All File Changes

v439_preview2 to v439_base (2022-10-24 to 2022-10-31) v439

• confs/hgwdev.hg.conf
  • lines changed 1, context: html, text, full: html, text
    7104bf898d48ee95c2d0958ab2d35e35341d7b7d Sun Oct 30 01:11:23 2022 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cgilib/cartJson.c
  • lines changed 6, context: html, text, full: html, text
    536e32480cf89093ba8b82ff4e73b0a9ca6ac389 Fri Oct 28 13:29:33 2022 -0700
    Fix multiTerm searches and plain chromosome searches, refs #29693
  • lines changed 1, context: html, text, full: html, text
    dbf64ebe4a5118f6ce418f0beb42fbd20821113a Fri Oct 28 17:15:59 2022 -0700
    Fix erroneous trix prefixing problem. When looking for snippets we use a larger trixPrefixSize for a speedup, but I was forgetting to reset the size when opening up the next trix index later on. Fix missing highlights on search results page. refs #26963
• src/hg/gar/gar.cgi.pl
  • lines changed 16, context: html, text, full: html, text
    137efea9b2a2dc6ade4965e5ab76309ec642635e Tue Oct 25 21:02:06 2022 -0700
    now with Reply-to Return-path and a bounce email and strict protection against usage only by assemblyRequest.html system refs #30184
  • lines changed 2, context: html, text, full: html, text
    a074b645168bba6d6f814b0475d63a0c4372aa0f Tue Oct 25 21:33:16 2022 -0700
    need to remove arguments from assemblyRequest.html?args refs #30184
  • lines changed 2, context: html, text, full: html, text
    edacf5fea5a549502094904f2b255229e6daef51 Wed Oct 26 15:15:27 2022 -0700
    can be done without a From: line refs #30184
• src/hg/hgPhyloPlace/hgPhyloPlace.c
  • lines changed 150, context: html, text, full: html, text
    0fffa3c31de4845a9bd3f06c0992f971e4d8a7a3 Fri Oct 28 15:08:06 2022 -0700
    Performance improvements for trees with millions of sequences: * Use @yceh's usher-sampled-server if configured; it preloads protobufs and can start placing sequences immediately using usher-sampled, a faster version of usher * Use usher-sampled instead of usher if server is not configured but usher-sampled is available * Load sample metadata file in a pthread while usher(-sampled(-server)) or matUtils is running * Skip checking for sample name clashes in uploaded fasta when using usher-sampled(-server)'s new --no-ignore-prefix option (but look for the prefix when parsing results) * Avoid parsing the protobuf and traversing the big tree unless absolutely necessary ** Subtrees from usher/matUtils have not included condensed nodes in a long time; remove lots of condensedNodes/summarization code from phyloPlace.c, runUsher.c, writeCustomTracks.c ** Use subtrees instead of big tree when possible (in findNearestNeighbor, treeToBaseAlleles, uploadedSamplesTree) ** Skip the informativeBases stuff that inhibits masking of sites from Problematic Sites set when the tree was built with an earlier version -- that pretty much never applies anymore now that only daily-updated trees are offered, not a range from old to new. ** Allow config.ra to specify a flat file of sample names (needed for searching user's uploaded names/IDs before calling matUtils) instead of getting names from the big tree
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 256, context: html, text, full: html, text
    0fffa3c31de4845a9bd3f06c0992f971e4d8a7a3 Fri Oct 28 15:08:06 2022 -0700
    Performance improvements for trees with millions of sequences: * Use @yceh's usher-sampled-server if configured; it preloads protobufs and can start placing sequences immediately using usher-sampled, a faster version of usher * Use usher-sampled instead of usher if server is not configured but usher-sampled is available * Load sample metadata file in a pthread while usher(-sampled(-server)) or matUtils is running * Skip checking for sample name clashes in uploaded fasta when using usher-sampled(-server)'s new --no-ignore-prefix option (but look for the prefix when parsing results) * Avoid parsing the protobuf and traversing the big tree unless absolutely necessary ** Subtrees from usher/matUtils have not included condensed nodes in a long time; remove lots of condensedNodes/summarization code from phyloPlace.c, runUsher.c, writeCustomTracks.c ** Use subtrees instead of big tree when possible (in findNearestNeighbor, treeToBaseAlleles, uploadedSamplesTree) ** Skip the informativeBases stuff that inhibits masking of sites from Problematic Sites set when the tree was built with an earlier version -- that pretty much never applies anymore now that only daily-updated trees are offered, not a range from old to new. ** Allow config.ra to specify a flat file of sample names (needed for searching user's uploaded names/IDs before calling matUtils) instead of getting names from the big tree
