All File Changes

v471_preview2 to v471_base (2024-09-09 to 2024-09-16) v471

• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 49, context: html, text, full: html, text
    466d876c3308a789b3abd3e2ae559d1413ea5fc5 Thu Sep 12 10:01:15 2024 -0700
    nextclade sort's scoring function, for short similar reference sequences, gives too much weight to reference sequence length and not enough to numHits. So, instead of using nextclade sort's top-scoring match for each input sequence, run nextclade sort --all-matches and choose the ref with the highest (score * numHits). This does a better job when distinguishing between 7 RefSeq assemblies for influenza A segments.
• src/hg/hgPhyloPlace/runUsher.c
  • lines changed 30, context: html, text, full: html, text
    6b482d67559bf0e2f7c27eed5182a18f85f0db2b Fri Sep 13 13:55:38 2024 -0700
    Add config setting enableOptimization (for small trees). Since there are now too many configurable usher-sampled options to handle by truncating a list, instead we now add options if configured.
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
  • lines changed 31, context: html, text, full: html, text
    5dd22774eea1a954815f0a32797d5a1dbfdcecc8 Tue Sep 10 14:01:20 2024 -0700
    When writing the auspice JSON tree, if a sample is found in the optional config file anchorSamples, then add an empty 'vaccine' attribute to get the X icon in auspice display.
• src/hg/hgPhyloPlace/vcfFromFasta.c
  • lines changed 1, context: html, text, full: html, text
    e4e4f9d3a53e8bc8b1354be2267031d392d09886 Fri Sep 13 12:57:40 2024 -0700
    Fix the way basesAligned is calculated: insBases were never part of (tEnd - tStart).
• src/hg/hgTables/hgTables.c
  • lines changed 29, context: html, text, full: html, text
    898fdeaa1667f0840890881a70f6ad37d9d0a0d6 Fri Sep 13 13:14:15 2024 -0700
    Reverting Max's change because it was breaking sequence table browser output, refs #33415
• src/hg/hgTables/hgTables.h
  • lines changed 3, context: html, text, full: html, text
    898fdeaa1667f0840890881a70f6ad37d9d0a0d6 Fri Sep 13 13:14:15 2024 -0700
    Reverting Max's change because it was breaking sequence table browser output, refs #33415
• src/hg/hgTables/mainPage.c
  • lines changed 3, context: html, text, full: html, text
    898fdeaa1667f0840890881a70f6ad37d9d0a0d6 Fri Sep 13 13:14:15 2024 -0700
    Reverting Max's change because it was breaking sequence table browser output, refs #33415
• src/hg/hgTables/seqOut.c
  • lines changed 14, context: html, text, full: html, text
    898fdeaa1667f0840890881a70f6ad37d9d0a0d6 Fri Sep 13 13:14:15 2024 -0700
    Reverting Max's change because it was breaking sequence table browser output, refs #33415
• src/hg/htdocs/assemblySearch.html
  • lines changed 27, context: html, text, full: html, text
    7147d370964619773bfd7a7761281240262aebe4 Tue Sep 10 15:05:22 2024 -0700
    adding pop up help text refs #32596
  • lines changed 8, context: html, text, full: html, text
    ee44defec68c55c48cf35268d29bdd9392923542 Wed Sep 11 13:30:48 2024 -0700
    js/assemblySearch.js
  • lines changed 5, context: html, text, full: html, text
    ccb13e0ba375da8b3ce296ec2813b1ff519bd88e Wed Sep 11 15:30:51 2024 -0700
    adjustments per feedback refs #32596
  • lines changed 7, context: html, text, full: html, text
    82be17cac081d3c6b3cc13407b570ad265fa6ad6 Thu Sep 12 11:38:02 2024 -0700
    proper delay on the pop ups and margins around elements remove the priority in the status column refs #32596
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 1, context: html, text, full: html, text
    826c2023c85f0829e3a131971666e6d643d94fb5 Tue Sep 10 13:55:14 2024 -0700
    Fixing broken link as pointed out by a user, refs #34414
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 4, context: html, text, full: html, text
    164341f2268fb461ad11b02336af844d6b930ae6 Tue Sep 10 14:10:46 2024 -0700
    Doc'ing new interact setting that allows default behavior showing only all interactions with both ends in current region. Refs #34164
