All File Changes

v469_base to v470_preview (2024-08-05 to 2024-08-12) v470

• confs/hgwbeta.hg.conf
  • lines changed 3, context: html, text, full: html, text
    f1914a4a85fd811ec33a9ce380b4e91f81f2f9e5 Sun Aug 11 01:11:17 2024 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cgilib/bedCart.c
  • lines changed 1, context: html, text, full: html, text
    cbc53920d6182a0aa1a9f12f9d0f4b53b9f20fe1 Wed Aug 7 03:01:18 2024 -0700
    allowing off in addition to Off in itemRgb setting, refs #28498
• src/hg/hgTables/filterFields.c
  • lines changed 1, context: html, text, full: html, text
    f805cfddece1b469753005f8007f75d5f644ed26 Mon Aug 12 08:20:46 2024 -0700
    not showing mysql query form for bigBed files, refs #21799
• src/hg/hgTables/mainPage.c
  • lines changed 4, context: html, text, full: html, text
    d11695558ca61844bc4fcccee30701d1e535c90b Mon Aug 12 08:36:52 2024 -0700
    promoting the data integrator from hgTables, refs #34268
• src/hg/hgTracks/hgTracks.c
  • lines changed 5, context: html, text, full: html, text
    6cb29beead43fd47d57c739ea19b62990c1a87e5 Tue Jun 25 15:14:30 2024 -0700
    Making a javascript tutorial for clinicians. Creating a URL parameter to start the tutorial. refs #33732
  • lines changed 3, context: html, text, full: html, text
    f72cf5a493f28ff5613e2d0d06ec1cc708db44b9 Thu Aug 8 08:54:18 2024 -0700
    another braindead Max bug again, refs #34249
• src/hg/hgTracks/interactTrack.c
  • lines changed 1, context: html, text, full: html, text
    2e122ca3817920fe44d27f86628c84a2908fdd04 Mon Aug 12 07:25:28 2024 -0700
    trying to add endsVisible to trackDb for interact, refs #34164
• src/hg/htdocs/goldenPath/help/mirrorManual.html
  • lines changed 49, context: html, text, full: html, text
    6426a655644fe5e06de5cebdc4f01c7b0deb2686 Thu Aug 8 06:47:16 2024 -0700
    adding note about security problems, refs #34166
  • lines changed 6, context: html, text, full: html, text
    8ae57fb027f43538412376ac1c4435b247d95f75 Thu Aug 8 07:20:50 2024 -0700
    typos, refs #34166
  • lines changed 23, context: html, text, full: html, text
    8f16c04099f371f3c1ba035b1f7b73ffe52e6370 Fri Aug 9 00:40:08 2024 -0700
    Committing derived files from mirrorManual.txt, refs #34166
• src/hg/htdocs/mirror.html
  • lines changed 7, context: html, text, full: html, text
    6426a655644fe5e06de5cebdc4f01c7b0deb2686 Thu Aug 8 06:47:16 2024 -0700
    adding note about security problems, refs #34166
• src/hg/js/hgSearch.js
  • lines changed 1, context: html, text, full: html, text
    17fc72a70e64f33d1a23b697ba99a2e008860ec5 Mon Aug 5 13:56:30 2024 -0700
    Make the show more search results link not be huge, #33503
• src/hg/js/hgTracks.js
  • lines changed 5, context: html, text, full: html, text
    6cb29beead43fd47d57c739ea19b62990c1a87e5 Tue Jun 25 15:14:30 2024 -0700
    Making a javascript tutorial for clinicians. Creating a URL parameter to start the tutorial. refs #33732
  • lines changed 33, context: html, text, full: html, text
    dc88954b3214a3b414711c9e73dfa654bf0dffd9 Tue Aug 6 12:58:18 2024 -0700
    fixup mouseOver wiggle track when a track in wiggle mode switches to not wiggle mode, do not display the mouseOver. refs #34222
  • lines changed 1, context: html, text, full: html, text
    21a18bb99f000d0da8cfbb15cc33138f4127947a Wed Aug 7 10:26:30 2024 -0700
    correct for loop variable declaration no redmine
• src/hg/js/tutorials/clinicalTutorial.js
  • lines changed 191, context: html, text, full: html, text
    6cb29beead43fd47d57c739ea19b62990c1a87e5 Tue Jun 25 15:14:30 2024 -0700
    Making a javascript tutorial for clinicians. Creating a URL parameter to start the tutorial. refs #33732
• src/hg/lib/hui.c
  • lines changed 3, context: html, text, full: html, text
