All File Changes

v486_base to v487_preview (2025-08-11 to 2025-08-18) v487

• confs/hgwbeta.hg.conf
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    b138708088517105f8ff45aa2f31b084da587ece Sun Aug 17 01:11:15 2025 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 4, context: html, text, full: html, text
    b138708088517105f8ff45aa2f31b084da587ece Sun Aug 17 01:11:15 2025 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html
  • lines changed 1, context: html, text, full: html, text
    07881adb0f70ae507b3d6c184b77e74df8395446 Tue Aug 12 14:36:04 2025 -0700
    Removing likely accidental ANSI escape code ESC[?1;95;0c. insert
• src/hg/hgConvert/hgConvert.c
  • lines changed 9, context: html, text, full: html, text
    325f711f30c884459738f065f3415ce2914ec828 Wed Aug 13 16:18:51 2025 -0700
    get hgConvert and hgLiftOver to use genark assemblies that are not in the UCSC taxId list
• src/hg/hgLiftOver/hgLiftOver.c
  • lines changed 19, context: html, text, full: html, text
    325f711f30c884459738f065f3415ce2914ec828 Wed Aug 13 16:18:51 2025 -0700
    get hgConvert and hgLiftOver to use genark assemblies that are not in the UCSC taxId list
• src/hg/hgTables/schema.c
  • lines changed 2, context: html, text, full: html, text
    5a34c495d5fe1db2aab6d1785c0b0239dbed2520 Sat Aug 16 21:21:02 2025 -0700
    New track type lorax: details page embeds Lorax multi-tree viewer. The trees are subtrees of an Ancestral Recombination Graph (ARG). This commit also adds a track with 1000 Genomes data, tgpLorax. The details page uses an iframe to embed the Lorax viewer from a separate server (most likely will run in a docker container on the GB server hosts; that will make this track more complicated for mirror operators than other tracks).
• src/hg/hgTracks/bedTrack.c
  • lines changed 69, context: html, text, full: html, text
    0fbc4aeaa5dc8cc1be2ddf15500790407ed9df91 Sat Aug 16 11:18:40 2025 -0700
    support bed8 and bed9 in quickLift
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 9, context: html, text, full: html, text
    6bd9e5d7816b693462f8db468253aea8f999fb81 Mon Aug 18 04:32:11 2025 -0700
    initial check-in minimal bigBedTrack
  • lines changed 45, context: html, text, full: html, text
    b6ef83c2f06ae1928e9fabf8ee84a72b3ef1d2a0 Mon Aug 18 09:58:52 2025 -0700
    Remove preload since it adds complications for multi-region without any improvement since the automatic wiggle code works fine without it.. Fixes #35580
• src/hg/hgTracks/hgTracks.h
  • lines changed 3, context: html, text, full: html, text
    5a34c495d5fe1db2aab6d1785c0b0239dbed2520 Sat Aug 16 21:21:02 2025 -0700
    New track type lorax: details page embeds Lorax multi-tree viewer. The trees are subtrees of an Ancestral Recombination Graph (ARG). This commit also adds a track with 1000 Genomes data, tgpLorax. The details page uses an iframe to embed the Lorax viewer from a separate server (most likely will run in a docker container on the GB server hosts; that will make this track more complicated for mirror operators than other tracks).
• src/hg/hgTracks/loraxTrack.c
  • lines changed 100, context: html, text, full: html, text
    5a34c495d5fe1db2aab6d1785c0b0239dbed2520 Sat Aug 16 21:21:02 2025 -0700
    New track type lorax: details page embeds Lorax multi-tree viewer. The trees are subtrees of an Ancestral Recombination Graph (ARG). This commit also adds a track with 1000 Genomes data, tgpLorax. The details page uses an iframe to embed the Lorax viewer from a separate server (most likely will run in a docker container on the GB server hosts; that will make this track more complicated for mirror operators than other tracks).
• src/hg/hgTracks/makefile
  • lines changed 1, context: html, text, full: html, text
    5a34c495d5fe1db2aab6d1785c0b0239dbed2520 Sat Aug 16 21:21:02 2025 -0700
    New track type lorax: details page embeds Lorax multi-tree viewer. The trees are subtrees of an Ancestral Recombination Graph (ARG). This commit also adds a track with 1000 Genomes data, tgpLorax. The details page uses an iframe to embed the Lorax viewer from a separate server (most likely will run in a docker container on the GB server hosts; that will make this track more complicated for mirror operators than other tracks).
