All File Changes

v465_preview to v465_preview2 (2024-04-29 to 2024-05-06) v465

• confs/asia.hg.conf
  • lines changed 3, context: html, text, full: html, text
    bbd2de3e1bd74881c478c8a80da3f770386dfab2 Sun May 5 01:11:20 2024 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 3, context: html, text, full: html, text
    bbd2de3e1bd74881c478c8a80da3f770386dfab2 Sun May 5 01:11:20 2024 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta.hg.conf
  • lines changed 5, context: html, text, full: html, text
    bbd2de3e1bd74881c478c8a80da3f770386dfab2 Sun May 5 01:11:20 2024 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 4, context: html, text, full: html, text
    bbd2de3e1bd74881c478c8a80da3f770386dfab2 Sun May 5 01:11:20 2024 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 3, context: html, text, full: html, text
    bbd2de3e1bd74881c478c8a80da3f770386dfab2 Sun May 5 01:11:20 2024 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/getRnaPred/getRnaPred.c
  • lines changed 3, context: html, text, full: html, text
    191a740d41e1bcaf9d012380f0ec5d23904f223d Fri May 3 02:38:26 2024 -0700
    updated confusing doc
• src/hg/hgBlat/hgBlat.c
  • lines changed 2, context: html, text, full: html, text
    0773256839bbb83ac8143ee7e2ffbf86cb06be9c Mon May 6 02:09:53 2024 -0700
    add mouseover to blat details link, refs #19668
• src/hg/hgGateway/hgGateway.c
  • lines changed 89, context: html, text, full: html, text
    b62fb9699fbc8ae0ef6ac9bf8e8760831e6f5ba2 Tue Apr 30 13:24:22 2024 -0700
    Add genark assemblies to species search on hgGateway, refs #33572
  • lines changed 3, context: html, text, full: html, text
    c3c0b288edd697b9631d8236bc27091d0ae6c8ff Tue Apr 30 13:41:00 2024 -0700
    Get clicks from autocomplete to genark hubs working, refs #33572
  • lines changed 1, context: html, text, full: html, text
    94fd2b4a65a39182e0c820849113307771f9fdb5 Tue Apr 30 14:37:47 2024 -0700
    Make genark list of results ordered by commonName, refs Hiram
  • lines changed 1, context: html, text, full: html, text
    919ecaa0c76c01938c9e9091ecef58581ea9c8f1 Wed May 1 08:49:55 2024 -0700
    Sort genark species in asc order instead of desc order, refs #33572
  • lines changed 2, context: html, text, full: html, text
    75c3553ad54a75adcf41248feb8330a34c96171a Mon May 6 06:23:09 2024 -0700
    adapting category names, refs #33572
• src/hg/hgGene/hgGeneData/Human/links.ra
  • lines changed 1, context: html, text, full: html, text
    abf27625ea432f351c680c8ceb0e6dadd2a15b71 Thu May 2 16:21:52 2024 -0700
    Fixing Malacards link for human hgGene, refs #33080
• src/hg/hgPhyloPlace/hgPhyloPlace.c
  • lines changed 168, context: html, text, full: html, text
    705420e703b067fbcad43ab67ed3e131552e7ac8 Wed Apr 24 14:23:03 2024 -0700
    Pathogen drop-down choices can now be groups of references/trees, for example 'Dengue (types 1 - 4)' instead of a separate choice for each type. Instead of config.ra, each group has an organism.ra and subdirectories named after reference accessions that contain reference.ra files. nextclade sort is used to match the user's uploaded sequences against available references for the selected pathogen. SARS-CoV-2, M. tuberculosis and hMPXV still have only one reference and still use config.ra, but RSV, Dengue and Influenza will become groups. Presentation is still kinda rough, just a loop on the original results output. The server commands part needs testing and will not work yet for groups (currently used only for SARS-CoV-2).
