All File Changes

v417_preview to v417_preview2 (2021-06-21 to 2021-06-28) v417

• README
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    4badcdf42740fdbfa694e118718e38558192c9ff Thu Jun 10 05:16:04 2021 -0700
    remove a few outdated instructions in top level README, github #56
• src/hg/cartDump/cartDump.c
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    dfd69d02b4d35ccafd84a4d712086ef61a9db487 Mon Jun 21 14:12:34 2021 -0700
    replacing hgBotDelay with earlyBotCheck refs #23217
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    d991ba970c957cf1cf454ddb19257fdb0a56bf82 Mon Jun 21 14:25:38 2021 -0700
    do not need the extra comment about the elimination of the hgBotDelay refs #23217
• src/hg/hgBlat/hgBlat.c
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    f73e7f5ce028d89c0ccb0a19268dc4c739746a79 Mon Jun 21 13:44:01 2021 -0700
    replacing hgBotDelayFrac with earlyBotCheck refs #23217
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    b36d37d0d18dbb63cbbeefd4d22bd70046526382 Mon Jun 21 14:23:58 2021 -0700
    do not need the extra comment about the elimination of the hgBotDelay refs #23217
• src/hg/hgGene/hgGene.c
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    dcba97b3f88e88e9e59b85f87647d0ba9f2d4503 Mon Jun 21 10:56:49 2021 -0700
    replacing hgBotDelay with earlyBotCheck refs #23217
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    9ff484f7f73c81550c994b66450266b94f0d24b1 Mon Jun 21 13:44:38 2021 -0700
    replacing hgBotDelayFrac with earlyBotCheck refs #23217
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    b36d37d0d18dbb63cbbeefd4d22bd70046526382 Mon Jun 21 14:23:58 2021 -0700
    do not need the extra comment about the elimination of the hgBotDelay refs #23217
• src/hg/hgPcr/hgPcr.c
  • lines changed 16, context: html, text, full: html, text
    82b4ffe1c64351dea31fbda82f186ce0fd30675e Mon Jun 21 14:08:24 2021 -0700
    replacing hgBotDelay with earlyBotCheck refs #23217
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    b36d37d0d18dbb63cbbeefd4d22bd70046526382 Mon Jun 21 14:23:58 2021 -0700
    do not need the extra comment about the elimination of the hgBotDelay refs #23217
• src/hg/hgPhyloPlace/phyloPlace.c
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    3e968a25a2e9635f916fb3eeac0b3e2147cfba7c Mon Jun 28 08:43:35 2021 -0700
    Add links to outbreak.info for lineages in results table & details.
• src/hg/hgPhyloPlace/phyloPlace.h
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    3e968a25a2e9635f916fb3eeac0b3e2147cfba7c Mon Jun 28 08:43:35 2021 -0700
    Add links to outbreak.info for lineages in results table & details.
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
  • lines changed 21, context: html, text, full: html, text
    b0914531bd4294d1cf0a746601f080cd53d159a2 Sun Jun 27 20:17:40 2021 -0700
    Add link from lineage to outbreak.info. Better labels for subtree links.
