All File Changes

v420_preview2 to v420_base (2021-08-30 to 2021-09-07) v420

• confs/hgwbeta.hg.conf
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    9a3ad98bbf8087975cc238c59472e95fec583d30 Sun Sep 5 01:11:44 2021 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 20, context: html, text, full: html, text
    9a3ad98bbf8087975cc238c59472e95fec583d30 Sun Sep 5 01:11:44 2021 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgBlat/hgBlat.c
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    209bf66e17a1caece85b4001ecaa554675fb36af Wed Sep 1 14:59:35 2021 -0700
    change citation to avoid redirect. Refs #28082
• src/hg/hgGene/hgGeneData/Human/hg38/otherOrgs.ra
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    21ecc89a7989c1f60d6da19c6e9eeb2dbe65525d Wed Sep 1 12:07:30 2021 -0700
    update to blastTabs to mm39 from mm10
• src/hg/hgGene/hgGeneData/S_cerevisiae/sacCer3/otherOrgs.ra
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    21ecc89a7989c1f60d6da19c6e9eeb2dbe65525d Wed Sep 1 12:07:30 2021 -0700
    update to blastTabs to mm39 from mm10
• src/hg/hgPhyloPlace/hgPhyloPlace.c
  • lines changed 5, context: html, text, full: html, text
    49fafa484293682f56ca08a0d902d8366fc476f7 Thu Sep 2 17:43:32 2021 -0700
    Link to client-side UShER implementation ShUShER.
• src/hg/hgTracks/hgTracks.c
  • lines changed 2, context: html, text, full: html, text
    a767f7035297137ff676dc149993c150cf511858 Fri Sep 3 06:49:08 2021 -0700
    changes after code review, refs #28080
• src/hg/hgc/bigBedClick.c
  • lines changed 11, context: html, text, full: html, text
    7f7a1e6ecc12149c8e55a619ce556836fdee8ad2 Fri Sep 3 14:59:09 2021 -0700
    add sequence logos to Jaspar track
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    9119dbe1ceda814b1ffe259d5c2c7739ea962337 Thu Sep 2 12:10:44 2021 -0700
    Fix missing hReplaceGbdb, refs #28019
• src/hg/htdocs/goldenPath/help/hubQuickStartFilter.html
  • lines changed 3, context: html, text, full: html, text
    bba85430ba9d52187d9737178b1e61f9d8b2ebc8 Fri Sep 3 13:32:44 2021 -0700
    Adding a note about how + and . are needed for filters in type bigBed declarations
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    ba9f7f2713b990c40b25d0f94ebeee2e44be1a73 Fri Sep 3 14:34:22 2021 -0700
    Small edits to Lou's beautiful filter page refs #24327
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 2, context: html, text, full: html, text
    fc9f1f64afcb86e19360832a7c9a8060d0ba2ee1 Wed Sep 1 13:58:05 2021 -0700
    Adding note about . and + in type bigBed # discussion
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    86cb28ab770d0af6370ad503639f160d931eeca3 Fri Sep 3 09:40:28 2021 -0700
    Fixing extraTableFields so that it matches what's in trackDbDoc.html, otherwise it's a duplicate of what's there for extraDetailsTable. Seems like a copy/paste error. no redmine.
• src/hg/htdocs/redmineWidget.html
  • lines changed 3, context: html, text, full: html, text
    3fc7f51f1200bccbd84d904d53c15957ee8fe293 Tue Aug 31 15:47:45 2021 -0700
    Tweaking some of the widget fields for organization purposes refs #28034
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    7bed054cfdb04e465c779db571df4c9768341368 Wed Sep 1 12:01:34 2021 -0700
    Swapping both widget creation categories to Widget refs #28034
• src/hg/htdocs/style/HGStyle.css
  • lines changed 1, context: html, text, full: html, text
    964ba602f775e2417cf537b501327bff415001cd Wed Sep 1 05:29:29 2021 -0700
    tweaking CSS of optional help search link, refs #28072
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    d95e67f834bfb8d2c96646f49c03c10a6a07d73b Thu Sep 2 08:23:41 2021 -0700
    moving search help link closer to go buttons, refs #28072
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    4069de964171b015cdf61e9a4cdb7cd2c4bf8a3b Tue Sep 7 10:08:34 2021 -0700
    New version number v420
• src/hg/lib/bed5SourceVals.sql
  • lines changed 2, context: html, text, full: html, text
    5a9e9854a89ac8e2dd7d2e0660dbd699f4de6404 Fri Sep 3 23:50:30 2021 -0700
    Got Angies original version which is better.