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 563, context: html, text, full: html, text
    705420e703b067fbcad43ab67ed3e131552e7ac8 Wed Apr 24 14:23:03 2024 -0700
    Pathogen drop-down choices can now be groups of references/trees, for example 'Dengue (types 1 - 4)' instead of a separate choice for each type. Instead of config.ra, each group has an organism.ra and subdirectories named after reference accessions that contain reference.ra files. nextclade sort is used to match the user's uploaded sequences against available references for the selected pathogen. SARS-CoV-2, M. tuberculosis and hMPXV still have only one reference and still use config.ra, but RSV, Dengue and Influenza will become groups. Presentation is still kinda rough, just a loop on the original results output. The server commands part needs testing and will not work yet for groups (currently used only for SARS-CoV-2).
  • lines changed 19, context: html, text, full: html, text
    da3772f3615ae3aa407af6aa2215a1b2ff480183 Mon Apr 29 13:40:41 2024 -0700
    If configured, use nextclade to align sequences (better for more diverged viruses like influenza). Also fix some buttons that the last change broke.
  • lines changed 19, context: html, text, full: html, text
    834653e22227fcea282e12a48910bb73068b34df Mon Apr 29 15:33:06 2024 -0700
    Don't depend on having a PSL alignment for the results table, precompute the same values whether aligning with gf/blat or nextclade.
  • lines changed 91, context: html, text, full: html, text
    eed992e6dfb41dffe0102882d47300c904aaf1de Mon Apr 29 19:17:50 2024 -0700
    When multiple reference sequences are matched, sort them alphabetically by description.
  • lines changed 18, context: html, text, full: html, text
    09ba8a42df0be5b65518715f8f499e4ac965a4ef Tue Apr 30 11:10:37 2024 -0700
    When multiple references are matched, make navigation links at the top of the results page.
• src/hg/hgPhyloPlace/phyloPlace.h
  • lines changed 45, context: html, text, full: html, text
    705420e703b067fbcad43ab67ed3e131552e7ac8 Wed Apr 24 14:23:03 2024 -0700
    Pathogen drop-down choices can now be groups of references/trees, for example 'Dengue (types 1 - 4)' instead of a separate choice for each type. Instead of config.ra, each group has an organism.ra and subdirectories named after reference accessions that contain reference.ra files. nextclade sort is used to match the user's uploaded sequences against available references for the selected pathogen. SARS-CoV-2, M. tuberculosis and hMPXV still have only one reference and still use config.ra, but RSV, Dengue and Influenza will become groups. Presentation is still kinda rough, just a loop on the original results output. The server commands part needs testing and will not work yet for groups (currently used only for SARS-CoV-2).
  • lines changed 4, context: html, text, full: html, text
    da3772f3615ae3aa407af6aa2215a1b2ff480183 Mon Apr 29 13:40:41 2024 -0700
    If configured, use nextclade to align sequences (better for more diverged viruses like influenza). Also fix some buttons that the last change broke.
  • lines changed 4, context: html, text, full: html, text
    834653e22227fcea282e12a48910bb73068b34df Mon Apr 29 15:33:06 2024 -0700
    Don't depend on having a PSL alignment for the results table, precompute the same values whether aligning with gf/blat or nextclade.
• src/hg/hgPhyloPlace/phyloPlaceMain.c
  • lines changed 10, context: html, text, full: html, text
    705420e703b067fbcad43ab67ed3e131552e7ac8 Wed Apr 24 14:23:03 2024 -0700
    Pathogen drop-down choices can now be groups of references/trees, for example 'Dengue (types 1 - 4)' instead of a separate choice for each type. Instead of config.ra, each group has an organism.ra and subdirectories named after reference accessions that contain reference.ra files. nextclade sort is used to match the user's uploaded sequences against available references for the selected pathogen. SARS-CoV-2, M. tuberculosis and hMPXV still have only one reference and still use config.ra, but RSV, Dengue and Influenza will become groups. Presentation is still kinda rough, just a loop on the original results output. The server commands part needs testing and will not work yet for groups (currently used only for SARS-CoV-2).