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    3e968a25a2e9635f916fb3eeac0b3e2147cfba7c Mon Jun 28 08:43:35 2021 -0700
    Add links to outbreak.info for lineages in results table & details.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 16, context: html, text, full: html, text
    39be885d6a194b49917e1d01b5aee2f9db114805 Mon Jun 21 13:13:22 2021 -0700
    replacing hgBotDelayFrac with earlyBotCheck refs #23217
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    9ff484f7f73c81550c994b66450266b94f0d24b1 Mon Jun 21 13:44:38 2021 -0700
    replacing hgBotDelayFrac with earlyBotCheck refs #23217
• src/hg/hgTracks/hgTracks.c
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    fb761d3895124a6052c3a71102eac03f9235f990 Fri Jun 25 03:52:26 2021 -0700
    moving the udcTimeout message to a notification box, refs #27677
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    ce8386426971b15c8c4e3a091fea3635fcf2df54 Fri Jun 25 08:00:43 2021 -0700
    fixing typo in last commit, refs #27677
• src/hg/hgc/hgc.c
  • lines changed 16, context: html, text, full: html, text
    2f97e349bcd569b1da7a53ba82570f47ae32c365 Mon Jun 21 13:55:18 2021 -0700
    replacing hgBotDelayFrac with earlyBotCheck refs #23217
  • lines changed 4, context: html, text, full: html, text
    b36d37d0d18dbb63cbbeefd4d22bd70046526382 Mon Jun 21 14:23:58 2021 -0700
    do not need the extra comment about the elimination of the hgBotDelay refs #23217
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    29f4bd09d8e89fdebee291c6ff2601cdb0adcf57 Mon Jun 21 14:29:46 2021 -0700
    there was another hgBotDelay in mafClick replaced by earlyBotCheck() system refs #23217
• src/hg/hgc/mafClick.c
  • lines changed 6, context: html, text, full: html, text
    29f4bd09d8e89fdebee291c6ff2601cdb0adcf57 Mon Jun 21 14:29:46 2021 -0700
    there was another hgBotDelay in mafClick replaced by earlyBotCheck() system refs #23217
• src/hg/htdocs/FAQ/FAQgenes.html
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    0c195e055727ab6baf38b80224f7cfd522c621ab Thu Jun 17 02:30:09 2021 -0700
    adding a bit of text for the user in ML 2;2D#7703 to explain transcripts
• src/hg/htdocs/goldenPath/help/trackDb/README.txt
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    2ef08a1cd112ef2b01d2047f176062ca6909b38e Tue Jun 22 14:50:58 2021 -0700
    Adding an emphasis about adding the new trackDbvNew#.html to the goldenPath/help/trackDb/makefile when versioning
• src/hg/htdocs/goldenPath/help/trackDb/makefile
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    88e575ca6d6806029c7dfb580657971a55885c94 Tue Jun 22 14:25:13 2021 -0700
    Documenting extraTableFields and extraDetailsTable settings in use by the gnomad tracks, refs #26837
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 8, context: html, text, full: html, text
    88e575ca6d6806029c7dfb580657971a55885c94 Tue Jun 22 14:25:13 2021 -0700
    Documenting extraTableFields and extraDetailsTable settings in use by the gnomad tracks, refs #26837
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 8, context: html, text, full: html, text
    88e575ca6d6806029c7dfb580657971a55885c94 Tue Jun 22 14:25:13 2021 -0700
    Documenting extraTableFields and extraDetailsTable settings in use by the gnomad tracks, refs #26837
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 88, context: html, text, full: html, text
    88e575ca6d6806029c7dfb580657971a55885c94 Tue Jun 22 14:25:13 2021 -0700
    Documenting extraTableFields and extraDetailsTable settings in use by the gnomad tracks, refs #26837
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 1, context: html, text, full: html, text
    d989e06c01ea0ec07b4d1fb71582b1c158a33ef2 Tue Jun 22 12:30:38 2021 -0700
    Fixing date typo NO RM
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    2fd50ddc65d39ab4d7e7b4860f2840d66ea014e4 Thu Jun 24 14:27:08 2021 -0700
    Releasing REVEL regfs #27141
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    f3ccc9b7200915518d9437f3718fd5b2097d9539 Thu Jun 24 15:46:28 2021 -0700
    Fixing inaccurate description refs #27142
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    6c3f3f0988717d3e5fea2f2670351b3e19f51a3d Fri Jun 25 17:23:09 2021 -0700
    Trying to clean up some htmlCheck validate newsarch.html items before adding trackDb v3 announcement.
• src/hg/htdocs/indexNews.html
  • lines changed 10, context: html, text, full: html, text
    2fd50ddc65d39ab4d7e7b4860f2840d66ea014e4 Thu Jun 24 14:27:08 2021 -0700
    Releasing REVEL regfs #27141
• src/hg/htdocs/staff.html
  • lines changed 8, context: html, text, full: html, text
    9e562858ace8bfed19032e903a04e97b2b158ef2 Mon Jun 21 13:55:13 2021 -0700
    Adding a link to Contact Us on staff.html, after MLQ user emailed Max directly (maybe related to 12c7c56 where About Us changed) refs #27739
• src/hg/htdocs/style/HGStyle.css
  • lines changed 15, context: html, text, full: html, text
    fb761d3895124a6052c3a71102eac03f9235f990 Fri Jun 25 03:52:26 2021 -0700
    moving the udcTimeout message to a notification box, refs #27677
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    577a2c68aee5d65c5b3e7bf92427c8ed6074dab5 Fri Jun 25 04:16:55 2021 -0700
    moving the main warning box back to the middle of the screen, refs #27677
• src/hg/js/utils.js
  • lines changed 9, context: html, text, full: html, text
    fb761d3895124a6052c3a71102eac03f9235f990 Fri Jun 25 03:52:26 2021 -0700
    moving the udcTimeout message to a notification box, refs #27677
• src/hg/lib/cartRewrite.c
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    eb728a6583bf2f2151e4ebe2e418cb103011814c Mon Jun 21 12:24:36 2021 -0700
    tweak to cartRewrite at Jonathans suggestion. Now it does as many rewrites as it has rather than not doing any if it can't do them all.
