All File Changes

v422_base to v423_preview (2021-10-18 to 2021-10-25) v423

• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 432, context: html, text, full: html, text
    a8f29caea973a2482924c38c981b59a28e22e8ec Fri Oct 22 05:14:38 2021 -0700
    making hgHubConnect more self-explanatory, with more text. The development tab is revamped to provide a visual indicator of what's going on while hubCheck is running. (The concept with an IFRAME could well be applied to hgc links from hgTracks, to avoid a full page reload.), refs #28324
  • lines changed 1, context: html, text, full: html, text
    7cdced87bd7680c51b327560aff3bb3cf414733a Sat Oct 23 08:59:02 2021 -0700
    Fixing the broken build for max, some little bits not checked in.
  • lines changed 4, context: html, text, full: html, text
    561f452458624b64c61e2ead5cdcb705b5fcadd1 Sat Oct 23 13:22:18 2021 -0700
    fixing up missing files in last commit, refs #28324
• src/hg/hgHubConnect/makefile
  • lines changed 1, context: html, text, full: html, text
    b08c92a020528ee45601b53582dbcaf70d41b03d Tue Oct 19 00:43:02 2021 -0700
    error in makefile was including HALLIBS twice
• src/hg/hgPhyloPlace/phyloPlace.h
  • lines changed 1, context: html, text, full: html, text
    8bc5f2734824f3c46de7cab1f48c9012c7146ff0 Wed Oct 20 14:41:56 2021 -0700
    Increase single subtree size to 2000. There are >4M samples in the big tree; 1000 is just too few to get a good overview anymore.
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
  • lines changed 6, context: html, text, full: html, text
    b83116855bd919a0da2b417f07d4473828c94845 Wed Oct 20 13:37:23 2021 -0700
    Oops, lookupCodon returns '\0' for stop codon but we want to display '*'. Reported by Cornelius Roemer in https://github.com/yatisht/usher/issues/178
• src/hg/hgTables/makefile
  • lines changed 1, context: html, text, full: html, text
    b08c92a020528ee45601b53582dbcaf70d41b03d Tue Oct 19 00:43:02 2021 -0700
    error in makefile was including HALLIBS twice
• src/hg/hgTrackUi/makefile
  • lines changed 1, context: html, text, full: html, text
    b08c92a020528ee45601b53582dbcaf70d41b03d Tue Oct 19 00:43:02 2021 -0700
    error in makefile was including HALLIBS twice
• src/hg/hgTracks/makefile
  • lines changed 1, context: html, text, full: html, text
    e9af54d1ab1699eeb44bb835e2c3ed770fbe6eb2 Tue Oct 19 00:36:20 2021 -0700
    error in makefile was including HALLIBS twice
• src/hg/htdocs/FAQ/FAQblat.html
  • lines changed 1, context: html, text, full: html, text
    466b66ad1df60b0f76a5cdedec047bf21c449141 Wed Oct 20 15:51:52 2021 -0700
    tiny typo
• src/hg/htdocs/goldenPath/help/ftp.html
  • lines changed 1, context: html, text, full: html, text
    c6477c2f3e0e7b960bfa58c95f93288c54619381 Tue Oct 19 16:42:36 2021 -0700
    Removing mention of ENCODE, feedback from CR refs #28359
• src/hg/htdocs/goldenPath/help/mirrorManual.html
  • lines changed 109, context: html, text, full: html, text
    96c23d22e15631da16fcf1069f0f30249910b533 Thu Oct 21 05:45:43 2021 -0700
    Updating mirrorManual and mirror.html / README.txt for Mysql support retirement, refs #28373
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 45, context: html, text, full: html, text
    6cdc3f8d72e6f83675f24cf18df1dbcfb97c7743 Tue Oct 19 12:34:30 2021 -0700
    Updating news for the hg38 patch 13 announcement, refs #25091
  • lines changed 52, context: html, text, full: html, text
    cb69f436621e81c835b31bd83f83cd43433bda92 Tue Oct 19 19:35:04 2021 -0700
    Announcing VOC track #27926
• src/hg/htdocs/images/GIlogo.png
  • lines changed 0, context: html, text, full: html, text
    d7c9d081bf4db4ea32f199e1bed6ece6ae367fcc Tue Oct 19 11:58:03 2021 -0700
    Updating GI logo, refs #28371
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    6cdc3f8d72e6f83675f24cf18df1dbcfb97c7743 Tue Oct 19 12:34:30 2021 -0700
    Updating news for the hg38 patch 13 announcement, refs #25091
  • lines changed 11, context: html, text, full: html, text
    cb69f436621e81c835b31bd83f83cd43433bda92 Tue Oct 19 19:35:04 2021 -0700
    Announcing VOC track #27926
• src/hg/htdocs/style/hgHubConnect.css
  • lines changed 8, context: html, text, full: html, text
    a8f29caea973a2482924c38c981b59a28e22e8ec Fri Oct 22 05:14:38 2021 -0700
    making hgHubConnect more self-explanatory, with more text. The development tab is revamped to provide a visual indicator of what's going on while hubCheck is running. (The concept with an IFRAME could well be applied to hgc links from hgTracks, to avoid a full page reload.), refs #28324
• src/hg/htdocs/training/openHouse.html
  • lines changed 17, context: html, text, full: html, text
    652871f2edc8d07560e54bc1eb16dc748f852225 Mon Oct 18 12:47:29 2021 -0700
    changing openHouse page to say thanks
• src/hg/inc/hubConnect.h
  • lines changed 1, context: html, text, full: html, text
    7cdced87bd7680c51b327560aff3bb3cf414733a Sat Oct 23 08:59:02 2021 -0700
    Fixing the broken build for max, some little bits not checked in.
