All File Changes

v463_preview to v463_preview2 (2024-03-18 to 2024-03-25) v463

• src/browserbox/root/updateBrowser.sh
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    24af8bffea6c499bbea60b989d81278c414781d0 Tue Mar 19 07:44:13 2024 -0700
    removing registration.txt file on gbib updates, as per hiram
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    7623f8078aef4173058b6ec1911f93714d7b906f Wed Mar 20 07:47:29 2024 -0700
    protecting blatservers table against duplicates created by a future generation of engineers who are not as afraid to change things as we are, refs #33230
• src/hg/hgPcr/hgPcr.c
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    7149c3be130a904c8bae3802b15cda69833c52a0 Mon Mar 18 17:00:30 2024 -0700
    Adding some info to hgPcr to be wary of primer identification using only this tool. We have had users who used hgPcr, ordered primers, and then found they had off-targets. Refs #25202
• src/hg/hgPhyloPlace/phyloPlace.c
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    66a1a82f72f9f3295bb4007b1b5681013976a694 Wed Mar 20 15:20:27 2024 -0700
    Overhaul struct sampleMetadata: instead of one struct member per anticipated column, use an array of column values and a shared array of column names. As we support more species, the available metadata gets more divergent so this needs to be more general. We still need to make aggregation of attributes on branches more generic / config-driven.
• src/hg/hgPhyloPlace/phyloPlace.h
  • lines changed 21, context: html, text, full: html, text
    66a1a82f72f9f3295bb4007b1b5681013976a694 Wed Mar 20 15:20:27 2024 -0700
    Overhaul struct sampleMetadata: instead of one struct member per anticipated column, use an array of column values and a shared array of column names. As we support more species, the available metadata gets more divergent so this needs to be more general. We still need to make aggregation of attributes on branches more generic / config-driven.
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
  • lines changed 56, context: html, text, full: html, text
    66a1a82f72f9f3295bb4007b1b5681013976a694 Wed Mar 20 15:20:27 2024 -0700
    Overhaul struct sampleMetadata: instead of one struct member per anticipated column, use an array of column values and a shared array of column names. As we support more species, the available metadata gets more divergent so this needs to be more general. We still need to make aggregation of attributes on branches more generic / config-driven.
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    b4460ce8ea85171693750dd217ba805870b0b93d Thu Mar 21 08:54:51 2024 -0700
    Branch attributes (used for coloring branches by majority lineage/clade) are now specified by a new config setting branchAttributes instead of being hardcoded.
• src/hg/hgPhyloPlace/vcfFromFasta.c
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    9ee0dbb8ed4ffb54cdd9fb8bb473548ae9cf276b Wed Mar 20 15:16:13 2024 -0700
    M. tuberculosis gets lots of BLAT alignments; tweak warning message, make sure we keep only the first.
• src/hg/hgSession/hgSession.c
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    2eb840e2f6321346a970fc26e010158f57ff7602 Mon Mar 25 07:21:48 2024 -0700
    showing view counts in session list and adding the copy to clipboard button here, too, refs #33248
• src/hg/hgTables/filterFields.c
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    2395162eb448f802868450e7c2201988e8e1671f Wed Mar 20 14:34:27 2024 -0700
    showing only tables from the db knownGeneVx in TB if user selected a knownGeneVx track, refs #33269
• src/hg/hgTracks/bedTrack.c
  • lines changed 16, context: html, text, full: html, text
    1cbb143dea2cf4ece990707556b4c2caac7f0311 Thu Mar 21 13:50:58 2024 -0700
    fixing bugs in quickLift
• src/hg/hgTracks/chainTrack.c
  • lines changed 3, context: html, text, full: html, text
    1cbb143dea2cf4ece990707556b4c2caac7f0311 Thu Mar 21 13:50:58 2024 -0700
    fixing bugs in quickLift
• src/hg/hgTracks/variation.c
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    88370fb4e8dfd1915a22d3d086a92060e7286b6c Thu Mar 21 11:52:55 2024 -0700
    bigDbSnp should use summary levels if load failed
• src/hg/hgc/hgc.c
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    96c4625c9810fd946a852d4e85d343cd2b0e5717 Thu Mar 21 16:08:25 2024 -0700
    get sequence links from hgc to work with quickLift
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    a00e505a58aefda679ed9a8a2a74687a93861a47 Fri Mar 22 08:22:51 2024 -0700
    adding database name to title on hgc, especially useful for shortmatch track, Jairo requested this in some ticket, do not remember the redmine ticket
• src/hg/htdocs/FAQ/FAQmaillist.html
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    c89f2b179cb5052739a8194a970696e09e8901cb Tue Mar 19 04:00:10 2024 -0700
    future proof the mailing list FAQ, no redmine
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    e8a896540cd06508afeee8b70668dd296644b65f Tue Mar 19 04:04:31 2024 -0700
    fixing up ML FAQ, no redmine
• src/hg/htdocs/goldenPath/help/hgGeneGraph.html
  • lines changed 1, context: html, text, full: html, text
    d2f09bfc70b10ed51f71ed23c096e8e74162ca63 Thu Mar 21 13:44:49 2024 -0700
    Remove unneeded id from Credits header in hgGeneGraph help page so the pandoc html to plain text conversion step stops complaining, refs #32812
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 23, context: html, text, full: html, text