• src/hg/hgPhyloPlace/runUsher.c
  • lines changed 51, context: html, text, full: html, text
    705420e703b067fbcad43ab67ed3e131552e7ac8 Wed Apr 24 14:23:03 2024 -0700
    Pathogen drop-down choices can now be groups of references/trees, for example 'Dengue (types 1 - 4)' instead of a separate choice for each type. Instead of config.ra, each group has an organism.ra and subdirectories named after reference accessions that contain reference.ra files. nextclade sort is used to match the user's uploaded sequences against available references for the selected pathogen. SARS-CoV-2, M. tuberculosis and hMPXV still have only one reference and still use config.ra, but RSV, Dengue and Influenza will become groups. Presentation is still kinda rough, just a loop on the original results output. The server commands part needs testing and will not work yet for groups (currently used only for SARS-CoV-2).
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
  • lines changed 8, context: html, text, full: html, text
    705420e703b067fbcad43ab67ed3e131552e7ac8 Wed Apr 24 14:23:03 2024 -0700
    Pathogen drop-down choices can now be groups of references/trees, for example 'Dengue (types 1 - 4)' instead of a separate choice for each type. Instead of config.ra, each group has an organism.ra and subdirectories named after reference accessions that contain reference.ra files. nextclade sort is used to match the user's uploaded sequences against available references for the selected pathogen. SARS-CoV-2, M. tuberculosis and hMPXV still have only one reference and still use config.ra, but RSV, Dengue and Influenza will become groups. Presentation is still kinda rough, just a loop on the original results output. The server commands part needs testing and will not work yet for groups (currently used only for SARS-CoV-2).
• src/hg/hgPhyloPlace/vcfFromFasta.c
  • lines changed 4, context: html, text, full: html, text
    705420e703b067fbcad43ab67ed3e131552e7ac8 Wed Apr 24 14:23:03 2024 -0700
    Pathogen drop-down choices can now be groups of references/trees, for example 'Dengue (types 1 - 4)' instead of a separate choice for each type. Instead of config.ra, each group has an organism.ra and subdirectories named after reference accessions that contain reference.ra files. nextclade sort is used to match the user's uploaded sequences against available references for the selected pathogen. SARS-CoV-2, M. tuberculosis and hMPXV still have only one reference and still use config.ra, but RSV, Dengue and Influenza will become groups. Presentation is still kinda rough, just a loop on the original results output. The server commands part needs testing and will not work yet for groups (currently used only for SARS-CoV-2).
  • lines changed 376, context: html, text, full: html, text
    da3772f3615ae3aa407af6aa2215a1b2ff480183 Mon Apr 29 13:40:41 2024 -0700
    If configured, use nextclade to align sequences (better for more diverged viruses like influenza). Also fix some buttons that the last change broke.
  • lines changed 20, context: html, text, full: html, text
    834653e22227fcea282e12a48910bb73068b34df Mon Apr 29 15:33:06 2024 -0700
    Don't depend on having a PSL alignment for the results table, precompute the same values whether aligning with gf/blat or nextclade.
• src/hg/hgPhyloPlace/writeCustomTracks.c
  • lines changed 4, context: html, text, full: html, text
    705420e703b067fbcad43ab67ed3e131552e7ac8 Wed Apr 24 14:23:03 2024 -0700
    Pathogen drop-down choices can now be groups of references/trees, for example 'Dengue (types 1 - 4)' instead of a separate choice for each type. Instead of config.ra, each group has an organism.ra and subdirectories named after reference accessions that contain reference.ra files. nextclade sort is used to match the user's uploaded sequences against available references for the selected pathogen. SARS-CoV-2, M. tuberculosis and hMPXV still have only one reference and still use config.ra, but RSV, Dengue and Influenza will become groups. Presentation is still kinda rough, just a loop on the original results output. The server commands part needs testing and will not work yet for groups (currently used only for SARS-CoV-2).