• src/hg/hgTracks/quickLift.c
  • lines changed 67, context: html, text, full: html, text
    953748cd6cac972d5472b72e07e579dd6abc90dc Sat Aug 16 14:23:50 2025 -0700
    make the indel track for quickLift a little more useful
• src/hg/hgTracks/simpleTracks.c
  • lines changed 4, context: html, text, full: html, text
    5a34c495d5fe1db2aab6d1785c0b0239dbed2520 Sat Aug 16 21:21:02 2025 -0700
    New track type lorax: details page embeds Lorax multi-tree viewer. The trees are subtrees of an Ancestral Recombination Graph (ARG). This commit also adds a track with 1000 Genomes data, tgpLorax. The details page uses an iframe to embed the Lorax viewer from a separate server (most likely will run in a docker container on the GB server hosts; that will make this track more complicated for mirror operators than other tracks).
• src/hg/hgc/barChartClick.c
  • lines changed 86, context: html, text, full: html, text
    0b780ebaab52c71cce8e8dc15c8540eb94e3a1bf Tue Aug 5 15:23:07 2025 -0700
    Draw the barChart svgs on the client so the table can take advantage of the full screen width, refs #36124
• src/hg/hgc/hgc.c
  • lines changed 4, context: html, text, full: html, text
    5a34c495d5fe1db2aab6d1785c0b0239dbed2520 Sat Aug 16 21:21:02 2025 -0700
    New track type lorax: details page embeds Lorax multi-tree viewer. The trees are subtrees of an Ancestral Recombination Graph (ARG). This commit also adds a track with 1000 Genomes data, tgpLorax. The details page uses an iframe to embed the Lorax viewer from a separate server (most likely will run in a docker container on the GB server hosts; that will make this track more complicated for mirror operators than other tracks).
• src/hg/hgc/hgc.h
  • lines changed 3, context: html, text, full: html, text
    5a34c495d5fe1db2aab6d1785c0b0239dbed2520 Sat Aug 16 21:21:02 2025 -0700
    New track type lorax: details page embeds Lorax multi-tree viewer. The trees are subtrees of an Ancestral Recombination Graph (ARG). This commit also adds a track with 1000 Genomes data, tgpLorax. The details page uses an iframe to embed the Lorax viewer from a separate server (most likely will run in a docker container on the GB server hosts; that will make this track more complicated for mirror operators than other tracks).
• src/hg/hgc/loraxClick.c
  • lines changed 48, context: html, text, full: html, text
    5a34c495d5fe1db2aab6d1785c0b0239dbed2520 Sat Aug 16 21:21:02 2025 -0700
    New track type lorax: details page embeds Lorax multi-tree viewer. The trees are subtrees of an Ancestral Recombination Graph (ARG). This commit also adds a track with 1000 Genomes data, tgpLorax. The details page uses an iframe to embed the Lorax viewer from a separate server (most likely will run in a docker container on the GB server hosts; that will make this track more complicated for mirror operators than other tracks).
  • lines changed 2, context: html, text, full: html, text
    fca649f40a04767fbd9c331ef4e4b37f25882bf0 Mon Aug 18 09:16:01 2025 -0700
    Changing tdb setting name from loraxBackendUrl (misnomer) to loraxIframeUrlBase.
• src/hg/hgc/makefile
  • lines changed 1, context: html, text, full: html, text
    5a34c495d5fe1db2aab6d1785c0b0239dbed2520 Sat Aug 16 21:21:02 2025 -0700
    New track type lorax: details page embeds Lorax multi-tree viewer. The trees are subtrees of an Ancestral Recombination Graph (ARG). This commit also adds a track with 1000 Genomes data, tgpLorax. The details page uses an iframe to embed the Lorax viewer from a separate server (most likely will run in a docker container on the GB server hosts; that will make this track more complicated for mirror operators than other tracks).