    6b5d81231f6dcb4895d9522b80b2552711a4e87e Tue Aug 6 03:22:14 2024 -0700
    adding resolvPrefix to our hg.conf statements for the udc resolver, refs #34240
• src/hg/lib/straw/cStraw.cpp
  • lines changed 11, context: html, text, full: html, text
    0f42d7fc723850694dd33dc22be6817a6c9446f0 Mon Aug 12 09:49:39 2024 -0700
    Adding hReplaceGbdb call to cStraw to handle local hic files in GBiB, refs #27851
• src/hg/lib/straw/hReplaceGbdb.h
  • lines changed 13, context: html, text, full: html, text
    0f42d7fc723850694dd33dc22be6817a6c9446f0 Mon Aug 12 09:49:39 2024 -0700
    Adding hReplaceGbdb call to cStraw to handle local hic files in GBiB, refs #27851
• src/hg/lib/straw/straw.cpp
  • lines changed 1, context: html, text, full: html, text
    0f42d7fc723850694dd33dc22be6817a6c9446f0 Mon Aug 12 09:49:39 2024 -0700
    Adding hReplaceGbdb call to cStraw to handle local hic files in GBiB, refs #27851
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 67, context: html, text, full: html, text
    8796500caefe26d7872e2d6a8ffbed913d70a8f0 Wed Aug 7 11:30:21 2024 -0700
    an update for VGP to add 67 assemblies refs #29545
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 21, context: html, text, full: html, text
    8796500caefe26d7872e2d6a8ffbed913d70a8f0 Wed Aug 7 11:30:21 2024 -0700
    an update for VGP to add 67 assemblies refs #29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 11, context: html, text, full: html, text
    8796500caefe26d7872e2d6a8ffbed913d70a8f0 Wed Aug 7 11:30:21 2024 -0700
    an update for VGP to add 67 assemblies refs #29545
• src/hg/makeDb/doc/hg38/gnomad.txt
  • lines changed 56, context: html, text, full: html, text
    b2223b223d36a5a9fa31014dab284d6212cfb4e8 Wed Aug 7 16:36:26 2024 -0700
    Adding the gnomAD v4.1 Structural Variants track, refs #33823
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    8796500caefe26d7872e2d6a8ffbed913d70a8f0 Wed Aug 7 11:30:21 2024 -0700
    an update for VGP to add 67 assemblies refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 9, context: html, text, full: html, text
    8796500caefe26d7872e2d6a8ffbed913d70a8f0 Wed Aug 7 11:30:21 2024 -0700
    an update for VGP to add 67 assemblies refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 10, context: html, text, full: html, text
    8796500caefe26d7872e2d6a8ffbed913d70a8f0 Wed Aug 7 11:30:21 2024 -0700
    an update for VGP to add 67 assemblies refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 26, context: html, text, full: html, text
    8796500caefe26d7872e2d6a8ffbed913d70a8f0 Wed Aug 7 11:30:21 2024 -0700
    an update for VGP to add 67 assemblies refs #29545
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    8796500caefe26d7872e2d6a8ffbed913d70a8f0 Wed Aug 7 11:30:21 2024 -0700
    an update for VGP to add 67 assemblies refs #29545
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 16, context: html, text, full: html, text
    8796500caefe26d7872e2d6a8ffbed913d70a8f0 Wed Aug 7 11:30:21 2024 -0700
    an update for VGP to add 67 assemblies refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.alternate.orderList.tsv
  • lines changed 25, context: html, text, full: html, text
    344c5e2d07b4517677ea9a70fbededda133fc34f Wed Aug 7 16:01:44 2024 -0700
    VGP update with 48 added primary assemblies and 25 alternates refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv
  • lines changed 48, context: html, text, full: html, text
    344c5e2d07b4517677ea9a70fbededda133fc34f Wed Aug 7 16:01:44 2024 -0700
    VGP update with 48 added primary assemblies and 25 alternates refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt
  • lines changed 70, context: html, text, full: html, text
    344c5e2d07b4517677ea9a70fbededda133fc34f Wed Aug 7 16:01:44 2024 -0700