• src/hg/lib/trackDbCustom.c
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    1eb615411838193436b51e2a8a177b865544d85d Fri Jun 25 14:33:38 2021 -0700
    Fix bug in trackDb include processing, when a bigDataUrl is referenced relative to it's trackDb file, and the trackDb file is referenced via an include statement, CGIs were trying to expand bigDataUrl relative to the top level trackDb instead of it's correct parent, refs #27767
• src/hg/makeDb/doc/asmHubs/master.run.list
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    a491bbd44d8008ea1c97f3e100d34d97484e1909 Thu Jun 24 10:44:43 2021 -0700
    building the mouseStrains assemblies refs #27731
• src/hg/makeDb/doc/mm10.patchUpdate.6.txt
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    662a15da12048f67428d67e010d61bfc6ea202fa Tue Jun 22 17:24:25 2021 -0700
    updated the tables list
• src/hg/makeDb/doc/viralAsmHub/hub.txt
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    f419336d3cf8ed5a96aa852c9f3e56f408b96f49 Thu Jun 24 12:51:01 2021 -0700
    the nascient virus assembly hubs refs #27758
• src/hg/makeDb/doc/viralAsmHub/makefile
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    f419336d3cf8ed5a96aa852c9f3e56f408b96f49 Thu Jun 24 12:51:01 2021 -0700
    the nascient virus assembly hubs refs #27758
• src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
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    f419336d3cf8ed5a96aa852c9f3e56f408b96f49 Thu Jun 24 12:51:01 2021 -0700
    the nascient virus assembly hubs refs #27758
• src/hg/makeDb/trackDb/human/cadd.ra
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    9c70d91534dd8366a57c563718c715308d3dac78 Mon Jun 21 16:03:47 2021 -0700
    Code review edits, shorting longLabel’s within 80 characters, refs #27743
• src/hg/makeDb/trackDb/human/caddSuper.html
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    9c70d91534dd8366a57c563718c715308d3dac78 Mon Jun 21 16:03:47 2021 -0700
    Code review edits, shorting longLabel’s within 80 characters, refs #27743
• src/hg/makeDb/trackDb/human/hg19/dbSnpArchiveHg19.ra
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    ccf434551cc2ced3b6d25bc18a013ea7d7ec1898 Thu Jun 24 15:01:51 2021 -0700
    Fixing minor typo for CR refs #27744
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    9c70d91534dd8366a57c563718c715308d3dac78 Mon Jun 21 16:03:47 2021 -0700
    Code review edits, shorting longLabel’s within 80 characters, refs #27743
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    2fd50ddc65d39ab4d7e7b4860f2840d66ea014e4 Thu Jun 24 14:27:08 2021 -0700
    Releasing REVEL regfs #27141
• src/hg/makeDb/trackDb/human/revel.ra
  • lines changed 1, context: html, text, full: html, text
    2fd50ddc65d39ab4d7e7b4860f2840d66ea014e4 Thu Jun 24 14:27:08 2021 -0700
    Releasing REVEL regfs #27141
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    1381766f491bf545cadd81a3dbae38c8194ea04a Thu Jun 24 14:39:44 2021 -0700
    Adding to longLabel to signify anotations only on CDS refs #27142
• src/hg/makeDb/trackDb/trackDb.ra
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    b5704bfd9c58bd4bd650da05c2da4068f5ce2d63 Thu Jun 24 02:13:13 2021 -0700
    making uniprot work with the new-style filters for the uniprot otto job, refs #27464
• src/hg/makeDb/trackDb/uniprot.alpha.ra
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    b5704bfd9c58bd4bd650da05c2da4068f5ce2d63 Thu Jun 24 02:13:13 2021 -0700
    making uniprot work with the new-style filters for the uniprot otto job, refs #27464
• src/hg/utils/faToVcf/faToVcf.c
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    0410ce3f2bff7c04762f60551db166f4cae460f7 Tue Jun 22 10:13:57 2021 -0700
    faToVcf: added -maxDiff to exclude sequences with too many mismatches w/reference (causes usher mem usage increase, no good placement).