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 3, context: html, text, full: html, text
    8aa967cc374a546b89bc60c39ca138a6e8d338ff Thu Aug 14 14:49:42 2025 -0700
    Adding a new example that shows how to have a multiview composite inside of a superTrack, refs #36210
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 2, context: html, text, full: html, text
    ac9015d3fb6b96fc1e6e68398883b8e76ddcecb8 Tue Aug 12 15:36:46 2025 -0700
    Adding a note that you can add literal commas by adding two commas at once.
  • lines changed 79, context: html, text, full: html, text
    8aa967cc374a546b89bc60c39ca138a6e8d338ff Thu Aug 14 14:49:42 2025 -0700
    Adding a new example that shows how to have a multiview composite inside of a superTrack, refs #36210
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 3, context: html, text, full: html, text
    859337c16046d447561d96df437d21967043240e Wed Aug 13 09:45:57 2025 -0700
    Typo and improved wording, no RM.
• src/hg/htdocs/inc/hgMyData.html
  • lines changed 4, context: html, text, full: html, text
    3a0e8244d3863116f69114e3f7c21f212a0b7a4c Thu Aug 14 16:20:09 2025 -0700
    Fixing broken links on the Hub Space page, Changing the 'Where to host your track hub' to 'External hosting space for your track hub', refs #31058
• src/hg/js/hgMyData.js
  • lines changed 12, context: html, text, full: html, text
    7fe593ea07a74ee88c5ad5a7c09763f4e86b2a7a Thu Aug 14 13:53:15 2025 -0700
    Change displayed quota upon deleting/uploading file sucess, refs #31058
  • lines changed 19, context: html, text, full: html, text
    942d5c5f4dac131598bfc04d6077c53bb74a337f Thu Aug 14 14:39:11 2025 -0700
    Add client side checks for preventing uploading files associated with two different genomes to the same hub (right now only support one genome per hub), and prevent uploading a hub.txt to a hub that already has a hub.txt, refs #31058
  • lines changed 3, context: html, text, full: html, text
    b7f8440d095182812999bab176e7d4fbc68b49ea Thu Aug 14 15:19:43 2025 -0700
    Fix hs1 label to set the right dropdown value to hs1 in the default genome choices dropdown. Fix bug bug that we should only check for pre-existing hub.txt when we are uploading to an already existing hub, refs #31058
  • lines changed 1, context: html, text, full: html, text
    b462b3f2747d45e71716563dcbf57e0634eb6e9b Thu Aug 14 16:00:03 2025 -0700
    Do not create track stanzas for vcf and bam index files, refs #31054
• src/hg/js/hgc.js
  • lines changed 160, context: html, text, full: html, text
    0b780ebaab52c71cce8e8dc15c8540eb94e3a1bf Tue Aug 5 15:23:07 2025 -0700
    Draw the barChart svgs on the client so the table can take advantage of the full screen width, refs #36124
• src/hg/js/lorax.js
  • lines changed 8, context: html, text, full: html, text
    5a34c495d5fe1db2aab6d1785c0b0239dbed2520 Sat Aug 16 21:21:02 2025 -0700
    New track type lorax: details page embeds Lorax multi-tree viewer. The trees are subtrees of an Ancestral Recombination Graph (ARG). This commit also adds a track with 1000 Genomes data, tgpLorax. The details page uses an iframe to embed the Lorax viewer from a separate server (most likely will run in a docker container on the GB server hosts; that will make this track more complicated for mirror operators than other tracks).
• src/hg/js/makefile
  • lines changed 1, context: html, text, full: html, text
    5a34c495d5fe1db2aab6d1785c0b0239dbed2520 Sat Aug 16 21:21:02 2025 -0700
    New track type lorax: details page embeds Lorax multi-tree viewer. The trees are subtrees of an Ancestral Recombination Graph (ARG). This commit also adds a track with 1000 Genomes data, tgpLorax. The details page uses an iframe to embed the Lorax viewer from a separate server (most likely will run in a docker container on the GB server hosts; that will make this track more complicated for mirror operators than other tracks).
