All File Changes

v440_base to v441_preview (2022-11-21 to 2022-11-28) v441

• confs/hgwbeta.hg.conf
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    5a6fb43a17ad1a68e6d3d7296537dcc138d6cad0 Sun Nov 27 01:11:21 2022 -0800
    Installing updated hg.conf files from UCSC servers
• src/browserbox/root/fetchCramReference.sh
  • lines changed 13, context: html, text, full: html, text
    154f871dec4299c79113834fd45f17a4521ad8c6 Wed Nov 23 22:07:55 2022 -0800
    Replacing lockfile in fetchCramReference with flock, to remove the procmail dependency. Also updating the browserbox version to match the current server version. refs #17547, #14717
• src/hg/hgSearch/hgSearch.c
  • lines changed 27, context: html, text, full: html, text
    660387765d7bd58729c204580b26bd016b0afeaa Mon Nov 21 14:30:49 2022 -0800
    Do a quick async chromosome name lookup before sending a full search request from hgTracks/hgGateway
• src/hg/hgTracks/config.c
  • lines changed 3, context: html, text, full: html, text
    6a0a4de569da7ed5c63d2781badccdd5249149a1 Thu Nov 24 09:16:29 2022 -0800
    gracefully accept trackDbs that have superTrack children in different groups.
• src/hg/hgTracks/hgTracks.c
  • lines changed 6, context: html, text, full: html, text
    6a0a4de569da7ed5c63d2781badccdd5249149a1 Thu Nov 24 09:16:29 2022 -0800
    gracefully accept trackDbs that have superTrack children in different groups.
• src/hg/hgTracks/hgTracks.h
  • lines changed 1, context: html, text, full: html, text
    6a0a4de569da7ed5c63d2781badccdd5249149a1 Thu Nov 24 09:16:29 2022 -0800
    gracefully accept trackDbs that have superTrack children in different groups.
• src/hg/hgTracks/searchTracks.c
  • lines changed 3, context: html, text, full: html, text
    6a0a4de569da7ed5c63d2781badccdd5249149a1 Thu Nov 24 09:16:29 2022 -0800
    gracefully accept trackDbs that have superTrack children in different groups.
• src/hg/js/hgGateway.js
  • lines changed 34, context: html, text, full: html, text
    660387765d7bd58729c204580b26bd016b0afeaa Mon Nov 21 14:30:49 2022 -0800
    Do a quick async chromosome name lookup before sending a full search request from hgTracks/hgGateway
  • lines changed 15, context: html, text, full: html, text
    85de86d688b23d0663ee6c4e3376fe6708148550 Mon Nov 28 09:55:49 2022 -0800
    Forgot to check for an empty search string when deciding whether to go from hgGateway to hgSearch/hgTracks
• src/hg/js/hgTracks.js
  • lines changed 26, context: html, text, full: html, text
    660387765d7bd58729c204580b26bd016b0afeaa Mon Nov 21 14:30:49 2022 -0800
    Do a quick async chromosome name lookup before sending a full search request from hgTracks/hgGateway
• src/hg/js/model/lib/cart.js
  • lines changed 5, context: html, text, full: html, text
    660387765d7bd58729c204580b26bd016b0afeaa Mon Nov 21 14:30:49 2022 -0800
    Do a quick async chromosome name lookup before sending a full search request from hgTracks/hgGateway
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 3, context: html, text, full: html, text
    3cc17c13ddc05a2dbb8b6d1d917c56d3b829c9df Mon Nov 21 11:58:27 2022 -0800
    catching up three RefSeq VGP assemblies refs #29545
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    696803d5e4b71ea8b2c2d7e75f655b5d6e08dca1 Wed Nov 23 11:32:46 2022 -0800
    running up an E.coli sequence per user request refs #29545
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    29d094212da4beb5ba75141066116a9dfaa52dbb Wed Nov 23 14:57:01 2022 -0800
    correct GCF assembly for GCA_000750555.1 for user request refs #29545
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    696803d5e4b71ea8b2c2d7e75f655b5d6e08dca1 Wed Nov 23 11:32:46 2022 -0800
    running up an E.coli sequence per user request refs #29545
  • lines changed 1, context: html, text, full: html, text
    29d094212da4beb5ba75141066116a9dfaa52dbb Wed Nov 23 14:57:01 2022 -0800
    correct GCF assembly for GCA_000750555.1 for user request refs #29545
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    3cc17c13ddc05a2dbb8b6d1d917c56d3b829c9df Mon Nov 21 11:58:27 2022 -0800
    catching up three RefSeq VGP assemblies refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    3cc17c13ddc05a2dbb8b6d1d917c56d3b829c9df Mon Nov 21 11:58:27 2022 -0800
    catching up three RefSeq VGP assemblies refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    3cc17c13ddc05a2dbb8b6d1d917c56d3b829c9df Mon Nov 21 11:58:27 2022 -0800
    catching up three RefSeq VGP assemblies refs #29545