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 6, context: html, text, full: html, text
    164341f2268fb461ad11b02336af844d6b930ae6 Tue Sep 10 14:10:46 2024 -0700
    Doc'ing new interact setting that allows default behavior showing only all interactions with both ends in current region. Refs #34164
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 80, context: html, text, full: html, text
    a9883c85708472dcd0be71920acdd2b0c2cd31c7 Tue Sep 10 15:00:35 2024 -0700
    Announcing the ENIGMA and BRCA Exchange hubs, refs #34352
  • lines changed 2, context: html, text, full: html, text
    397aad19c80dcc088077ed13360f7300ef182db6 Tue Sep 10 15:03:32 2024 -0700
    Updating the dates for the announcement, refs #34352 and #32914
• src/hg/htdocs/inc/gbPageStartHardcoded.html
  • lines changed 2, context: html, text, full: html, text
    3307a39e169e86190666dba88d4e6521880d49f2 Fri Aug 16 17:32:50 2024 -0700
    Adding Anna's suggestions to the tutorial. The final tool tip was too large, so I broke it up into smaller pieces: track search, vai, sessions, hgConvert, highlights, refs #33732 Fixing the RTS popup missing a title by adding the title in the tutorial, Fixing the ending buttons
  • lines changed 1, context: html, text, full: html, text
    52aa3333e45260142657abe8389a9504d5262cb9 Thu Sep 12 14:36:52 2024 -0700
    Writing to the error log when the tutorial starts and finishes
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 1, context: html, text, full: html, text
    d844b02530ce38cd6118c985b80d07ad59066cc8 Wed Sep 11 16:50:12 2024 -0700
    Adding an id for the 'Contact us' link in the Help Menu, refs #33732
  • lines changed 1, context: html, text, full: html, text
    3307a39e169e86190666dba88d4e6521880d49f2 Fri Aug 16 17:32:50 2024 -0700
    Adding Anna's suggestions to the tutorial. The final tool tip was too large, so I broke it up into smaller pieces: track search, vai, sessions, hgConvert, highlights, refs #33732 Fixing the RTS popup missing a title by adding the title in the tutorial, Fixing the ending buttons
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    397aad19c80dcc088077ed13360f7300ef182db6 Tue Sep 10 15:03:32 2024 -0700
    Updating the dates for the announcement, refs #34352 and #32914
• src/hg/htdocs/style/assemblySearch.css
  • lines changed 7, context: html, text, full: html, text
    7147d370964619773bfd7a7761281240262aebe4 Tue Sep 10 15:05:22 2024 -0700
    adding pop up help text refs #32596
  • lines changed 4, context: html, text, full: html, text
    ee44defec68c55c48cf35268d29bdd9392923542 Wed Sep 11 13:30:48 2024 -0700
    js/assemblySearch.js
  • lines changed 28, context: html, text, full: html, text
    ccb13e0ba375da8b3ce296ec2813b1ff519bd88e Wed Sep 11 15:30:51 2024 -0700
    adjustments per feedback refs #32596
  • lines changed 8, context: html, text, full: html, text
    82be17cac081d3c6b3cc13407b570ad265fa6ad6 Thu Sep 12 11:38:02 2024 -0700
    proper delay on the pop ups and margins around elements remove the priority in the status column refs #32596
• src/hg/hubApi/assemblyList.py
  • lines changed 37, context: html, text, full: html, text
    ff0ea8e2f1223e74bcb82b2426e6976bca6473b7 Thu Sep 12 20:50:47 2024 -0700
    get the year in the description if it is not in other fields and correctly lowerCase the category,status and level words refs #33720
  • lines changed 6, context: html, text, full: html, text
    456f4a30692d5db99a4b90e76b2f7a4f06bae0e1 Fri Sep 13 10:53:13 2024 -0700
    simple year match is good enough refs #33720
  • lines changed 5, context: html, text, full: html, text
    215ac86539ac6a12e2db96c777a7a1568817318a Fri Sep 13 16:07:46 2024 -0700
    getting the GC accessions into dbDb descriptions when possible refs #33720
• src/hg/hubApi/findGenome.c
  • lines changed 23, context: html, text, full: html, text
    6bd1b2f193f4cc37ac89a76582cb432e40988574 Thu Sep 12 15:42:26 2024 -0700