  • lines changed 1, context: html, text, full: html, text
    561f452458624b64c61e2ead5cdcb705b5fcadd1 Sat Oct 23 13:22:18 2021 -0700
    fixing up missing files in last commit, refs #28324
• src/hg/js/hgHubConnect.js
  • lines changed 8, context: html, text, full: html, text
    a8f29caea973a2482924c38c981b59a28e22e8ec Fri Oct 22 05:14:38 2021 -0700
    making hgHubConnect more self-explanatory, with more text. The development tab is revamped to provide a visual indicator of what's going on while hubCheck is running. (The concept with an IFRAME could well be applied to hgc links from hgTracks, to avoid a full page reload.), refs #28324
• src/hg/js/hgTracks.js
  • lines changed 2, context: html, text, full: html, text
    009aed1c7b80108e75e1922430316e7c1cac39aa Fri Oct 22 05:59:18 2021 -0700
    making hlColor save syncronous, hopefully this will avoid the problem found by QA in note 34 of the ticket, refs #28098
• src/hg/lib/liftOver.c
  • lines changed 5, context: html, text, full: html, text
    17c3457c1ceec90005de6ff399c50a9c66c8ce50 Mon Oct 18 13:43:01 2021 -0700
    fixed silly oversight that failed to correct for zero width items
• src/hg/liftOver/tests/expected/zeroWidth.bed
  • lines changed 6, context: html, text, full: html, text
    17c3457c1ceec90005de6ff399c50a9c66c8ce50 Mon Oct 18 13:43:01 2021 -0700
    fixed silly oversight that failed to correct for zero width items
• src/hg/makeDb/doc/asmHubs/lastzRuns.txt
  • lines changed 243, context: html, text, full: html, text
    90af857c47a2063649df6d9526c94de4989f12ec Tue Oct 19 12:03:52 2021 -0700
    mouse and date palm lastz runs completed per user requests refs #28365 #28302
  • lines changed 505, context: html, text, full: html, text
    9d4bef0d3eb7ba60d763868e2db43256281e38ab Fri Oct 22 13:31:37 2021 -0700
    lastz runs to golden hamster refs #28333
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 54, context: html, text, full: html, text
    0fd53fc90dcc6fd4deca96abee94ea5344a73f39 Sat Oct 23 15:25:09 2021 -0700
    adding Paramecium_tetraurelia_strain_d4-2 no redmine
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    10495af5529be614efb01145d78ce0509c2c9b67 Sat Oct 23 15:28:37 2021 -0700
    adding Paramecium tetraurelia (d4-2 2017) no redmine
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 6, context: html, text, full: html, text
    7610a0636c1fb8160a412f89fefc9929d005373a Mon Oct 18 16:54:54 2021 -0700
    Update hg38 patch 13 genbank file references, refs #25091
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
  • lines changed 2, context: html, text, full: html, text
    37993dc79a851fd6a443d8c0fe8bb4264b8e4191 Fri Oct 22 16:21:42 2021 -0700
    Woops forgot to restore the old setting name to actual tracks after testing rename of trackDb variable, refs BrianLee email
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 2, context: html, text, full: html, text
    37993dc79a851fd6a443d8c0fe8bb4264b8e4191 Fri Oct 22 16:21:42 2021 -0700
    Woops forgot to restore the old setting name to actual tracks after testing rename of trackDb variable, refs BrianLee email
• src/hg/makeDb/trackDb/human/hg38/t2t.ra
  • lines changed 31, context: html, text, full: html, text
    8f84137f9fba8bf1eaa585cb8325ab61f7efd302 Fri Oct 22 05:45:18 2021 -0700
    adding T2T alignment chains received from Mark. We got at least one ML question about this, refs #28098
• src/hg/makeDb/trackDb/human/hg38/t2tChain.html
  • lines changed 236, context: html, text, full: html, text
    5bf878e63284b8c825a75a4ddff4a0c56a088a5c Mon Oct 25 08:05:22 2021 -0700
    adding t2t docs page, refs #28380
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    8f84137f9fba8bf1eaa585cb8325ab61f7efd302 Fri Oct 22 05:45:18 2021 -0700
    adding T2T alignment chains received from Mark. We got at least one ML question about this, refs #28098
• src/hg/makeDb/trackDb/human/orphadata.html