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    3cc17c13ddc05a2dbb8b6d1d917c56d3b829c9df Mon Nov 21 11:58:27 2022 -0800
    catching up three RefSeq VGP assemblies refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.legacy.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    22b32cdaa6887807ed99855a69b1c76dc557357b Mon Nov 21 15:02:16 2022 -0800
    updated one and added two VGP assemblies refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    22b32cdaa6887807ed99855a69b1c76dc557357b Mon Nov 21 15:02:16 2022 -0800
    updated one and added two VGP assemblies refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt
  • lines changed 4, context: html, text, full: html, text
    22b32cdaa6887807ed99855a69b1c76dc557357b Mon Nov 21 15:02:16 2022 -0800
    updated one and added two VGP assemblies refs #29545
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    02061d6c491453d05b5e79d02fa4db9e75c15ecb Mon Nov 21 14:04:59 2022 -0800
    Adding beta to release tag, refs #30252
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    02061d6c491453d05b5e79d02fa4db9e75c15ecb Mon Nov 21 14:04:59 2022 -0800
    Adding beta to release tag, refs #30252
• src/hg/utils/otto/otto.crontab
  • lines changed 1, context: html, text, full: html, text
    46f725e19a2ba40e0c662936986fc0d08fea103a Wed Nov 23 10:59:15 2022 -0800
    Adding Gerardo to the thumbnail cron as a redundancy if I'm away, refs #30312
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    68acb387bdc14ff22cb70d1d38ec40cbbd699a8f Wed Nov 23 11:00:38 2022 -0800
    Changing the thumbail day to Thursday to allow us to catch any errors for a few days before the autoPush on Tuesday. Refs #30312
• src/lib/rudp.c
  • lines changed 1, context: html, text, full: html, text
    235b09c3dbc2a911c48639c01cbfe5b3447d635f Wed Nov 23 16:21:51 2022 -0800
    fixup correct argument to sendto() function as found on BSD system on Mac laptops refs #29651
• src/product/scripts/fetchCramReference.sh
  • lines changed 8, context: html, text, full: html, text
    154f871dec4299c79113834fd45f17a4521ad8c6 Wed Nov 23 22:07:55 2022 -0800
    Replacing lockfile in fetchCramReference with flock, to remove the procmail dependency. Also updating the browserbox version to match the current server version. refs #17547, #14717
• src/utils/bigGuessDb/bigGuessDb
  • lines changed 164, context: html, text, full: html, text
    a6961f6d0aa8579910afb52dec6f333a0113328c Tue Nov 22 03:48:11 2022 -0800
    adding bigGuessDb tool, refs #30316
  • lines changed 2, context: html, text, full: html, text
    db09ffb4f2f00a9391334ce3e8b3cbe5fcc98cb5 Tue Nov 22 03:50:26 2022 -0800
    shorten arg for bigGuessDb tool, refs #30316
  • lines changed 28, context: html, text, full: html, text
    ab5e63af16ca6461e7853f9a665abb74bbe40a7f Mon Nov 28 05:26:07 2022 -0800
    adding bigBed to bigGuessDb, fixing stupid makefile error and checking missing tools with an error message, refs #30316
• src/utils/bigGuessDb/makefile
  • lines changed 14, context: html, text, full: html, text
    a6961f6d0aa8579910afb52dec6f333a0113328c Tue Nov 22 03:48:11 2022 -0800
    adding bigGuessDb tool, refs #30316
  • lines changed 1, context: html, text, full: html, text
    f75f891d0f7d1cb2ebd8fcd35fa94984cdd6f444 Wed Nov 23 10:13:08 2022 -0800
    adding clean command
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    ab5e63af16ca6461e7853f9a665abb74bbe40a7f Mon Nov 28 05:26:07 2022 -0800
    adding bigBed to bigGuessDb, fixing stupid makefile error and checking missing tools with an error message, refs #30316
• src/utils/makefile
  • lines changed 2, context: html, text, full: html, text
    a6961f6d0aa8579910afb52dec6f333a0113328c Tue Nov 22 03:48:11 2022 -0800
    adding bigGuessDb tool, refs #30316
  • lines changed 4, context: html, text, full: html, text
    ab5e63af16ca6461e7853f9a665abb74bbe40a7f Mon Nov 28 05:26:07 2022 -0800
    adding bigBed to bigGuessDb, fixing stupid makefile error and checking missing tools with an error message, refs #30316
• src/utils/qa/buildPublicSessionThumbnailsIndexPage.py
  • lines changed 16, context: html, text, full: html, text
    18de809f70db46cfe42a72b76433af3325016c81 Wed Nov 23 10:57:02 2022 -0800
    Removing bash subprocess calls and other general improvements to thumbnail script in response to CR. Refs #30312
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    c9b6626d10c0da573b51bc3aa8bbea283432ad70 Mon Nov 28 10:17:38 2022 -0800
    v441 preview1, refs #30323

• lines changed: 403
• files changed: 39