• src/hg/lib/customTrack.c
  • lines changed 20, context: html, text, full: html, text
    cde87e3d79ee923945b80b85d708ab9d07475263 Wed Sep 1 13:26:02 2021 -0700
    improved bottleneck penalty for custom track loading even when they fail to load refs #28049
  • lines changed 2, context: html, text, full: html, text
    054ce7806ed2e09aa1e24d1a126fedfb96bd1348 Thu Sep 2 14:22:15 2021 -0700
    show current botDelay millis after the ct loading penalty refs #28049
  • lines changed 1, context: html, text, full: html, text
    bc60ecbf3126d1c8502d28b45dde545bf8467d8b Fri Sep 3 15:14:40 2021 -0700
    not a good idea to add delay for zero custom tracks loaded, something in hgc is calling this repeatedly for no custom tracks refs #28049
  • lines changed 4, context: html, text, full: html, text
    4ff52b737cc301bc1f66518cdc6336c8b976bb16 Mon Sep 6 09:31:38 2021 -0700
    do not penalize for each custom track, just one penalty per submissiong refs #28049
• src/hg/lib/hgHgvs.c
  • lines changed 8, context: html, text, full: html, text
    ce891d7726cb07920b5072bb5b4ca9faf44c6e61 Fri Sep 3 16:39:47 2021 -0700
    Translating protein coords to CDS might result in coords that fall off the end of CDS but not off the end of the transcript. Avoid showing 3'UTR results for a protein search by requiring results in the coding region for protein searches. refs #28107
• src/hg/lib/tests/expected/hgvs/validTerms.txt
  • lines changed 2, context: html, text, full: html, text
    ce891d7726cb07920b5072bb5b4ca9faf44c6e61 Fri Sep 3 16:39:47 2021 -0700
    Translating protein coords to CDS might result in coords that fall off the end of CDS but not off the end of the transcript. Avoid showing 3'UTR results for a protein search by requiring results in the coding region for protein searches. refs #28107
• src/hg/lib/tests/hgvsTester.c
  • lines changed 8, context: html, text, full: html, text
    ce891d7726cb07920b5072bb5b4ca9faf44c6e61 Fri Sep 3 16:39:47 2021 -0700
    Translating protein coords to CDS might result in coords that fall off the end of CDS but not off the end of the transcript. Avoid showing 3'UTR results for a protein search by requiring results in the coding region for protein searches. refs #28107
• src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
  • lines changed 14, context: html, text, full: html, text
    8b6ee6734404f7ab681577f5044559dd2ce8bc08 Fri Sep 3 12:24:45 2021 -0700
    print heredoc need to have ; on the print line refs #23891
• src/hg/makeDb/doc/hg19.txt
  • lines changed 2, context: html, text, full: html, text
    078373be43b3261bd2d3b282e15c11599cd45964 Thu Sep 2 12:02:34 2021 -0700
    Adding info to makeDoc refs #27061
• src/hg/makeDb/trackDb/buildRelatedTracks
  • lines changed 1, context: html, text, full: html, text
    a359b0401955c02ce8c7f3880c354648d5caa349 Mon Sep 6 06:32:03 2021 -0700
    adding error message to related tracks script, no redmine.
• src/hg/makeDb/trackDb/chimp/panTro2/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/cow/bosTau4/trackDb.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/dog/canFam2/trackDb.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/dbSnp153Composite.html
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    58f9a8971053e464cfefcfff018e491cae5dd8f3 Mon Aug 30 11:27:36 2021 -0700
    Setting width of Tables at b0b's request No RM
• src/hg/makeDb/trackDb/human/encodeTest/wgEncodeMetaCheckTest.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeAffyRnaChip.patch.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeAffyRnaChip.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeq.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadHmm.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBuOrchid.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMap.new.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMap.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlLongRnaSeq.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlShortRnaSeq.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeDukeAffyExon.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisDnaPet.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisPet.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisRnaSeq.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHelicosRnaSeq.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.new.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaCnv.new.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaCnv.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethyl27.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethylSeq.new.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethylSeq.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaRnaSeq.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeMapability.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeSuper.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwAffyExonArray.patch.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwAffyExonArray.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwChIPSeq.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDGF.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.new.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseq.new.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseq.patch.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseq.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleRnaSeq.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg19/encode3.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAffyRnaChip.patch.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAffyRnaChip.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwg.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseMasterSites.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseUniform.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgSegmentation.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgTfbsUniform.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release2.ra
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• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuRnaSeq.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
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• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
