (Carolina Gold Select 2019) per user request refs #29545
• src/hg/makeDb/doc/hg38/gnomad.txt
  • lines changed 34, context: html, text, full: html, text
    63da25eccd720eec2319fa50cfa381335671856d Tue Mar 12 11:12:47 2024 -0700
    Adding actual steps into the gnomAD v4 constraint makedoc instead of just a link to hive, refs #33084
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 81, context: html, text, full: html, text
    365e31c93a680e12bf42b06632d77f166f15f78d Tue Mar 12 10:52:24 2024 -0700
    Adding the lines used to create the liftOver files hg38/GCF_009762305.2, refs #33198
• src/hg/makeDb/doc/hg38/makeExportHubs.txt
  • lines changed 27, context: html, text, full: html, text
    8ccceea1c52492b6a869af8de3190a387d4b6550 Tue Mar 12 13:41:09 2024 -0700
    added exportedDataHubs dialog and code to deal with quickLifted hubs
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    067fb83d75952110057ca62ab59c231e46ddc6e8 Fri Mar 15 14:36:33 2024 -0700
    adding GCA_004007595.1_JHU_CGRice_1.0 Asian cultivated rice (Carolina Gold Select 2019) per user request refs #29545
• src/hg/makeDb/trackDb/ailMel1_trackDb.offsets
  • lines changed 130, context: html, text, full: html, text
    f1beb8040b180a7792173f00422f73335ea3385b Tue Mar 12 10:47:53 2024 -0700
    Adding some missing lines to the JASPAR mouse trackDb files, refs #32537
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    754114543c12fe5bcb44180dcf89899256d7905b Tue Mar 12 10:50:05 2024 -0700
    Accidentally pushed junk, no Redmine.
• src/hg/makeDb/trackDb/ailMel1_trackDb.offsets.ixx
  • lines changed 1, context: html, text, full: html, text
    f1beb8040b180a7792173f00422f73335ea3385b Tue Mar 12 10:47:53 2024 -0700
    Adding some missing lines to the JASPAR mouse trackDb files, refs #32537
  • lines changed 1, context: html, text, full: html, text
    754114543c12fe5bcb44180dcf89899256d7905b Tue Mar 12 10:50:05 2024 -0700
    Accidentally pushed junk, no Redmine.
• src/hg/makeDb/trackDb/human/enigma.html
  • lines changed 9, context: html, text, full: html, text
    106ce8e3a43c932f7a6485f81935620e0a21cf70 Wed Mar 13 13:56:47 2024 -0700
    Grammar corrections from CR feedback, refs #33223
• src/hg/makeDb/trackDb/human/hg38/gnomad.constraint.alpha.ra
  • lines changed 133, context: html, text, full: html, text
    13f34e881b68f17416c4574d5357d96d8de56acb Tue Mar 12 13:06:22 2024 -0700
    Move the gnomAD constraint track re-org into a separate file so we can play with the organization on hgwdev before pushing, refs #33084
  • lines changed 1, context: html, text, full: html, text
    6259faa455bb7d9c823bb73107330f521eacacd9 Tue Mar 12 13:24:14 2024 -0700
    Add an alpha only version of gnomAD PLI description page, refs #33084
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    19ca3b614f0a8ed286fb387b5ad3ff0d9287984a Thu Mar 14 14:08:55 2024 -0700
    Adding v2 to the previous gnomAD release. Moving a note in the track description page after the image, refs #33084
  • lines changed 2, context: html, text, full: html, text
    8df029566f5f9ad912fe89e045b72ba44d6ee943 Thu Mar 14 15:28:53 2024 -0700
    Updating the names of the bigBed files used, refs #33084
• src/hg/makeDb/trackDb/human/hg38/gnomad.constraint.public.ra
  • lines changed 77, context: html, text, full: html, text
    13f34e881b68f17416c4574d5357d96d8de56acb Tue Mar 12 13:06:22 2024 -0700
    Move the gnomAD constraint track re-org into a separate file so we can play with the organization on hgwdev before pushing, refs #33084
  • lines changed 63, context: html, text, full: html, text
    29b6f07dd2be9444f6dac51078b46282aecc357c Fri Mar 15 14:21:32 2024 -0700
    Releasing the gnomAD constraints track to the RR, refs #33084
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 110, context: html, text, full: html, text
    13f34e881b68f17416c4574d5357d96d8de56acb Tue Mar 12 13:06:22 2024 -0700