  • lines changed 85, context: html, text, full: html, text
    9ff1cfb85060858263a0978407de64c2715a4722 Fri Oct 22 11:50:35 2021 -0700
    Staging orphanet track ready for QA, refs #14319
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 15, context: html, text, full: html, text
    9ff1cfb85060858263a0978407de64c2715a4722 Fri Oct 22 11:50:35 2021 -0700
    Staging orphanet track ready for QA, refs #14319
• src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra
  • lines changed 95, context: html, text, full: html, text
    e7c438c709822b66b2cad226d2a58940823e7b00 Fri Oct 22 14:06:41 2021 -0700
    adding chainNet for golden hamster GCF_000349665.1 refs #28333
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    29acb9da18cc7c3a4f649cc736b088c74ebba64e Tue Oct 19 19:25:43 2021 -0700
    releasing variantMuts track update refs #27926
  • lines changed 1, context: html, text, full: html, text
    2335e9761a17e9b1dc1d720ca8f63d85a5be9352 Fri Oct 22 10:58:27 2021 -0700
    Fixing a tiny spelling mistake noticed by a user in ref #28388
• src/hg/makeDb/trackDb/virus/wuhCor1/variantMutsV2.html
  • lines changed 25, context: html, text, full: html, text
    c8b0ee76649b8b7430afeb713a3a2cb560247b57 Tue Oct 19 11:02:09 2021 -0700
    Small format changes to variantMutsV2 refs #27926
• src/hg/makeDb/trackDb/virus/wuhCor1/variantMutsV2.ra
  • lines changed 1, context: html, text, full: html, text
    29acb9da18cc7c3a4f649cc736b088c74ebba64e Tue Oct 19 19:25:43 2021 -0700
    releasing variantMuts track update refs #27926
• src/hg/utils/automation/asmHubChainNetTrackDb.sh
  • lines changed 5, context: html, text, full: html, text
    f3236a4aa3d7e74b63c7d2cb2f9e3b37ac7858b8 Tue Oct 19 12:22:57 2021 -0700
    beware the name date vs. date palm refs #28365
• src/hg/utils/automation/n50.pl
  • lines changed 4, context: html, text, full: html, text
    ed292c11c5008eec8dd80894e385fead2d77a97c Thu Oct 21 11:59:45 2021 -0700
    correct result when the first contig satisifies the measurement no redmine
• src/hg/utils/otto/grcIncident/README.txt
  • lines changed 57, context: html, text, full: html, text
    8a0a3fdc82e2a1362e24e91a2f5de0ee9c1931fe Thu Oct 21 11:17:30 2021 -0700
    scripts for the GRC Incident otto job no redmine
  • lines changed 6, context: html, text, full: html, text
    7ca589e9eb061fa0b78b02f616c6b28c85fc15e5 Thu Oct 21 11:18:31 2021 -0700
    indicate the cron tab entry
• src/hg/utils/otto/grcIncident/grcUpdate.sh
  • lines changed 120, context: html, text, full: html, text
    8a0a3fdc82e2a1362e24e91a2f5de0ee9c1931fe Thu Oct 21 11:17:30 2021 -0700
    scripts for the GRC Incident otto job no redmine
• src/hg/utils/otto/grcIncident/parseGff.pl
  • lines changed 44, context: html, text, full: html, text
    8a0a3fdc82e2a1362e24e91a2f5de0ee9c1931fe Thu Oct 21 11:17:30 2021 -0700
    scripts for the GRC Incident otto job no redmine
• src/hg/utils/otto/grcIncident/runUpdate.sh
  • lines changed 112, context: html, text, full: html, text
    8a0a3fdc82e2a1362e24e91a2f5de0ee9c1931fe Thu Oct 21 11:17:30 2021 -0700
    scripts for the GRC Incident otto job no redmine
• src/hg/utils/otto/grcIncident/verifyTransfer.sh
  • lines changed 47, context: html, text, full: html, text
    8a0a3fdc82e2a1362e24e91a2f5de0ee9c1931fe Thu Oct 21 11:17:30 2021 -0700
    scripts for the GRC Incident otto job no redmine
• src/hg/utils/otto/lovd/download.sh
  • lines changed 1, context: html, text, full: html, text
    d5cc9995f1311fb06dd8291222c892da6084f4d6 Tue Oct 19 07:31:47 2021 -0700
    now that LOVD has fixed their server, can remove the hacks again, no redmine, email with Lou
• src/hg/utils/otto/ncbiRefSeq/README.txt
  • lines changed 5, context: html, text, full: html, text
    d5dd5a3cb96a68a3bc78d07e8247fc03036e2a73 Tue Oct 19 14:01:21 2021 -0700
    scripts to run the NCBI RefSeq update automatically refs #24735