• src/hg/hgPhyloPlace/phyloPlace.h
  • lines changed 34, context: html, text, full: html, text
    0fffa3c31de4845a9bd3f06c0992f971e4d8a7a3 Fri Oct 28 15:08:06 2022 -0700
    Performance improvements for trees with millions of sequences: * Use @yceh's usher-sampled-server if configured; it preloads protobufs and can start placing sequences immediately using usher-sampled, a faster version of usher * Use usher-sampled instead of usher if server is not configured but usher-sampled is available * Load sample metadata file in a pthread while usher(-sampled(-server)) or matUtils is running * Skip checking for sample name clashes in uploaded fasta when using usher-sampled(-server)'s new --no-ignore-prefix option (but look for the prefix when parsing results) * Avoid parsing the protobuf and traversing the big tree unless absolutely necessary ** Subtrees from usher/matUtils have not included condensed nodes in a long time; remove lots of condensedNodes/summarization code from phyloPlace.c, runUsher.c, writeCustomTracks.c ** Use subtrees instead of big tree when possible (in findNearestNeighbor, treeToBaseAlleles, uploadedSamplesTree) ** Skip the informativeBases stuff that inhibits masking of sites from Problematic Sites set when the tree was built with an earlier version -- that pretty much never applies anymore now that only daily-updated trees are offered, not a range from old to new. ** Allow config.ra to specify a flat file of sample names (needed for searching user's uploaded names/IDs before calling matUtils) instead of getting names from the big tree
• src/hg/hgPhyloPlace/phyloPlaceMain.c
  • lines changed 9, context: html, text, full: html, text
    12ed3c2212ad565ac6ad2a713cf10ca455d5db27 Fri Oct 28 10:52:59 2022 -0700
    Add options -db and -protobuf for more flexible testing
• src/hg/hgPhyloPlace/runUsher.c
  • lines changed 842, context: html, text, full: html, text
    0fffa3c31de4845a9bd3f06c0992f971e4d8a7a3 Fri Oct 28 15:08:06 2022 -0700
    Performance improvements for trees with millions of sequences: * Use @yceh's usher-sampled-server if configured; it preloads protobufs and can start placing sequences immediately using usher-sampled, a faster version of usher * Use usher-sampled instead of usher if server is not configured but usher-sampled is available * Load sample metadata file in a pthread while usher(-sampled(-server)) or matUtils is running * Skip checking for sample name clashes in uploaded fasta when using usher-sampled(-server)'s new --no-ignore-prefix option (but look for the prefix when parsing results) * Avoid parsing the protobuf and traversing the big tree unless absolutely necessary ** Subtrees from usher/matUtils have not included condensed nodes in a long time; remove lots of condensedNodes/summarization code from phyloPlace.c, runUsher.c, writeCustomTracks.c ** Use subtrees instead of big tree when possible (in findNearestNeighbor, treeToBaseAlleles, uploadedSamplesTree) ** Skip the informativeBases stuff that inhibits masking of sites from Problematic Sites set when the tree was built with an earlier version -- that pretty much never applies anymore now that only daily-updated trees are offered, not a range from old to new. ** Allow config.ra to specify a flat file of sample names (needed for searching user's uploaded names/IDs before calling matUtils) instead of getting names from the big tree
• src/hg/hgPhyloPlace/vcfFromFasta.c
  • lines changed 14, context: html, text, full: html, text
    0fffa3c31de4845a9bd3f06c0992f971e4d8a7a3 Fri Oct 28 15:08:06 2022 -0700