    VGP update with 48 added primary assemblies and 25 alternates refs #29545
• src/hg/makeDb/trackDb/human/hg38/gnomadSv.alpha.ra
  • lines changed 288, context: html, text, full: html, text
    b2223b223d36a5a9fa31014dab284d6212cfb4e8 Wed Aug 7 16:36:26 2024 -0700
    Adding the gnomAD v4.1 Structural Variants track, refs #33823
  • lines changed 2, context: html, text, full: html, text
    50c7584becf246a8ce1b05377c7b20d3a656f492 Wed Aug 7 16:50:48 2024 -0700
    Updating longLabel and adding dataVersion. Adding the gnomAD v4.1 SV track to trackDb.ra with alpha tag, refs #33823
• src/hg/makeDb/trackDb/human/hg38/gnomadSv.html
  • lines changed 173, context: html, text, full: html, text
    b2223b223d36a5a9fa31014dab284d6212cfb4e8 Wed Aug 7 16:36:26 2024 -0700
    Adding the gnomAD v4.1 Structural Variants track, refs #33823
• src/hg/makeDb/trackDb/human/hg38/primates11way.html
  • lines changed 277, context: html, text, full: html, text
    e12feaeaef7d5378709131fd36f53b7b87e48d72 Fri Aug 9 16:44:52 2024 -0700
    adding 11-way multiz and cactus alignments no redmine
• src/hg/makeDb/trackDb/human/hg38/primates11way.ra
  • lines changed 90, context: html, text, full: html, text
    e12feaeaef7d5378709131fd36f53b7b87e48d72 Fri Aug 9 16:44:52 2024 -0700
    adding 11-way multiz and cactus alignments no redmine
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    de958458900052c5ab2ef799c2b203b63a2b3497 Tue Jul 23 16:34:42 2024 -0700
    adding mouseover field to vista track, no redmine
  • lines changed 3, context: html, text, full: html, text
    50c7584becf246a8ce1b05377c7b20d3a656f492 Wed Aug 7 16:50:48 2024 -0700
    Updating longLabel and adding dataVersion. Adding the gnomAD v4.1 SV track to trackDb.ra with alpha tag, refs #33823
  • lines changed 2, context: html, text, full: html, text
    e12feaeaef7d5378709131fd36f53b7b87e48d72 Fri Aug 9 16:44:52 2024 -0700
    adding 11-way multiz and cactus alignments no redmine
• src/hg/makeDb/trackDb/human/hs1/primates11way.html
  • lines changed 277, context: html, text, full: html, text
    624d014a418548f0a73d8400eee3cae42e81bdaf Fri Aug 9 16:46:10 2024 -0700
    adding 11-way multiz and cactus alignments no redmine
• src/hg/makeDb/trackDb/human/hs1/primates11way.ra
  • lines changed 89, context: html, text, full: html, text
    624d014a418548f0a73d8400eee3cae42e81bdaf Fri Aug 9 16:46:10 2024 -0700
    adding 11-way multiz and cactus alignments no redmine
• src/hg/makeDb/trackDb/human/hs1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    624d014a418548f0a73d8400eee3cae42e81bdaf Fri Aug 9 16:46:10 2024 -0700
    adding 11-way multiz and cactus alignments no redmine
• src/hg/makeDb/trackDb/human/spliceAI.ra
  • lines changed 3, context: html, text, full: html, text
    9400a988d1680e6c5b6e2bae4978f602beda0404 Thu Aug 8 17:08:00 2024 -0700
    Lowering the priority range so the tracks show together, before OMIM was slipping in between two of them. Refs #27141
• src/hg/mouseStuff/axtBest/axtBest.c
  • lines changed 2, context: html, text, full: html, text
    584b7af6bcac17cc116ca2c4801e60a149d49c2c Wed Aug 7 15:23:41 2024 -0700
    BIGNUM needs to be a bit larger for chain/net processing on sequences over 1 Gb refs #34248
• src/hg/mouseStuff/axtBestNear/axtBestNear.c
  • lines changed 3, context: html, text, full: html, text
    584b7af6bcac17cc116ca2c4801e60a149d49c2c Wed Aug 7 15:23:41 2024 -0700
    BIGNUM needs to be a bit larger for chain/net processing on sequences over 1 Gb refs #34248
• src/hg/mouseStuff/axtFilter/axtFilter.c
  • lines changed 2, context: html, text, full: html, text
    584b7af6bcac17cc116ca2c4801e60a149d49c2c Wed Aug 7 15:23:41 2024 -0700
    BIGNUM needs to be a bit larger for chain/net processing on sequences over 1 Gb refs #34248
• src/hg/mouseStuff/chainFilter/chainFilter.c