• src/hg/hgTracks/bedTrack.c
  • lines changed 23, context: html, text, full: html, text
    b818160961573cd7b8902303ca4dc532d1366513 Mon Apr 29 11:14:47 2024 -0700
    adding name filter and color track options to hgTrackUi, refs #20460
• src/hg/hgTracks/hgTracks.h
  • lines changed 8, context: html, text, full: html, text
    a774bc0d5ae571159bc1a764fcabd26c877ac523 Mon Apr 29 11:18:29 2024 -0700
    adding file forgot in previous commit
• src/hg/hgTracks/simpleTracks.c
  • lines changed 54, context: html, text, full: html, text
    b818160961573cd7b8902303ca4dc532d1366513 Mon Apr 29 11:14:47 2024 -0700
    adding name filter and color track options to hgTrackUi, refs #20460
• src/hg/htdocs/cite.html
  • lines changed 101, context: html, text, full: html, text
    579039309916a4c6c76ff97933b69eac88bba9ff Wed May 1 14:34:54 2024 -0700
    Adding more citations to the cite.html page (GenArk, REST API, GBiB, DI, VAI, LiftOver). Moving sections around because of the new additions. refs #19925
• src/hg/htdocs/goldenPath/help/decorator.html
  • lines changed 236, context: html, text, full: html, text
    0277340826c2caf3883e29dc80d4a28192029a43 Sat May 4 17:15:18 2024 -0700
    Code review edits for the decorator help page, refs #33564
• src/hg/htdocs/images/favicon.ico
  • lines changed 0, context: html, text, full: html, text
    f3d85fb0cf7e3e1f8a48158f7c0ea34413c275d4 Wed May 1 15:59:29 2024 -0700
    Removing the fav icon I committed so the different machines can go back to having individual icons.
• src/hg/htdocs/style/HGStyle.css
  • lines changed 1, context: html, text, full: html, text
    27399ac08ce72fbb526a871f894748072da72985 Tue Apr 30 14:37:16 2024 -0700
    Changing the hub group label color (hubToggleBar) to a different blue color which was the popular vote, refs #33039
• src/hg/inc/hubConnect.h
  • lines changed 4, context: html, text, full: html, text
    c1c6aafb9931704385d0c341c3fbebd50f0ba4fc Mon Apr 29 13:22:09 2024 -0700
    response to code review #33561
• src/hg/js/autocompleteCat.js
  • lines changed 3, context: html, text, full: html, text
    1fe39bbec78cdd5c5162f901b9ed11a7595545b1 Tue Apr 30 09:36:27 2024 -0700
    Fix bug in autocomplete render that was showing null for top level hits to assembly hubs in the species search
• src/hg/js/hgGateway.js
  • lines changed 4, context: html, text, full: html, text
    c3c0b288edd697b9631d8236bc27091d0ae6c8ff Tue Apr 30 13:41:00 2024 -0700
    Get clicks from autocomplete to genark hubs working, refs #33572
• src/hg/js/hgTracks.js
  • lines changed 10, context: html, text, full: html, text
    b818160961573cd7b8902303ca4dc532d1366513 Mon Apr 29 11:14:47 2024 -0700
    adding name filter and color track options to hgTrackUi, refs #20460
  • lines changed 1, context: html, text, full: html, text
    dbb3262ff0bcf115017d3f0abe5bfc26ae1a8dc1 Thu May 2 17:10:15 2024 -0700
    Fix drag select opening page in a new window, caused by mistakenly deleting a line that was important when merging the open hgc pages on hgTracks commit, refs #33584
  • lines changed 1, context: html, text, full: html, text
    76d24868211e2ef4be9717e9e98429cba45143a0 Fri May 3 09:39:56 2024 -0700
    Revert "Fix drag select opening page in a new window, caused by mistakenly deleting a line that was important when merging the open hgc pages on hgTracks commit, refs #33584" This reverts commit dbb3262ff0bcf115017d3f0abe5bfc26ae1a8dc1.