    Performance improvements for trees with millions of sequences: * Use @yceh's usher-sampled-server if configured; it preloads protobufs and can start placing sequences immediately using usher-sampled, a faster version of usher * Use usher-sampled instead of usher if server is not configured but usher-sampled is available * Load sample metadata file in a pthread while usher(-sampled(-server)) or matUtils is running * Skip checking for sample name clashes in uploaded fasta when using usher-sampled(-server)'s new --no-ignore-prefix option (but look for the prefix when parsing results) * Avoid parsing the protobuf and traversing the big tree unless absolutely necessary ** Subtrees from usher/matUtils have not included condensed nodes in a long time; remove lots of condensedNodes/summarization code from phyloPlace.c, runUsher.c, writeCustomTracks.c ** Use subtrees instead of big tree when possible (in findNearestNeighbor, treeToBaseAlleles, uploadedSamplesTree) ** Skip the informativeBases stuff that inhibits masking of sites from Problematic Sites set when the tree was built with an earlier version -- that pretty much never applies anymore now that only daily-updated trees are offered, not a range from old to new. ** Allow config.ra to specify a flat file of sample names (needed for searching user's uploaded names/IDs before calling matUtils) instead of getting names from the big tree
• src/hg/hgPhyloPlace/writeCustomTracks.c
  • lines changed 35, context: html, text, full: html, text
    0fffa3c31de4845a9bd3f06c0992f971e4d8a7a3 Fri Oct 28 15:08:06 2022 -0700
    Performance improvements for trees with millions of sequences: * Use @yceh's usher-sampled-server if configured; it preloads protobufs and can start placing sequences immediately using usher-sampled, a faster version of usher * Use usher-sampled instead of usher if server is not configured but usher-sampled is available * Load sample metadata file in a pthread while usher(-sampled(-server)) or matUtils is running * Skip checking for sample name clashes in uploaded fasta when using usher-sampled(-server)'s new --no-ignore-prefix option (but look for the prefix when parsing results) * Avoid parsing the protobuf and traversing the big tree unless absolutely necessary ** Subtrees from usher/matUtils have not included condensed nodes in a long time; remove lots of condensedNodes/summarization code from phyloPlace.c, runUsher.c, writeCustomTracks.c ** Use subtrees instead of big tree when possible (in findNearestNeighbor, treeToBaseAlleles, uploadedSamplesTree) ** Skip the informativeBases stuff that inhibits masking of sites from Problematic Sites set when the tree was built with an earlier version -- that pretty much never applies anymore now that only daily-updated trees are offered, not a range from old to new. ** Allow config.ra to specify a flat file of sample names (needed for searching user's uploaded names/IDs before calling matUtils) instead of getting names from the big tree
• src/hg/hgSearch/hgSearch.c
  • lines changed 15, context: html, text, full: html, text
    536e32480cf89093ba8b82ff4e73b0a9ca6ac389 Fri Oct 28 13:29:33 2022 -0700
    Fix multiTerm searches and plain chromosome searches, refs #29693
  • lines changed 45, context: html, text, full: html, text
    324020eced2a302856ea0cbec8942b374337a3f8 Mon Oct 31 10:02:26 2022 -0700
    When a user has entered a search term that resolves to a single position, such as an empty chromosome name or HGVS term, have the client redirect straight to hgTracks, refs #29693
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    9f8ea883fadb1ffa03ca78aab524f8235b5d4e67 Mon Oct 31 09:34:56 2022 -0700
    change to using mean instead of max for density coverage
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 1, context: html, text, full: html, text
    6efc703aec6bbfaeb2c1550f1cb45b3771629f86 Mon Oct 24 17:05:08 2022 -0700
    Updating documentation from 'My Hubs' to the new name 'Connected Hubs' refs #29870
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 2, context: html, text, full: html, text
    6efc703aec6bbfaeb2c1550f1cb45b3771629f86 Mon Oct 24 17:05:08 2022 -0700
    Updating documentation from 'My Hubs' to the new name 'Connected Hubs' refs #29870