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    b69d77d71d0bf2464ed68a165fd1988a7044753e Sun Jun 27 20:20:21 2021 -0700
    Added -includeNoAltN option to include info about Ns in the VCF.
• src/hg/utils/makefile
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    0363a87914ad142f466788f47b4006eea73e1f3b Thu Jun 24 10:33:34 2021 -0700
    demote scaffoldFaToAgp from the userApps list to the UCSC only list refs #27498
• src/hg/utils/otto/sarscov2phylo/getCogUk.sh
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    179775232ff5fe31323f984619b75cbc77204c00 Sun Jun 27 20:22:29 2021 -0700
    Update nextclade to 1.0 (new required command line args).
• src/hg/utils/otto/sarscov2phylo/getNcbi.sh
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    179775232ff5fe31323f984619b75cbc77204c00 Sun Jun 27 20:22:29 2021 -0700
    Update nextclade to 1.0 (new required command line args).
• src/hg/utils/otto/sarscov2phylo/gisaidFromChunks.sh
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    1e6e36834dceedd5c2cb79834bcc84ee0bac4be5 Mon Jun 28 08:44:36 2021 -0700
    Use make -j for pangolin (no multithreading at this point).
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
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    83f9e814d5441d0ba86d5fa735aed67d264a771f Sun Jun 27 20:27:52 2021 -0700
    Skip building new.masked.vcf.gz if it already exists (go straight to usher). More prevention of empty-grep crashes. Use faToVcf new -maxDiff option to prevent memory usage blowup for sequences that are so diverged/erroneous that we won't keep them anyway. Exclude sequences with 10 or more equally parsimonious placements so we don't keep trying in vain (and wasting time). Handle new nextstrain clade names with spaces etc.
• src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh
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    dc65a1eecd5e15e136536571af19bf7ccd77726e Sun Jun 27 20:21:39 2021 -0700
    Clean up hardcoded paths a tiny bit.
• src/lib/freeType.c
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    6be368acfff1be013b63beffd4d9129abaf62d6f Wed Jun 23 20:02:48 2021 -0700
    Two variables were defined in a header that was include by multiple .o files. This caused multiple defined symbols when compiling with GCC on MacOS ARM64. This is the correct way to declare an global shared by modules. I just have no idea how this ever worked.
• src/lib/freeType.h
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    6be368acfff1be013b63beffd4d9129abaf62d6f Wed Jun 23 20:02:48 2021 -0700
    Two variables were defined in a header that was include by multiple .o files. This caused multiple defined symbols when compiling with GCC on MacOS ARM64. This is the correct way to declare an global shared by modules. I just have no idea how this ever worked.
• src/utils/qa/weeklybld/buildEnv.csh
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    4227c91d6b331f97709e6f17edd48859da8ab6e2 Mon Jun 28 10:01:16 2021 -0700
    v417 preview2, refs #27752
• src/utils/qa/weeklybld/buildHgCentralSql.csh
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    1c051a9c4893791adf1c277cc77ff5f6ea520364 Thu Jun 24 14:27:57 2021 -0700
    Add hgdownload2 to list of hgdownload machines for users apps and other build targets, refs Hiram email
• src/utils/qa/weeklybld/doZip.csh
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    1c051a9c4893791adf1c277cc77ff5f6ea520364 Thu Jun 24 14:27:57 2021 -0700
    Add hgdownload2 to list of hgdownload machines for users apps and other build targets, refs Hiram email
• src/utils/qa/weeklybld/makeUserApps.csh
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    1c051a9c4893791adf1c277cc77ff5f6ea520364 Thu Jun 24 14:27:57 2021 -0700
    Add hgdownload2 to list of hgdownload machines for users apps and other build targets, refs Hiram email
• src/utils/qa/weeklybld/userApps.sh
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    1c051a9c4893791adf1c277cc77ff5f6ea520364 Thu Jun 24 14:27:57 2021 -0700
    Add hgdownload2 to list of hgdownload machines for users apps and other build targets, refs Hiram email

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