  • lines changed 2, context: html, text, full: html, text
    584b7af6bcac17cc116ca2c4801e60a149d49c2c Wed Aug 7 15:23:41 2024 -0700
    BIGNUM needs to be a bit larger for chain/net processing on sequences over 1 Gb refs #34248
• src/hg/mouseStuff/chainNet/chainNet.c
  • lines changed 2, context: html, text, full: html, text
    584b7af6bcac17cc116ca2c4801e60a149d49c2c Wed Aug 7 15:23:41 2024 -0700
    BIGNUM needs to be a bit larger for chain/net processing on sequences over 1 Gb refs #34248
• src/hg/mouseStuff/chainToAxt/chainToAxt.c
  • lines changed 2, context: html, text, full: html, text
    584b7af6bcac17cc116ca2c4801e60a149d49c2c Wed Aug 7 15:23:41 2024 -0700
    BIGNUM needs to be a bit larger for chain/net processing on sequences over 1 Gb refs #34248
• src/hg/mouseStuff/lavToAxt/lavToAxt.c
  • lines changed 3, context: html, text, full: html, text
    584b7af6bcac17cc116ca2c4801e60a149d49c2c Wed Aug 7 15:23:41 2024 -0700
    BIGNUM needs to be a bit larger for chain/net processing on sequences over 1 Gb refs #34248
• src/hg/mouseStuff/lavToPsl/lavToPsl.c
  • lines changed 3, context: html, text, full: html, text
    584b7af6bcac17cc116ca2c4801e60a149d49c2c Wed Aug 7 15:23:41 2024 -0700
    BIGNUM needs to be a bit larger for chain/net processing on sequences over 1 Gb refs #34248
• src/hg/mouseStuff/netFilter/netFilter.c
  • lines changed 2, context: html, text, full: html, text
    584b7af6bcac17cc116ca2c4801e60a149d49c2c Wed Aug 7 15:23:41 2024 -0700
    BIGNUM needs to be a bit larger for chain/net processing on sequences over 1 Gb refs #34248
• src/hg/mouseStuff/netToAxt/netToAxt.c
  • lines changed 2, context: html, text, full: html, text
    584b7af6bcac17cc116ca2c4801e60a149d49c2c Wed Aug 7 15:23:41 2024 -0700
    BIGNUM needs to be a bit larger for chain/net processing on sequences over 1 Gb refs #34248
• src/hg/mouseStuff/netToBed/netToBed.c
  • lines changed 2, context: html, text, full: html, text
    584b7af6bcac17cc116ca2c4801e60a149d49c2c Wed Aug 7 15:23:41 2024 -0700
    BIGNUM needs to be a bit larger for chain/net processing on sequences over 1 Gb refs #34248
• src/hg/mouseStuff/regionPicker/regionPicker.c
  • lines changed 2, context: html, text, full: html, text
    a56a50def2f2b52b39edf28d23ee8c4df43ad157 Sat Aug 10 02:08:21 2024 -0700
    fix issue found by Angie where some of the bit function would SEGV because the bit count type was change from and int an unsigned 64-bit int and some code counted on it going negative. This provides a typedef for bit counts which is a signed 64-bit types
• src/hg/utils/automation/doBlastzChainNet.pl
  • lines changed 6, context: html, text, full: html, text
    e83574e4d897147878ee3f50d7c37e49e30effa8 Fri Aug 9 09:16:55 2024 -0700
    eliminate the /gbdb/GC* symlinks for bigBed files no redmine
• src/hg/utils/otto/genArk/addAssemblyList.sh
  • lines changed 35, context: html, text, full: html, text
    9cea4ceb4ee3f5c28c3315f63f0c696e82f6a8d4 Thu Aug 8 12:57:18 2024 -0700
    adding the assemblyList table creation to the cron job refs #32596
• src/hg/utils/otto/genArk/updateHgcentral.sh
  • lines changed 14, context: html, text, full: html, text
    9cea4ceb4ee3f5c28c3315f63f0c696e82f6a8d4 Thu Aug 8 12:57:18 2024 -0700
    adding the assemblyList table creation to the cron job refs #32596
• src/hg/utils/otto/panelApp/tandRep.py
  • lines changed 3, context: html, text, full: html, text
    da2a89e8c4b23469cb35ec86b066bca2c4504745 Wed Aug 7 15:39:34 2024 -0700
    Adding a new check to panelApp otto that started failing, before all panelApp genes had an OMIM ID associated with it, so that field of the JSON file was a list with (usually) just one OMIM ID. But now there is a single gene with no associated ID so it returns None instead of a list. No RM.