• src/hg/js/subCfg.js
  • lines changed 1, context: html, text, full: html, text
    f3a764b6e4ef3322a64b3989e9d0733fff73c311 Thu Aug 14 03:04:28 2025 -0700
    giving subtrack configure div more width, refs #36227
• src/hg/lib/genark.c
  • lines changed 1, context: html, text, full: html, text
    325f711f30c884459738f065f3415ce2914ec828 Wed Aug 13 16:18:51 2025 -0700
    get hgConvert and hgLiftOver to use genark assemblies that are not in the UCSC taxId list
• src/hg/lib/hdb.c
  • lines changed 24, context: html, text, full: html, text
    325f711f30c884459738f065f3415ce2914ec828 Wed Aug 13 16:18:51 2025 -0700
    get hgConvert and hgLiftOver to use genark assemblies that are not in the UCSC taxId list
  • lines changed 2, context: html, text, full: html, text
    abaf0c7fca09364bf38dfbdcf2c49e910b3b01f6 Sat Aug 16 10:56:58 2025 -0700
    ongoing work on quickLift
• src/hg/lib/hubConnect.c
  • lines changed 20, context: html, text, full: html, text
    abaf0c7fca09364bf38dfbdcf2c49e910b3b01f6 Sat Aug 16 10:56:58 2025 -0700
    ongoing work on quickLift
• src/hg/lib/userdata.c
  • lines changed 4, context: html, text, full: html, text
    b462b3f2747d45e71716563dcbf57e0634eb6e9b Thu Aug 14 16:00:03 2025 -0700
    Do not create track stanzas for vcf and bam index files, refs #31054
• src/hg/lib/web.c
  • lines changed 1, context: html, text, full: html, text
    325f711f30c884459738f065f3415ce2914ec828 Wed Aug 13 16:18:51 2025 -0700
    get hgConvert and hgLiftOver to use genark assemblies that are not in the UCSC taxId list
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 16, context: html, text, full: html, text
    59b3611355a9a0ce350c4394976fbba6627c9f51 Wed Aug 13 14:29:44 2025 -0700
    BRC update and user requests refs #34337
  • lines changed 3, context: html, text, full: html, text
    520d88aed2d40477f654e3c9ac340e6a5224d847 Sat Aug 16 23:58:18 2025 -0700
    adding some per user requests refs #29545
  • lines changed 2, context: html, text, full: html, text
    f70000f503fe644133d077f22f7e3b8f3f95c93f Mon Aug 18 10:24:08 2025 -0700
    adding some per user requests refs #29545
• src/hg/makeDb/doc/genarkOrg.txt
  • lines changed 1, context: html, text, full: html, text
    325f711f30c884459738f065f3415ce2914ec828 Wed Aug 13 16:18:51 2025 -0700
    get hgConvert and hgLiftOver to use genark assemblies that are not in the UCSC taxId list
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 122, context: html, text, full: html, text
    2da466e720a8326977ce8e6456682fd45b82b9c3 Fri Aug 15 12:33:15 2025 -0700
    Moving the maveDb makedoc to its own file, refs #31812
• src/hg/makeDb/doc/hg38/maveDB.txt
  • lines changed 137, context: html, text, full: html, text
    9ab8b9c0cd6f2ff74c3187abce52e39a1309e51a Wed Aug 13 15:13:12 2025 -0700
    MaveDB trackdoc now in it's own file, with minor processing fixes, refs #31812
• src/hg/makeDb/doc/hg38/maveDb.txt
  • lines changed 125, context: html, text, full: html, text
    2da466e720a8326977ce8e6456682fd45b82b9c3 Fri Aug 15 12:33:15 2025 -0700
    Moving the maveDb makedoc to its own file, refs #31812
  • lines changed 125, context: html, text, full: html, text
    304286efb7b3569a7af96f8f3bea6ec5528fa5a1 Mon Aug 18 09:16:43 2025 -0700
    Removing the extra makedoc that I created since Jonathan also created one, refs #31812
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 15, context: html, text, full: html, text
    59b3611355a9a0ce350c4394976fbba6627c9f51 Wed Aug 13 14:29:44 2025 -0700
    BRC update and user requests refs #34337
  • lines changed 2, context: html, text, full: html, text
    520d88aed2d40477f654e3c9ac340e6a5224d847 Sat Aug 16 23:58:18 2025 -0700
    adding some per user requests refs #29545
  • lines changed 5, context: html, text, full: html, text