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 1, context: html, text, full: html, text
    6efc703aec6bbfaeb2c1550f1cb45b3771629f86 Mon Oct 24 17:05:08 2022 -0700
    Updating documentation from 'My Hubs' to the new name 'Connected Hubs' refs #29870
• src/hg/htdocs/goldenPath/help/hubQuickStart.html
  • lines changed 1, context: html, text, full: html, text
    6efc703aec6bbfaeb2c1550f1cb45b3771629f86 Mon Oct 24 17:05:08 2022 -0700
    Updating documentation from 'My Hubs' to the new name 'Connected Hubs' refs #29870
• src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
  • lines changed 1, context: html, text, full: html, text
    6efc703aec6bbfaeb2c1550f1cb45b3771629f86 Mon Oct 24 17:05:08 2022 -0700
    Updating documentation from 'My Hubs' to the new name 'Connected Hubs' refs #29870
• src/hg/htdocs/goldenPath/help/hubQuickStartGroups.html
  • lines changed 1, context: html, text, full: html, text
    6efc703aec6bbfaeb2c1550f1cb45b3771629f86 Mon Oct 24 17:05:08 2022 -0700
    Updating documentation from 'My Hubs' to the new name 'Connected Hubs' refs #29870
• src/hg/htdocs/goldenPath/help/hubQuickStartSearch.html
  • lines changed 1, context: html, text, full: html, text
    6efc703aec6bbfaeb2c1550f1cb45b3771629f86 Mon Oct 24 17:05:08 2022 -0700
    Updating documentation from 'My Hubs' to the new name 'Connected Hubs' refs #29870
• src/hg/htdocs/goldenPath/help/publicHubGuidelines.html
  • lines changed 257, context: html, text, full: html, text
    defacab8acb926ded12e379c9efb840ce3e31da2 Mon Oct 24 12:42:34 2022 -0700
    Creating a new GB page for public hub guidelines, Docs #28424
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 35, context: html, text, full: html, text
    243f2a513ccb6bd16b5ca51530e54791e220bdd7 Mon Oct 24 11:46:42 2022 -0700
    Announcing panelApp and HGNC refs #25568 and 29891
• src/hg/htdocs/images/panelApp.HGNC.png
  • lines changed 0, context: html, text, full: html, text
    243f2a513ccb6bd16b5ca51530e54791e220bdd7 Mon Oct 24 11:46:42 2022 -0700
    Announcing panelApp and HGNC refs #25568 and 29891
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    243f2a513ccb6bd16b5ca51530e54791e220bdd7 Mon Oct 24 11:46:42 2022 -0700
    Announcing panelApp and HGNC refs #25568 and 29891
• src/hg/inc/cartJson.h
  • lines changed 9, context: html, text, full: html, text
    536e32480cf89093ba8b82ff4e73b0a9ca6ac389 Fri Oct 28 13:29:33 2022 -0700
    Fix multiTerm searches and plain chromosome searches, refs #29693
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    683e63378776fb639a6de9d06eb6928500f4c378 Mon Oct 31 11:05:03 2022 -0700
    New version number v439
• src/hg/js/hgGateway.js
  • lines changed 26, context: html, text, full: html, text
    8539ceed63380177b62f366b975b829066aa5805 Wed Oct 26 15:30:53 2022 -0700
    make the onclick function create the button instead of being static no redmine
  • lines changed 3, context: html, text, full: html, text
    1812fed4d437f08a151d6e2cbe01ad565ae83925 Wed Oct 26 16:49:29 2022 -0700
    customized URL to refer to this host no redmine
  • lines changed 1, context: html, text, full: html, text
    536e32480cf89093ba8b82ff4e73b0a9ca6ac389 Fri Oct 28 13:29:33 2022 -0700
    Fix multiTerm searches and plain chromosome searches, refs #29693
• src/hg/js/hgSearch.js
  • lines changed 4, context: html, text, full: html, text
    696a2e28b77acdad5f799eb5aadd970f980299b7 Fri Oct 28 14:47:21 2022 -0700
    Fix bug with previous multiTerm fix and make tree checkboxes not auto collapse on click, refs #29693
  • lines changed 2, context: html, text, full: html, text
    6ebcc1b85cd5bd3a14205dc7552d35a80f1b3efa Fri Oct 28 14:53:40 2022 -0700
    Fix bogus no results message when entering hgSearch with no cgi arguments, refs #29693
  • lines changed 4, context: html, text, full: html, text
    dbf64ebe4a5118f6ce418f0beb42fbd20821113a Fri Oct 28 17:15:59 2022 -0700
    Fix erroneous trix prefixing problem. When looking for snippets we use a larger trixPrefixSize for a speedup, but I was forgetting to reset the size when opening up the next trix index later on. Fix missing highlights on search results page. refs #26963
  • lines changed 12, context: html, text, full: html, text