    c9401e6585d6b2dd85971d55120d7d7c3bc0d2e8 Tue Mar 19 11:13:11 2024 -0700
    Staging the gnomAD v4 constraints metrics announcemnt, refs #33084
• src/hg/js/hgSearch.js
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    7912833b68798e9a29c06efc6bd4df497108aaa6 Thu Mar 21 11:40:17 2024 -0700
    Refactor duplicate assignments in if else clauses after code review, good call Jonathan, refs #33254
• src/hg/js/utils.js
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    2eb840e2f6321346a970fc26e010158f57ff7602 Mon Mar 25 07:21:48 2024 -0700
    showing view counts in session list and adding the copy to clipboard button here, too, refs #33248
• src/hg/lib/jksql.c
  • lines changed 5, context: html, text, full: html, text
    5b207e2b6401af927d5c91ac1366b3212d54f427 Fri Mar 22 08:02:46 2024 -0700
    improving hgcentral down error message, suggestion by Lou
• src/hg/lib/quickLift.c
  • lines changed 5, context: html, text, full: html, text
    1cbb143dea2cf4ece990707556b4c2caac7f0311 Thu Mar 21 13:50:58 2024 -0700
    fixing bugs in quickLift
• src/hg/makeDb/doc/asmHubs/README.txt
  • lines changed 52, context: html, text, full: html, text
    b7f8218ec50729e9114674e07ac351f6c5a5a16b Tue Mar 19 10:08:46 2024 -0700
    updated instructions with refinements for genark assembly request handling refs #29545
• src/hg/makeDb/doc/asmHubs/commonNames.pl
  • lines changed 22, context: html, text, full: html, text
    5f396b55b70dd7faf0a76b2b96af95d7a79465f2 Wed Mar 20 10:48:22 2024 -0700
    better identification of haplotypes refs #29545
• src/hg/makeDb/doc/asmHubs/master.run.list
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    bcf17ae4e15479fb6142b4c253d9fd1107c50cc8 Sat Mar 23 14:20:19 2024 -0700
    adding invertebrate Hofstenia_miamia per user request, refs #29545
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
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    41d485270cf9979dd15c6d7395cee039644e971f Sat Mar 23 14:30:07 2024 -0700
    adding Hofstenia_miamia three-banded panther worm (2019) refs #29545
• src/hg/makeDb/schema/all.joiner
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    2395162eb448f802868450e7c2201988e8e1671f Wed Mar 20 14:34:27 2024 -0700
    showing only tables from the db knownGeneVx in TB if user selected a knownGeneVx track, refs #33269
• src/hg/makeDb/trackDb/chicken/galGal6/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    620a35451c58e0f130faa98b9dadb7fe0c1f9c6d Fri Mar 22 14:58:24 2024 -0700
    Fixing outlink to GRC page, refs #25576
• src/hg/makeDb/trackDb/human/cytoBand.html
  • lines changed 13, context: html, text, full: html, text
    18470eb8d3875f90afe85196e3582c394eaf2716 Wed Mar 20 17:07:49 2024 -0700
    Updating the chromosome band description page to clarify that we do not generate these data anymore, instead we download it from NCBI, refs #31551
• src/hg/makeDb/trackDb/human/hg19/gnomadExomesGenomes.html
  • lines changed 2, context: html, text, full: html, text
    ea6494737a0cd83794c8ff5820e214152f757b13 Thu Mar 21 13:55:59 2024 -0700
    Adding a description for the Non-Cancer filter to the gnomad pages, refs #32916
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
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    b0be4952b57643c5cd58f4bde82b2cd42d8da73e Sun Mar 24 22:33:28 2024 -0700
    Adding gnomAD non-cancer filter settings to hg38 v3.1.1 and hg19 v2.1.1, refs #32916
• src/hg/makeDb/trackDb/human/hg38/gnomad.constraint.public.ra
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    127474d5eea0b79b635d2e3b1b264dbaa28a1151 Thu Mar 21 09:10:38 2024 -0700
    Forgot to update the HTML pages when releasing, refs #33256
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 3, context: html, text, full: html, text
    b0be4952b57643c5cd58f4bde82b2cd42d8da73e Sun Mar 24 22:33:28 2024 -0700
    Adding gnomAD non-cancer filter settings to hg38 v3.1.1 and hg19 v2.1.1, refs #32916
• src/hg/makeDb/trackDb/human/hg38/gnomadPLI.html
  • lines changed 24, context: html, text, full: html, text
    127474d5eea0b79b635d2e3b1b264dbaa28a1151 Thu Mar 21 09:10:38 2024 -0700
    Forgot to update the HTML pages when releasing, refs #33256
• src/hg/makeDb/trackDb/human/hg38/gnomadV3_1_1.html
  • lines changed 2, context: html, text, full: html, text
    ea6494737a0cd83794c8ff5820e214152f757b13 Thu Mar 21 13:55:59 2024 -0700
    Adding a description for the Non-Cancer filter to the gnomad pages, refs #32916
• src/hg/makeDb/trackDb/human/hg38/gnomadV4.html
  • lines changed 2, context: html, text, full: html, text
    ea6494737a0cd83794c8ff5820e214152f757b13 Thu Mar 21 13:55:59 2024 -0700
    Adding a description for the Non-Cancer filter to the gnomad pages, refs #32916
• src/hg/utils/automation/doAugustus.pl
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    b02e6b88da8d3a3d306017183d22d63a22c3543e Thu Mar 21 22:03:37 2024 -0700
    adding ram and cpu arguments no redmine
• src/product/installer/browserSetup.sh
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    db6167f2bb6f7e666e48290a919254cb9f93b3cd Wed Mar 20 07:49:33 2024 -0700
    GBIC version: protecting blatservers table against duplicates created by a future generation of engineers who are not as afraid to change things as we are, refs #33230
• src/utils/qa/weeklybld/buildEnv.csh
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    59f89a79c486d68b92cec457a0f29a66dc570768 Mon Mar 25 10:52:21 2024 -0700
    v463 preview2, refs #33267

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• files changed: 40