  • lines changed 8, context: html, text, full: html, text
    12acb7943615ead2b77b0eebaedf70b8ca1d7a96 Fri May 3 09:54:02 2024 -0700
    Better fix for broken drag select. The map click code that now tries to open up hgc needs to first check whether we are currently allowed to click to begin with. Then we can try to open up the details pages. If we aren't doing a details page, then we need to submit the form like we would do before I added hgc pop ups, refs #33584
• src/hg/js/utils.js
  • lines changed 20, context: html, text, full: html, text
    b818160961573cd7b8902303ca4dc532d1366513 Mon Apr 29 11:14:47 2024 -0700
    adding name filter and color track options to hgTrackUi, refs #20460
• src/hg/lib/cart.c
  • lines changed 25, context: html, text, full: html, text
    4fc19c01ff119c7075ec8d474e37e6bfc8519792 Mon Apr 29 14:56:59 2024 -0700
    allow Genark hubs to be specified as "db"
• src/hg/lib/decoratorUi.c
  • lines changed 1, context: html, text, full: html, text
    a0d2406fe056fb89608bdf3ba8b970c44d472a44 Wed May 1 02:06:27 2024 -0700
    added missing newline in 'Decoration settings' to put 'Filter items by' at the start of a line
• src/hg/lib/hgHgvs.c
  • lines changed 48, context: html, text, full: html, text
    63bcbd28b1571a7efdb6628f80751481f3bd98f2 Tue Apr 30 01:15:16 2024 -0700
    adding n. notation to HGVS parser, refs #25982
• src/hg/lib/hui.c
  • lines changed 52, context: html, text, full: html, text
    b818160961573cd7b8902303ca4dc532d1366513 Mon Apr 29 11:14:47 2024 -0700
    adding name filter and color track options to hgTrackUi, refs #20460
• src/hg/lib/trackHub.c
  • lines changed 1, context: html, text, full: html, text
    c1c6aafb9931704385d0c341c3fbebd50f0ba4fc Mon Apr 29 13:22:09 2024 -0700
    response to code review #33561
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    4f4b20c6b02408923cb4856e887380a4a217fd5d Mon Apr 29 16:17:13 2024 -0700
    adding GCA_036010255.1_ASM3601025v1 mammals Myotis_ricketti per user request, refs #29545
  • lines changed 1, context: html, text, full: html, text
    94f0712f11c72e596510a7a6adfbea49d3ae7574 Wed May 1 15:26:56 2024 -0700
    adding GCF_000021865.1_ASM2186v1 bacteria Rhodobacter_capsulatus_SB_1003 per user request, refs #29545
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    cbcfaaa19062bc357dcbc5dabd90efa08709f865 Wed May 1 15:34:46 2024 -0700
    adding Rhodobacter_capsulatus_SB_1003, refs #29545
• src/hg/makeDb/doc/hg38/hprcInDel.txt
  • lines changed 3, context: html, text, full: html, text
    dfffa1b747f834032ed3af48b7cd00e7a493da7e Wed May 1 10:49:40 2024 -0700
    add human parseable names to the elements
• src/hg/makeDb/doc/hg38/hprcRearrange.txt
  • lines changed 4, context: html, text, full: html, text
    dfffa1b747f834032ed3af48b7cd00e7a493da7e Wed May 1 10:49:40 2024 -0700
    add human parseable names to the elements
• src/hg/makeDb/doc/hg38/multiz100way.txt
  • lines changed 9, context: html, text, full: html, text
    3b7094b836ca282f03f54eb70c3778efab444042 Wed May 1 10:54:51 2024 -0700
    did this work awhile ago but didn't commit the doc
• src/hg/makeDb/doc/hg38/multiz470way.txt
  • lines changed 1, context: html, text, full: html, text
    3b7094b836ca282f03f54eb70c3778efab444042 Wed May 1 10:54:51 2024 -0700
    did this work awhile ago but didn't commit the doc
  • lines changed 308, context: html, text, full: html, text
    ff4e923294201861dc037c70229a73b50e3c2cbc Wed May 1 21:29:23 2024 -0700