• src/hg/utils/pslToBigPsl/pslToBigPsl.c
  • lines changed 1, context: html, text, full: html, text
    55d9748b1ae610c7a16d106ca2bbf7485429ed0e Tue Jul 23 16:49:31 2024 -0700
    adding URL to command line tool doc, no redmine
• src/inc/bits.h
  • lines changed 28, context: html, text, full: html, text
    a56a50def2f2b52b39edf28d23ee8c4df43ad157 Sat Aug 10 02:08:21 2024 -0700
    fix issue found by Angie where some of the bit function would SEGV because the bit count type was change from and int an unsigned 64-bit int and some code counted on it going negative. This provides a typedef for bit counts which is a signed 64-bit types
• src/inc/udc.h
  • lines changed 1, context: html, text, full: html, text
    6b5d81231f6dcb4895d9522b80b2552711a4e87e Tue Aug 6 03:22:14 2024 -0700
    adding resolvPrefix to our hg.conf statements for the udc resolver, refs #34240
• src/lib/bits.c
  • lines changed 73, context: html, text, full: html, text
    a56a50def2f2b52b39edf28d23ee8c4df43ad157 Sat Aug 10 02:08:21 2024 -0700
    fix issue found by Angie where some of the bit function would SEGV because the bit count type was change from and int an unsigned 64-bit int and some code counted on it going negative. This provides a typedef for bit counts which is a signed 64-bit types
• src/lib/chain.c
  • lines changed 2, context: html, text, full: html, text
    584b7af6bcac17cc116ca2c4801e60a149d49c2c Wed Aug 7 15:23:41 2024 -0700
    BIGNUM needs to be a bit larger for chain/net processing on sequences over 1 Gb refs #34248
• src/lib/udc.c
  • lines changed 18, context: html, text, full: html, text
    6b5d81231f6dcb4895d9522b80b2552711a4e87e Tue Aug 6 03:22:14 2024 -0700
    adding resolvPrefix to our hg.conf statements for the udc resolver, refs #34240
• src/product/ex.hg.conf
  • lines changed 4, context: html, text, full: html, text
    6b5d81231f6dcb4895d9522b80b2552711a4e87e Tue Aug 6 03:22:14 2024 -0700
    adding resolvPrefix to our hg.conf statements for the udc resolver, refs #34240
• src/product/mirrorManual.txt
  • lines changed 44, context: html, text, full: html, text
    6426a655644fe5e06de5cebdc4f01c7b0deb2686 Thu Aug 8 06:47:16 2024 -0700
    adding note about security problems, refs #34166
  • lines changed 6, context: html, text, full: html, text
    8ae57fb027f43538412376ac1c4435b247d95f75 Thu Aug 8 07:20:50 2024 -0700
    typos, refs #34166
  • lines changed 1, context: html, text, full: html, text
    34221be37944fac0dfa79a676d280f3c0d6aa8d3 Thu Aug 8 07:24:46 2024 -0700
    typos2, refs #34166
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    608e46b17b501a42b7ca533aa95b0db15d93eb3e Fri Aug 9 00:38:51 2024 -0700
    A few small changes to the mirror manual security section, refs #34166
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    2ac88b3aa0e9b8c22387ffd29e2cf41475155903 Mon Aug 12 10:27:49 2024 -0700
    v470 preview1, refs #34168

• lines changed: 2217
• files changed: 73