    324020eced2a302856ea0cbec8942b374337a3f8 Mon Oct 31 10:02:26 2022 -0700
    When a user has entered a search term that resolves to a single position, such as an empty chromosome name or HGVS term, have the client redirect straight to hgTracks, refs #29693
• src/hg/js/hgTracks.js
  • lines changed 1, context: html, text, full: html, text
    536e32480cf89093ba8b82ff4e73b0a9ca6ac389 Fri Oct 28 13:29:33 2022 -0700
    Fix multiTerm searches and plain chromosome searches, refs #29693
• src/hg/lib/hgFind.c
  • lines changed 41, context: html, text, full: html, text
    536e32480cf89093ba8b82ff4e73b0a9ca6ac389 Fri Oct 28 13:29:33 2022 -0700
    Fix multiTerm searches and plain chromosome searches, refs #29693
  • lines changed 1, context: html, text, full: html, text
    696a2e28b77acdad5f799eb5aadd970f980299b7 Fri Oct 28 14:47:21 2022 -0700
    Fix bug with previous multiTerm fix and make tree checkboxes not auto collapse on click, refs #29693
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 8, context: html, text, full: html, text
    34301df1c5cadc9fafbfd5dcaa783323052a1665 Mon Oct 24 16:10:36 2022 -0700
    adding six assemblies per user request refs #29545
  • lines changed 2, context: html, text, full: html, text
    950dd9f87f20b0b5c014a980672965bfc9ddf58b Tue Oct 25 13:54:13 2022 -0700
    adding two assemblies per user request refs #29545
• src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh
  • lines changed 2, context: html, text, full: html, text
    950dd9f87f20b0b5c014a980672965bfc9ddf58b Tue Oct 25 13:54:13 2022 -0700
    adding two assemblies per user request refs #29545
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    34301df1c5cadc9fafbfd5dcaa783323052a1665 Mon Oct 24 16:10:36 2022 -0700
    adding six assemblies per user request refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    34301df1c5cadc9fafbfd5dcaa783323052a1665 Mon Oct 24 16:10:36 2022 -0700
    adding six assemblies per user request refs #29545
• src/hg/makeDb/doc/mm39/initialBuild.txt
  • lines changed 26, context: html, text, full: html, text
    5cd914bd3782a8a0a26ac2e8d7af9d13db79b2f8 Wed Oct 26 12:10:56 2022 -0700
    mm9 vs mm39 liftOvers in both directions
• src/hg/makeDb/doc/mm9.txt
  • lines changed 28, context: html, text, full: html, text
    5cd914bd3782a8a0a26ac2e8d7af9d13db79b2f8 Wed Oct 26 12:10:56 2022 -0700
    mm9 vs mm39 liftOvers in both directions
• src/hg/makeDb/doc/ortMon1/initialBuild.txt
  • lines changed 1274, context: html, text, full: html, text
    9b6753bad28dabd04e55ddddf77b229217d94a74 Mon Oct 24 14:16:51 2022 -0700
    delete initial build or ortMon1 (monkeypox)
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    950dd9f87f20b0b5c014a980672965bfc9ddf58b Tue Oct 25 13:54:13 2022 -0700
    adding two assemblies per user request refs #29545
• src/hg/makeDb/trackDb/human/hg38/crossTissueMaps.html
  • lines changed 143, context: html, text, full: html, text
    e1f33e28e4cebd6d10a2f693e8345b0ba6a387d9 Tue Oct 25 14:56:32 2022 -0700
    Use facets made by Jim and Brittney in gtex single cell track, refs #29954
• src/hg/makeDb/trackDb/human/hg38/crossTissueMaps.ra
  • lines changed 47, context: html, text, full: html, text
    e1f33e28e4cebd6d10a2f693e8345b0ba6a387d9 Tue Oct 25 14:56:32 2022 -0700
    Use facets made by Jim and Brittney in gtex single cell track, refs #29954
  • lines changed 2, context: html, text, full: html, text
    36cbaaaede3eb9bcd15b5ab27b0a401036fb331f Wed Oct 26 16:08:49 2022 -0700
    Fix release tags hopefully
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 2, context: html, text, full: html, text
    de2972fbe00fcd9f99920394633a4adde097c7ad Fri Oct 28 09:54:18 2022 -0700
    Updating the data/description of updated mutational constraints track, refs #30160
• src/hg/makeDb/trackDb/human/hg38/gnomadV3_1_1.html
  • lines changed 13, context: html, text, full: html, text
    de2972fbe00fcd9f99920394633a4adde097c7ad Fri Oct 28 09:54:18 2022 -0700
    Updating the data/description of updated mutational constraints track, refs #30160
• src/hg/makeDb/trackDb/human/hg38/gtexSnAtlas.html
  • lines changed 153, context: html, text, full: html, text