    reworking the phastCons and phyloP tracks
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    3e1fe07895299ad2677b082bbac446ca15d20533 Mon Apr 29 16:30:02 2024 -0700
    adding Myotis_ricketti Rickett's big-footed myotis (AB-2021 2024), refs #29545
  • lines changed 0, context: html, text, full: html, text
    aa63bca14f11e084b4edff89584d0bd25db701d4 Mon Apr 29 16:34:22 2024 -0700
    adding a tab-separated value for Myotis_ricketti Rickett's big-footed myotis (AB-2021 2024), refs #29545
• src/hg/makeDb/trackDb/human/hg19/knownGeneV45lift37.html
  • lines changed 16, context: html, text, full: html, text
    2ae08032da58150435266d0852373f9988321484 Mon Apr 29 12:07:22 2024 -0700
    fix hg19 knowngene description page to not have table with transcript type counts
• src/hg/utils/automation/asmHubChainNetComposite.pl
  • lines changed 114, context: html, text, full: html, text
    9904896e7b27b2bf0bd0d55377bf3aa1aa7c3ffb Fri May 3 12:06:42 2024 -0700
    improved description and now with table of feature bits identity
• src/hg/utils/automation/asmHubChainNetTrackDb.pl
  • lines changed 37, context: html, text, full: html, text
    973d987f021ce8ae4fbaa555f2f7ee611c341a10 Thu May 2 10:19:09 2024 -0700
    separate out the syn rbest and liftOver chains into their own view
  • lines changed 70, context: html, text, full: html, text
    4687e86792555ca063ea6d90d67adb7d583551d6 Thu May 2 11:45:57 2024 -0700
    now with correct common name
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    9eb381beb58a8f827bb0664bdcb8c643144fe7bd Thu May 2 12:32:49 2024 -0700
    the net tracks are not nets they are alignments
• src/hg/utils/automation/doBlastzChainNet.pl
  • lines changed 13, context: html, text, full: html, text
    2df46316a4bbb699e3c24bf57485b216e3c32af4 Fri May 3 12:06:07 2024 -0700
    making liftOver big files for track
• src/hg/utils/automation/featBitsSurvey.pl
  • lines changed 84, context: html, text, full: html, text
    819c30d6d5b5e898158949bb88d89026bd30bdf6 Fri May 3 15:53:04 2024 -0700
    initial version of a feature bits table
• src/hg/utils/chainArrangeCollect/chainArrangeCollect.c
  • lines changed 10, context: html, text, full: html, text
    5b9d61175695a6fdb016b877212a58fd6d8048de Wed May 1 11:12:38 2024 -0700
    added name prefix so elements can have human parseable names
• src/hg/utils/hgTracksDelta/hgTracksDelta.c
  • lines changed 71, context: html, text, full: html, text
    5aa51e4d2469b0277e03cc831915afb71f9635ea Wed May 1 11:13:38 2024 -0700
    some work I did a while ago on an image comparator. At this point this has been replaced with QA's version
• src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
  • lines changed 10, context: html, text, full: html, text
    7e6a7ad1f3194e32d9af0a87aff074aa01a859d3 Mon Apr 22 14:16:28 2024 -0700
    Added more sites by request, including new branch GE.1.2.1.
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
  • lines changed 74, context: html, text, full: html, text
    e2d2b97265d31fb70bbc473306eac28305d94a0e Tue Apr 30 08:30:48 2024 -0700
    New lineages -- up to pango-designation release v1.27.
• src/hg/utils/paSNP/pa.c
  • lines changed 1, context: html, text, full: html, text
    3ff74a4107b59f4d14c1e06025077dd24900888b Wed May 1 11:15:37 2024 -0700
    allow underbars in names

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• files changed: 71