    f70000f503fe644133d077f22f7e3b8f3f95c93f Mon Aug 18 10:24:08 2025 -0700
    adding some per user requests refs #29545
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    520d88aed2d40477f654e3c9ac340e6a5224d847 Sat Aug 16 23:58:18 2025 -0700
    adding some per user requests refs #29545
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    59b3611355a9a0ce350c4394976fbba6627c9f51 Wed Aug 13 14:29:44 2025 -0700
    BRC update and user requests refs #34337
• src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    59b3611355a9a0ce350c4394976fbba6627c9f51 Wed Aug 13 14:29:44 2025 -0700
    BRC update and user requests refs #34337
• src/hg/makeDb/trackDb/human/hg38/mavedb_maps.html
  • lines changed 6, context: html, text, full: html, text
    47863b1a0e3507e6bbdd1677f9defb46d247d7d2 Mon Aug 11 16:58:37 2025 -0700
    Adding a bit more detail on the MaveDB heatmap display, refs #31812
• src/hg/makeDb/trackDb/human/hg38/tgpArchive.ra
  • lines changed 12, context: html, text, full: html, text
    5a34c495d5fe1db2aab6d1785c0b0239dbed2520 Sat Aug 16 21:21:02 2025 -0700
    New track type lorax: details page embeds Lorax multi-tree viewer. The trees are subtrees of an Ancestral Recombination Graph (ARG). This commit also adds a track with 1000 Genomes data, tgpLorax. The details page uses an iframe to embed the Lorax viewer from a separate server (most likely will run in a docker container on the GB server hosts; that will make this track more complicated for mirror operators than other tracks).
  • lines changed 1, context: html, text, full: html, text
    fca649f40a04767fbd9c331ef4e4b37f25882bf0 Mon Aug 18 09:16:01 2025 -0700
    Changing tdb setting name from loraxBackendUrl (misnomer) to loraxIframeUrlBase.
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 4, context: html, text, full: html, text
    5a34c495d5fe1db2aab6d1785c0b0239dbed2520 Sat Aug 16 21:21:02 2025 -0700
    New track type lorax: details page embeds Lorax multi-tree viewer. The trees are subtrees of an Ancestral Recombination Graph (ARG). This commit also adds a track with 1000 Genomes data, tgpLorax. The details page uses an iframe to embed the Lorax viewer from a separate server (most likely will run in a docker container on the GB server hosts; that will make this track more complicated for mirror operators than other tracks).
  • lines changed 1, context: html, text, full: html, text
    fca649f40a04767fbd9c331ef4e4b37f25882bf0 Mon Aug 18 09:16:01 2025 -0700
    Changing tdb setting name from loraxBackendUrl (misnomer) to loraxIframeUrlBase.
• src/hg/oneShot/parseMave/parseMave.pl
  • lines changed 2, context: html, text, full: html, text
    9ab8b9c0cd6f2ff74c3187abce52e39a1309e51a Wed Aug 13 15:13:12 2025 -0700
    MaveDB trackdoc now in it's own file, with minor processing fixes, refs #31812
• src/hg/utils/otto/dengue/buildTree.sh
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    da068f4b13595bfb45af25849abab4d89f816b5b Tue Jun 3 08:40:49 2025 -0700
    Reduce threads to avoid lockup in usher-sampled and matOptimize. Update hgdownload2 --> hgdownload3 and tolerate hgdownload rsync failure.
• src/hg/utils/otto/fluA/buildConcatTree.sh
  • lines changed 22, context: html, text, full: html, text
    1a144b066558c8c401c4440635f0f4aa68707806 Tue Jun 3 08:43:18 2025 -0700
    Reduce threads to avoid lockup in usher-sampled and matOptimize. Remove items with bogus dates to avoid crashing chronumental. Specify B3.13 because there's also D1.1. Update hgdownload2 --> hgdownload3 and tolerate hgdownload rsync failure.
• src/hg/utils/otto/fluA/buildConcatTreeD1.1.sh
  • lines changed 320, context: html, text, full: html, text
    63452d3fc64291c480595973b542b279d32dd256 Tue Jun 3 08:44:00 2025 -0700
    Concatenated-segment build for genotype D1.1.