    better management of the addition of the compound words refs #32596
  • lines changed 3, context: html, text, full: html, text
    bd79f475d7a5bc2a54f40eed4c16db77dd28f14a Fri Sep 13 14:45:12 2024 -0700
    one word with wildcard* leave it as-is refs #32596
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    882e1939634c785f6b65c6e72eee66092020267a Mon Sep 16 10:49:59 2024 -0700
    New version number v471
• src/hg/js/assemblySearch.js
  • lines changed 9, context: html, text, full: html, text
    7147d370964619773bfd7a7761281240262aebe4 Tue Sep 10 15:05:22 2024 -0700
    adding pop up help text refs #32596
  • lines changed 13, context: html, text, full: html, text
    54ea59ee208f0e498cfeb3d6ca7f1478fca8d5a4 Wed Sep 11 13:31:29 2024 -0700
    adding documention for all pop up informations boxes refs #32596
  • lines changed 2, context: html, text, full: html, text
    d86274d116c9a29ddcf66f594c57bab80fb5a93c Wed Sep 11 15:31:27 2024 -0700
    adjustments per feedback refs #32596
  • lines changed 1, context: html, text, full: html, text
    82be17cac081d3c6b3cc13407b570ad265fa6ad6 Thu Sep 12 11:38:02 2024 -0700
    proper delay on the pop ups and margins around elements remove the priority in the status column refs #32596
• src/hg/js/tutorials/clinicalTutorial.js
  • lines changed 203, context: html, text, full: html, text
    3307a39e169e86190666dba88d4e6521880d49f2 Fri Aug 16 17:32:50 2024 -0700
    Adding Anna's suggestions to the tutorial. The final tool tip was too large, so I broke it up into smaller pieces: track search, vai, sessions, hgConvert, highlights, refs #33732 Fixing the RTS popup missing a title by adding the title in the tutorial, Fixing the ending buttons
  • lines changed 4, context: html, text, full: html, text
    52aa3333e45260142657abe8389a9504d5262cb9 Thu Sep 12 14:36:52 2024 -0700
    Writing to the error log when the tutorial starts and finishes
  • lines changed 15, context: html, text, full: html, text
    a1b6cfaff731641724453df38e50ad5921892fe9 Fri Sep 13 16:11:55 2024 -0700
    Adding an event listener to properly log that the clincial tutorial finished when they start the basic tutorial in the last step, refs #33732
• src/hg/lib/featureBits.c
  • lines changed 5, context: html, text, full: html, text
    33350fe38ad2c46108db7cd96e0ec0d956c7c6cb Fri Sep 13 12:14:25 2024 -0700
    Revert "show table browser only exons when track contains genes, refs #27633" This reverts commit e0cf10a674d7aac55aff8d39d169440716eb3f74.
• src/hg/makeDb/doc/asmHubs/lastzRuns.txt
  • lines changed 82, context: html, text, full: html, text
    1ac19241d8c26d55fe304ed17a3cc41d2c3c5115 Thu Sep 5 15:20:13 2024 -0700
    Adding makedocs for liftOver files created, refs #34305
  • lines changed 83, context: html, text, full: html, text
    0bcfab505e3e3fa981b3d220f0354128e7a8a2df Sun Sep 15 16:11:48 2024 -0700
    violet copper butterfly (GCA_963853865.1) to butterfly C.glycerion (GCA_963855885.1) lastz/chain/net run for user, refs #33991
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    67ad3f3b39146140aef1db15ea45c7c45200fec0 Wed Sep 11 14:40:33 2024 -0700
    adding one per user request refs #29545
• src/hg/makeDb/doc/asmHubs/tsvToJson.py
  • lines changed 1, context: html, text, full: html, text
    c0d655e157b7e29f988e6bb9416578d6ac08f40f Thu Sep 12 19:15:10 2024 -0700
    open the tsv file as latin-1 encoding to handle extended characters refs #34337
• src/hg/makeDb/doc/brcAsmHub/brc.orderList.tsv
  • lines changed 6, context: html, text, full: html, text
    3ef9201cf5cc70993b1e35a6b3aa4d9d85b470d7 Wed Sep 11 14:14:36 2024 -0700
    adding six more to help catch up refs #34337
  • lines changed 1, context: html, text, full: html, text
    a1387634d24e7ba1195bc31ba3339d1c98be018b Thu Sep 12 19:27:10 2024 -0700
    correcting some versions refs #29545
• src/hg/makeDb/doc/hg38/lastzRuns.txt
  • lines changed 403, context: html, text, full: html, text
    1ac19241d8c26d55fe304ed17a3cc41d2c3c5115 Thu Sep 5 15:20:13 2024 -0700