• src/hg/utils/otto/ncbiRefSeq/archiveOne.sh
  • lines changed 40, context: html, text, full: html, text
    a7b8d7430248b2898d2f79c40a49665b06c033c1 Tue Oct 19 14:00:23 2021 -0700
    scripts to run the NCBI RefSeq update automatically refs #24735
• src/hg/utils/otto/ncbiRefSeq/ottoNcbiRefSeq.sh
  • lines changed 11, context: html, text, full: html, text
    a7b8d7430248b2898d2f79c40a49665b06c033c1 Tue Oct 19 14:00:23 2021 -0700
    scripts to run the NCBI RefSeq update automatically refs #24735
• src/hg/utils/otto/ncbiRefSeq/prevHg19.sum
  • lines changed 1, context: html, text, full: html, text
    a7b8d7430248b2898d2f79c40a49665b06c033c1 Tue Oct 19 14:00:23 2021 -0700
    scripts to run the NCBI RefSeq update automatically refs #24735
• src/hg/utils/otto/ncbiRefSeq/prevHg38.sum
  • lines changed 1, context: html, text, full: html, text
    a7b8d7430248b2898d2f79c40a49665b06c033c1 Tue Oct 19 14:00:23 2021 -0700
    scripts to run the NCBI RefSeq update automatically refs #24735
• src/hg/utils/otto/ncbiRefSeq/prevMm10.sum
  • lines changed 1, context: html, text, full: html, text
    a7b8d7430248b2898d2f79c40a49665b06c033c1 Tue Oct 19 14:00:23 2021 -0700
    scripts to run the NCBI RefSeq update automatically refs #24735
• src/hg/utils/otto/ncbiRefSeq/prevMm39.sum
  • lines changed 1, context: html, text, full: html, text
    a7b8d7430248b2898d2f79c40a49665b06c033c1 Tue Oct 19 14:00:23 2021 -0700
    scripts to run the NCBI RefSeq update automatically refs #24735
• src/hg/utils/otto/ncbiRefSeq/runHg19.sh
  • lines changed 17, context: html, text, full: html, text
    a7b8d7430248b2898d2f79c40a49665b06c033c1 Tue Oct 19 14:00:23 2021 -0700
    scripts to run the NCBI RefSeq update automatically refs #24735
• src/hg/utils/otto/ncbiRefSeq/runHg38.sh
  • lines changed 17, context: html, text, full: html, text
    a7b8d7430248b2898d2f79c40a49665b06c033c1 Tue Oct 19 14:00:23 2021 -0700
    scripts to run the NCBI RefSeq update automatically refs #24735
• src/hg/utils/otto/ncbiRefSeq/runMm10.sh
  • lines changed 17, context: html, text, full: html, text
    a7b8d7430248b2898d2f79c40a49665b06c033c1 Tue Oct 19 14:00:23 2021 -0700
    scripts to run the NCBI RefSeq update automatically refs #24735
• src/hg/utils/otto/ncbiRefSeq/runMm39.sh
  • lines changed 17, context: html, text, full: html, text
    a7b8d7430248b2898d2f79c40a49665b06c033c1 Tue Oct 19 14:00:23 2021 -0700
    scripts to run the NCBI RefSeq update automatically refs #24735
• src/hg/utils/otto/ncbiRefSeq/runUcscDb.sh
  • lines changed 63, context: html, text, full: html, text
    a7b8d7430248b2898d2f79c40a49665b06c033c1 Tue Oct 19 14:00:23 2021 -0700
    scripts to run the NCBI RefSeq update automatically refs #24735
• src/hg/utils/otto/orphanet/checkOrphanet.sh
  • lines changed 61, context: html, text, full: html, text
    9ff1cfb85060858263a0978407de64c2715a4722 Fri Oct 22 11:50:35 2021 -0700
    Staging orphanet track ready for QA, refs #14319
• src/hg/utils/otto/orphanet/orphadata.as
  • lines changed 33, context: html, text, full: html, text
    9ff1cfb85060858263a0978407de64c2715a4722 Fri Oct 22 11:50:35 2021 -0700
    Staging orphanet track ready for QA, refs #14319
• src/hg/utils/otto/orphanet/orphanetWrapper.sh
  • lines changed 9, context: html, text, full: html, text
    9ff1cfb85060858263a0978407de64c2715a4722 Fri Oct 22 11:50:35 2021 -0700
    Staging orphanet track ready for QA, refs #14319
• src/hg/utils/otto/orphanet/parseOrphadata.py
  • lines changed 727, context: html, text, full: html, text
    9ff1cfb85060858263a0978407de64c2715a4722 Fri Oct 22 11:50:35 2021 -0700
    Staging orphanet track ready for QA, refs #14319
• src/hg/utils/otto/otto.crontab
  • lines changed 9, context: html, text, full: html, text
    9e91874973c9983e2bc43514478ba4beb46cc38e Fri Oct 22 08:22:44 2021 -0700
    Adding GRC Incident and NCBI RefSeq otto jobs, passed over from Hiram.