• src/hg/utils/otto/fluA/buildTree.sh
  • lines changed 112, context: html, text, full: html, text
    41e22d6a4bde0b7e897cb88724d4a27a14fe64e0 Tue Jun 3 09:26:25 2025 -0700
    Reduce threads to avoid lockup in usher-sampled and matOptimize. Add SRA assembly seqs to all segment builds. Pass VCF to matOptimize. Use cvstk to join with headers instead of complicated pipe. Add GenoFlu genotypes to metadata for H5N1. Update hgdownload2 --> hgdownload3 and tolerate hgdownload rsync failure.
• src/hg/utils/otto/fluA/concat.config.json
  • lines changed 2, context: html, text, full: html, text
    643a144d0cd42d469fb6181b59ba89e95972cce2 Tue Jun 3 09:28:49 2025 -0700
    Color by host by default.
• src/hg/utils/otto/fluA/genofluToSegmentMetadata.py
  • lines changed 58, context: html, text, full: html, text
    41e22d6a4bde0b7e897cb88724d4a27a14fe64e0 Tue Jun 3 09:26:25 2025 -0700
    Reduce threads to avoid lockup in usher-sampled and matOptimize. Add SRA assembly seqs to all segment builds. Pass VCF to matOptimize. Use cvstk to join with headers instead of complicated pipe. Add GenoFlu genotypes to metadata for H5N1. Update hgdownload2 --> hgdownload3 and tolerate hgdownload rsync failure.
• src/hg/utils/otto/fluA/h5n1_ha.config.json
  • lines changed 5, context: html, text, full: html, text
    f01307d6c89f243afd4e0eafe0d4421fb05f6039 Tue Jun 3 09:28:38 2025 -0700
    Add genoflu types to metadata. Color by serotype by default.
• src/hg/utils/otto/fluA/pb2.config.json
  • lines changed 5, context: html, text, full: html, text
    f01307d6c89f243afd4e0eafe0d4421fb05f6039 Tue Jun 3 09:28:38 2025 -0700
    Add genoflu types to metadata. Color by serotype by default.
• src/hg/utils/otto/fluA/runGenoFlu.sh
  • lines changed 63, context: html, text, full: html, text
    41e22d6a4bde0b7e897cb88724d4a27a14fe64e0 Tue Jun 3 09:26:25 2025 -0700
    Reduce threads to avoid lockup in usher-sampled and matOptimize. Add SRA assembly seqs to all segment builds. Pass VCF to matOptimize. Use cvstk to join with headers instead of complicated pipe. Add GenoFlu genotypes to metadata for H5N1. Update hgdownload2 --> hgdownload3 and tolerate hgdownload rsync failure.
• src/hg/utils/otto/fluA/updateAndersenLab.sh
  • lines changed 31, context: html, text, full: html, text
    236232f2b6c67b0ee2c39a9baa9480c9a500423f Tue Jun 3 09:27:37 2025 -0700
    Updated naming conventions
• src/hg/utils/otto/mpxv/buildTree.sh
  • lines changed 159, context: html, text, full: html, text
    f9ee0c7ea6540636411b7ff4a6ed54ab574701e2 Tue Jun 3 11:04:31 2025 -0700
    Add Clade I.
• src/hg/utils/otto/mpxv/getNcbiMpxv.sh
  • lines changed 33, context: html, text, full: html, text
    f9ee0c7ea6540636411b7ff4a6ed54ab574701e2 Tue Jun 3 11:04:31 2025 -0700
    Add Clade I.
• src/hg/utils/otto/mtb/buildTree.sh
  • lines changed 12, context: html, text, full: html, text
    8a0ebbbae627da20c8c7c65aa57d297e5a19529a Tue Jun 3 11:08:52 2025 -0700
    Tweak download dir name. Update hgdownload2 --> hgdownload3 and tolerate hgdownload rsync failure.
• src/hg/utils/otto/mtb/getNcbiMtb.sh
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    8a0ebbbae627da20c8c7c65aa57d297e5a19529a Tue Jun 3 11:08:52 2025 -0700
    Tweak download dir name. Update hgdownload2 --> hgdownload3 and tolerate hgdownload rsync failure.