    Adding makedocs for liftOver files created, refs #34305
  • lines changed 166, context: html, text, full: html, text
    a38890e725d62be014d276d490e710348a32cd6b Sun Sep 15 16:00:51 2024 -0700
    hg38 to GCA_023856395.1/GCF_030867095.1 lastz/chain/net run for users, refs #33276 #33786
  • lines changed 84, context: html, text, full: html, text
    1d41751e7047c66060c07042479d29cb82dd9c0b Sun Sep 15 23:27:57 2024 -0700
    Rabbit (GCF_009806435.1) to hg38/mm39 lastz/chain/net run for user, refs #34037
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    67ad3f3b39146140aef1db15ea45c7c45200fec0 Wed Sep 11 14:40:33 2024 -0700
    adding one per user request refs #29545
  • lines changed 1, context: html, text, full: html, text
    a1387634d24e7ba1195bc31ba3339d1c98be018b Thu Sep 12 19:27:10 2024 -0700
    correcting some versions refs #29545
  • lines changed 90, context: html, text, full: html, text
    2136bd857c7f0ce869fce9d10f6f412bc7eb1100 Fri Sep 13 16:09:16 2024 -0700
    adding 89 for the BRC project new type of invertebrate refs #34337
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 2, context: html, text, full: html, text
    a1387634d24e7ba1195bc31ba3339d1c98be018b Thu Sep 12 19:27:10 2024 -0700
    correcting some versions refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    a1387634d24e7ba1195bc31ba3339d1c98be018b Thu Sep 12 19:27:10 2024 -0700
    correcting some versions refs #29545
• src/hg/makeDb/doc/mm39/lastzRuns.txt
  • lines changed 83, context: html, text, full: html, text
    1d41751e7047c66060c07042479d29cb82dd9c0b Sun Sep 15 23:27:57 2024 -0700
    Rabbit (GCF_009806435.1) to hg38/mm39 lastz/chain/net run for user, refs #34037
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    a1387634d24e7ba1195bc31ba3339d1c98be018b Thu Sep 12 19:27:10 2024 -0700
    correcting some versions refs #29545
• src/hg/makeDb/trackDb/human/hg38/gnomad.alpha.ra
  • lines changed 1, context: html, text, full: html, text
    7c0839ed1101cbd7f6e2e592a94672ed4b38f5bd Fri Sep 13 15:32:35 2024 -0700
    Staging the the Transcript LoF v4.1 and Missense v4.1 tracks on hgwbeta, refs #34252
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 1, context: html, text, full: html, text
    7c0839ed1101cbd7f6e2e592a94672ed4b38f5bd Fri Sep 13 15:32:35 2024 -0700
    Staging the the Transcript LoF v4.1 and Missense v4.1 tracks on hgwbeta, refs #34252
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    7c0839ed1101cbd7f6e2e592a94672ed4b38f5bd Fri Sep 13 15:32:35 2024 -0700
    Staging the the Transcript LoF v4.1 and Missense v4.1 tracks on hgwbeta, refs #34252
• src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
  • lines changed 9, context: html, text, full: html, text
    9804a48d4ee019ce876c5eb2f98239830a2ef766 Tue Sep 10 14:03:32 2024 -0700
    Mask artifactual reversions in KP.3.1.1.
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    882e1939634c785f6b65c6e72eee66092020267a Mon Sep 16 10:49:59 2024 -0700
    New version number v471
• src/utils/qa/doPublicCrawl
  • lines changed 59, context: html, text, full: html, text
    696e68b89c07237e19c04ed974d0e0ee90dbc784 Wed Sep 11 13:56:30 2024 -0700
    Adding the doPublicCrawl which is part of the public hub search index process into the kent tree, refs #34415
• src/utils/qa/makefile
  • lines changed 1, context: html, text, full: html, text
    696e68b89c07237e19c04ed974d0e0ee90dbc784 Wed Sep 11 13:56:30 2024 -0700
    Adding the doPublicCrawl which is part of the public hub search index process into the kent tree, refs #34415
• src/utils/qa/qaTestScript.py
  • lines changed 13, context: html, text, full: html, text
    f51804811274cbfc28fe8a5b77bfcc3df95048bf Sun Sep 15 15:38:46 2024 -0700
    Code review feedback edit, refs #34409
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    38a124b56d4e47e1f4b42908b410c73e72f923d4 Mon Sep 16 10:49:19 2024 -0700
    v471 final build, refs #34382

• lines changed: 1789
• files changed: 65