    e1f33e28e4cebd6d10a2f693e8345b0ba6a387d9 Tue Oct 25 14:56:32 2022 -0700
    Use facets made by Jim and Brittney in gtex single cell track, refs #29954
• src/hg/makeDb/trackDb/human/hg38/omimGene2.html
  • lines changed 2, context: html, text, full: html, text
    c589b0bdd54008d5662cbdd2b5d0ed664415bad6 Mon Oct 24 10:41:29 2022 -0700
    Edits to replace refGene with ncbiRefSeq in the Methods section, refs #29616
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    e969fce11cec6cf6fb528a65c646576395bc864c Wed Oct 26 17:45:55 2022 -0700
    remove gencodeV19 from trackDb for hg38
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    e1f33e28e4cebd6d10a2f693e8345b0ba6a387d9 Tue Oct 25 14:56:32 2022 -0700
    Use facets made by Jim and Brittney in gtex single cell track, refs #29954
  • lines changed 1, context: html, text, full: html, text
    36cbaaaede3eb9bcd15b5ab27b0a401036fb331f Wed Oct 26 16:08:49 2022 -0700
    Fix release tags hopefully
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV19.ra
  • lines changed 247, context: html, text, full: html, text
    e969fce11cec6cf6fb528a65c646576395bc864c Wed Oct 26 17:45:55 2022 -0700
    remove gencodeV19 from trackDb for hg38
• src/hg/makeDb/trackDb/human/panelApp.ra
  • lines changed 1, context: html, text, full: html, text
    243f2a513ccb6bd16b5ca51530e54791e220bdd7 Mon Oct 24 11:46:42 2022 -0700
    Announcing panelApp and HGNC refs #25568 and 29891
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    243f2a513ccb6bd16b5ca51530e54791e220bdd7 Mon Oct 24 11:46:42 2022 -0700
    Announcing panelApp and HGNC refs #25568 and 29891
• src/hg/makeDb/trackDb/worm/ce11/description.html
  • lines changed 1, context: html, text, full: html, text
    2d6904c6c6fcfc68566926eb2a8a68faad0c4bd6 Wed Oct 26 16:52:02 2022 -0700
    trying out the Share this genome browser with the link function now customized for http_host no redmine
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
  • lines changed 126, context: html, text, full: html, text
    7e28b978133361b5bf86a3b0d13d41c83462e121 Mon Oct 24 09:34:04 2022 -0700
    Latest Cornelian deluge of lineages.
  • lines changed 6, context: html, text, full: html, text
    b7313108f102804030e287e76146971d9552c504 Fri Oct 28 15:18:29 2022 -0700
    A mere half-dozen new lineages.
• src/inc/pthreadWrap.h
  • lines changed 3, context: html, text, full: html, text
    b24c2a743b181481454816222301d0b832b5ccc9 Fri Oct 28 15:11:02 2022 -0700
    Add pthreadJoin for getting a thread worker function's return value.
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    683e63378776fb639a6de9d06eb6928500f4c378 Mon Oct 31 11:05:03 2022 -0700
    New version number v439
• src/index/trixSearch/trixSearch.c
  • lines changed 1, context: html, text, full: html, text
    dbf64ebe4a5118f6ce418f0beb42fbd20821113a Fri Oct 28 17:15:59 2022 -0700
    Fix erroneous trix prefixing problem. When looking for snippets we use a larger trixPrefixSize for a speedup, but I was forgetting to reset the size when opening up the next trix index later on. Fix missing highlights on search results page. refs #26963
• src/lib/pthreadWrap.c
  • lines changed 7, context: html, text, full: html, text
    b24c2a743b181481454816222301d0b832b5ccc9 Fri Oct 28 15:11:02 2022 -0700
    Add pthreadJoin for getting a thread worker function's return value.
• src/lib/trix.c
  • lines changed 6, context: html, text, full: html, text
    dbf64ebe4a5118f6ce418f0beb42fbd20821113a Fri Oct 28 17:15:59 2022 -0700
    Fix erroneous trix prefixing problem. When looking for snippets we use a larger trixPrefixSize for a speedup, but I was forgetting to reset the size when opening up the next trix index later on. Fix missing highlights on search results page. refs #26963
• src/utils/qa/userCount
  • lines changed 6, context: html, text, full: html, text
    bdae98b8683d0e559cb5765c52a95e2af42cffa8 Mon Oct 24 14:28:51 2022 -0700
    Checking in script No RM
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    c9a73bfbb3cdd3b32185bf4fd1a2105237180210 Mon Oct 31 11:04:06 2022 -0700
    v439 final build, refs #30145

• lines changed: 3968
• files changed: 71