• src/inc/common.h
  • lines changed 3, context: html, text, full: html, text
    7cdced87bd7680c51b327560aff3bb3cf414733a Sat Oct 23 08:59:02 2021 -0700
    Fixing the broken build for max, some little bits not checked in.
  • lines changed 3, context: html, text, full: html, text
    561f452458624b64c61e2ead5cdcb705b5fcadd1 Sat Oct 23 13:22:18 2021 -0700
    fixing up missing files in last commit, refs #28324
• src/index/ixIxx/ixIxx.c
  • lines changed 34, context: html, text, full: html, text
    51227ee6c9fcdd3f5917826122b0b24c9fa57a9f Fri Oct 22 15:11:27 2021 -0700
    ixIxx fulltext limit of 31 characters was making it silently throw out terms that would otherwise be searchable from the .ix index. Added an option -maxWordLength=N to override the default of 31. Added status to stderr reporting the number of unique words that were too long and thus discarded, and the longest word length of discarded words, plus a message that -verbose=2 will list all words and their lengths that failed because they exceeded the allowed length.
• src/lib/common.c
  • lines changed 13, context: html, text, full: html, text
    7cdced87bd7680c51b327560aff3bb3cf414733a Sat Oct 23 08:59:02 2021 -0700
    Fixing the broken build for max, some little bits not checked in.
  • lines changed 13, context: html, text, full: html, text
    561f452458624b64c61e2ead5cdcb705b5fcadd1 Sat Oct 23 13:22:18 2021 -0700
    fixing up missing files in last commit, refs #28324
• src/product/Note-To-QA.txt
  • lines changed 13, context: html, text, full: html, text
    96c23d22e15631da16fcf1069f0f30249910b533 Thu Oct 21 05:45:43 2021 -0700
    Updating mirrorManual and mirror.html / README.txt for Mysql support retirement, refs #28373
• src/product/README.txt
  • lines changed 10, context: html, text, full: html, text
    96c23d22e15631da16fcf1069f0f30249910b533 Thu Oct 21 05:45:43 2021 -0700
    Updating mirrorManual and mirror.html / README.txt for Mysql support retirement, refs #28373
• src/product/mirrorDocs/makefile
  • lines changed 5, context: html, text, full: html, text
    96c23d22e15631da16fcf1069f0f30249910b533 Thu Oct 21 05:45:43 2021 -0700
    Updating mirrorManual and mirror.html / README.txt for Mysql support retirement, refs #28373
• src/product/mirrorDocs/staticPage.html
  • lines changed 3, context: html, text, full: html, text
    96c23d22e15631da16fcf1069f0f30249910b533 Thu Oct 21 05:45:43 2021 -0700
    Updating mirrorManual and mirror.html / README.txt for Mysql support retirement, refs #28373
• src/product/mirrorManual.txt
  • lines changed 100, context: html, text, full: html, text
    96c23d22e15631da16fcf1069f0f30249910b533 Thu Oct 21 05:45:43 2021 -0700
    Updating mirrorManual and mirror.html / README.txt for Mysql support retirement, refs #28373
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    1868eae342f27a2efc6b9820e3d14719ba56e5b8 Mon Oct 25 10:06:42 2021 -0700
    v423 preview1, refs #28292

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• files changed: 79