• src/hg/utils/otto/mtb/taxonium.annotated.config.json
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    ba10a7b1b7fae45ac511702425528670042b8c9f Tue Jun 3 11:26:10 2025 -0700
    Taxonium config file for SRA Mtb tree with Ash's ranchero metadata.
• src/hg/utils/otto/nextstrainNcov/doUpdate.sh
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    47df01a42e26269a5c952013a35cb5633e3c0f45 Tue Jun 3 11:10:06 2025 -0700
    Check for existence of bedGraph file before running bedGraphToBigWig.
• src/hg/utils/otto/panelApp/doPanelApp.py
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    7910a15d66e4f34c5d155cf73fb3132868b33c37 Thu Aug 14 14:17:34 2025 -0700
    Updating panelApp based on collaborator feedback, refs #36219
• src/hg/utils/otto/rsv/buildTree.sh
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    5af316b0f05735ba8dfb8a8264fe634e16e5bb22 Tue Jun 3 11:07:21 2025 -0700
    Reduce threads to avoid lockup in usher-sampled and matOptimize. Remove Goya clades because they were removed from nextclade. Update hgdownload2 --> hgdownload3 and tolerate hgdownload rsync failure.
• src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
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    65e3f367ddcc011118e795f0b8623058051d4c43 Tue Jun 3 11:18:27 2025 -0700
    Compress Newick download file (as should have done from the beginning). Remove MSA download, it's flawed and apparently unused.
• src/hg/utils/otto/sarscov2phylo/getCncb.sh
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    22d7aeffdf9fcd45a7ec9acf96c57eafdd55b218 Tue Jun 3 11:16:28 2025 -0700
    tweak CGI-encoding of metadataUrl... to no avail, they seem to have shut down access.
• src/hg/utils/otto/sarscov2phylo/mapleMerge.py
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    ca72f8065c8d796eeaaa43955bde1c6dc2ce9487 Tue Jun 3 11:13:18 2025 -0700
    Maple utility scripts for merging in N bases from VCF files to maple dumped from UShER tree. This was for Nicola de Maio to run SPRTA on the UShER tree with merged MAPLE or reviewer comments on viridian tree manuscript.
• src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv
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    2ece0f9519a3322fec8ecb7a283645b2c690b337 Tue Jun 3 11:19:26 2025 -0700
    Added new clades 25A (LP.8.1) and 25B (NB.1.8.1).
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
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    9ae312b796eca29cd110e08ecc8506ca593fcbfd Tue Jun 3 11:22:47 2025 -0700
    Relax branch length filter again (for BA.3.2).
• src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh
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    9012336f7d4569de36ea47886405c770b23a1ea1 Tue Jun 3 11:15:43 2025 -0700
    CNCB apparently shut down access so just use last downloaded set.
• src/hg/utils/otto/sarscov2phylo/updateLineageTreePb.sh
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    3da34ac26ab54ab67a772579de61222237f99e85 Tue Jun 3 11:22:08 2025 -0700
    Exempt a couple lineages with few representatives, all of which have reversions, from the reversion-pruner. Update to use .pb.gz instead of .pb.
• src/hg/utils/otto/sarscov2phylo/updatePublic.sh
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    ed655b70beb98c16d99689a1485b511d0b27d408 Tue Jun 3 11:20:34 2025 -0700
    Tolerate updateIdMapping.sh failure (always caused by download failure) and let build proceed with latest available mapping.
• src/hg/utils/otto/sarscov2phylo/vcfToMaple.py
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    ca72f8065c8d796eeaaa43955bde1c6dc2ce9487 Tue Jun 3 11:13:18 2025 -0700
    Maple utility scripts for merging in N bases from VCF files to maple dumped from UShER tree. This was for Nicola de Maio to run SPRTA on the UShER tree with merged MAPLE or reviewer comments on viridian tree manuscript.
• src/utils/qa/weeklybld/buildEnv.csh
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    3e16b9e55f0eadb6cd27b7152cc7233f7a7de6f2 Mon Aug 18 14:15:37 2025 -0700
    v487 preview1, refs #36171

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