    Move the gnomAD constraint track re-org into a separate file so we can play with the organization on hgwdev before pushing, refs #33084
  • lines changed 2, context: html, text, full: html, text
    e337dd5be26fafa3e9ef6afeb9ad353683d857f9 Fri Mar 15 13:52:45 2024 -0700
    Staging the gnomAD constraints track on beta, refs #33084
  • lines changed 2, context: html, text, full: html, text
    b573bc2fa6c4645cfe321c30869590fc5d73ef83 Fri Mar 15 14:22:14 2024 -0700
    Releasing the gnomAD constraints track, refs #33084
• src/hg/makeDb/trackDb/human/hg38/gnomadPLI.alpha.html
  • lines changed 261, context: html, text, full: html, text
    6259faa455bb7d9c823bb73107330f521eacacd9 Tue Mar 12 13:24:14 2024 -0700
    Add an alpha only version of gnomAD PLI description page, refs #33084
  • lines changed 2, context: html, text, full: html, text
    19ca3b614f0a8ed286fb387b5ad3ff0d9287984a Thu Mar 14 14:08:55 2024 -0700
    Adding v2 to the previous gnomAD release. Moving a note in the track description page after the image, refs #33084
• src/hg/makeDb/trackDb/mouse/jaspar.ra
  • lines changed 3, context: html, text, full: html, text
    f1beb8040b180a7792173f00422f73335ea3385b Tue Mar 12 10:47:53 2024 -0700
    Adding some missing lines to the JASPAR mouse trackDb files, refs #32537
• src/hg/snp/dbSnpJsonToTab/dbSnpJsonToTab.c
  • lines changed 3, context: html, text, full: html, text
    b280493ca2969a1de7f3dd8322f49fac095e77ac Tue Mar 12 16:40:33 2024 -0700
    Call stripOldStudyVersions before addMissingRefAllele instead of after to avoid erroneous output when re-running on dbSnp 153 JSON. refs #33070 With this change, addMissingRefAllele is looking only at the latest version, and its added item does not get stripped back out due to having a default version of 0. Stripping the added ref allele back out caused downstream trouble in sortFrequencies; allele frequencies were lost, and then the Common subset included no indels (the variants that were missing ref alleles) for 153.
• src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
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    5ae4d83b976b96f74cc3e1846e525601b6473cb3 Fri Mar 15 13:43:16 2024 -0700
    Expand masked range for JN.1 after more discussion in cov-lineages/pango-designation#2510
• src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv
  • lines changed 20, context: html, text, full: html, text
    6beb5b798df04141d3a69e5b80285e35d547fb4f Fri Mar 15 13:43:53 2024 -0700
    Adding more recombinants to exempt from filter.
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
  • lines changed 20, context: html, text, full: html, text
    6b7815eee943235aa3fd850bf2ce4648755504d2 Fri Mar 15 13:42:16 2024 -0700
    More new lineages for pango-designation v1.26 and beyond.
• src/lib/basicBed.c
  • lines changed 29, context: html, text, full: html, text
    8e33b480ded84760b7c96de88ab953102fbff466 Fri Mar 15 10:56:11 2024 -0700
    replace code that was potentially allocating too much memory off the stack with memory allocated off the heap and never freed.
• src/product/ex.hg.conf
  • lines changed 6, context: html, text, full: html, text
    716d66bcce087e3ab5cc3d6b74cebd7cb8d72e6d Wed Mar 13 09:20:16 2024 -0700
    docing bigBedMaxItems, refs #33023
• src/utils/bamToPsl/tests/makefile
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    9cf7baf4bc2d17ad036d295fd96f137235915775 Fri Mar 15 10:57:07 2024 -0700
    removed stale FIXME
• src/utils/git-reports/git-reports.c
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    4966ea67f91dd60e9ac4125e84a11888eef516df Thu Mar 14 16:27:33 2024 -0700
    Special case Jairo's username for the git reports because of the hgwdev username/email mismatch, refs #33244
• src/utils/qa/weeklybld/buildEnv.csh
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    9c4165c5bcbffbdab0b88f0dabed60cc3c5253c2 Mon Mar 18 11:30:20 2024 -0700
    v463 preview1, refs #33051

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• files changed: 76