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• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.release2.ra
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• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHist.ra
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    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHist.release2.ra
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    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhRnaSeq.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhRnaSeq.release2.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
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• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.release3.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.release4.ra
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    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDgf.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.release2.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwRnaSeq.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
    Removing encode icons from hgTracks refs #25035
• src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
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• src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.ra
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• src/hg/makeDb/trackDb/tagTypes.tab
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    7f7a1e6ecc12149c8e55a619ce556836fdee8ad2 Fri Sep 3 14:59:09 2021 -0700
    add sequence logos to Jaspar track
• src/hg/makeDb/trackDb/trackDb.encode3.ra
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    6da4dce3a3a3c6e69b499b5a77781a650909bc8f Thu Sep 2 11:15:11 2021 -0700
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• src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainClade.html
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    b1e8a38c415af7804a13ce7b2db5b2abb6e8dbe0 Mon Sep 6 15:09:25 2021 -0700
    changing reference to moved file
• src/hg/utils/automation/doAssemblyHub.pl
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    9fb7e2a933dd0b378f251d348153730c9972ddcd Wed Sep 1 15:24:05 2021 -0700
    eliminate small errors in unlocalized scaffold names and genePredFilter for ncbiGene to eliminate problem gene definitions no redmine
• src/hg/utils/automation/doNcbiRefSeq.pl
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    1f92dad159673221d937c939cfabf4ac32534823 Wed Sep 1 15:22:44 2021 -0700
    use genePredFilter to eliminate the circular wrap around genes on chrMT and like chromosomes no redmine
• src/hg/utils/automation/doTandemDup.pl
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    fb5a1a487756e0535aef78cf7818c7ea9c5f09e7 Wed Sep 1 15:21:45 2021 -0700
    using ram=16g on the cluster jobs to help prevent cluster job failures no redmine
• src/hg/utils/automation/synBlastp.csh
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    9160ba77561829b8e213058680623b63d35262dc Fri Sep 3 10:40:47 2021 -0700
    get synBlast to work with bigBed
• src/hg/utils/otto/knownGene/buildBlast.sh
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    66b1030888d2fbc504ed737350256b20442367c7 Fri Sep 3 10:43:22 2021 -0700
    ongoing work on knownGene automation
• src/hg/utils/otto/knownGene/buildCore.sh
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    66b1030888d2fbc504ed737350256b20442367c7 Fri Sep 3 10:43:22 2021 -0700
    ongoing work on knownGene automation
• src/hg/utils/otto/knownGene/buildKnown.sh
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    66b1030888d2fbc504ed737350256b20442367c7 Fri Sep 3 10:43:22 2021 -0700
    ongoing work on knownGene automation
• src/hg/utils/otto/knownGene/buildLoadOther.sh
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    21ecc89a7989c1f60d6da19c6e9eeb2dbe65525d Wed Sep 1 12:07:30 2021 -0700
    update to blastTabs to mm39 from mm10
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    66b1030888d2fbc504ed737350256b20442367c7 Fri Sep 3 10:43:22 2021 -0700
    ongoing work on knownGene automation
• src/hg/utils/otto/knownGene/buildMafGene.sh
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    66b1030888d2fbc504ed737350256b20442367c7 Fri Sep 3 10:43:22 2021 -0700
    ongoing work on knownGene automation
• src/hg/utils/otto/knownGene/buildTo.sh
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    66b1030888d2fbc504ed737350256b20442367c7 Fri Sep 3 10:43:22 2021 -0700
    ongoing work on knownGene automation
• src/hg/utils/otto/knownGene/copyFilesToAssembly.sh
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    66b1030888d2fbc504ed737350256b20442367c7 Fri Sep 3 10:43:22 2021 -0700
    ongoing work on knownGene automation
• src/hg/utils/otto/sarscov2phylo/bioSampleJsonToTab.py
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    86c9c0072ad12699dfdcf8232ad812f1982d23d7 Thu Sep 2 17:47:47 2021 -0700
    NCBI Datasets now includes a biosample.jsonl file -- when it's stable we won't need EUtils anymore, yay!
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    c28af7c6bbe39c880c7e6dcc0f1c3ff2ee5b427c Fri Sep 3 12:11:22 2021 -0700
    Grab lab from obscure location found by Nextstrain team in ncov-ingest PR#208.
• src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
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    eeafd7b8b2ea5f34ee78bfe73b51ea7a1be5bce4 Thu Sep 2 17:51:46 2021 -0700
    Add the same filters that we've been using on the combined tree because when GISAID samples are removed, some branches become very long. (Russ & Yatish request)
• src/hg/utils/otto/sarscov2phylo/gbMetadataAddBioSample.pl
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    7f0ad33bd004bc5616a9214534d74371f9f51940 Thu Sep 2 17:48:56 2021 -0700
    Greatly increase tolerance for missing BioSample records. I reported this to NCBI; sounds like that's just the way it is with importing delays.
• src/hg/utils/otto/sarscov2phylo/getNcbi.sh
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    d49c83bd184000554d36f1ffd9c07a89fb856352 Thu Sep 2 17:53:52 2021 -0700
    Use the new bioSampleJsonToTab.py script but keep the EUtils stuff for now as a back up until biosample.jsonl looks stable and complete. Make a separate log file for gbMetadataAddBioSample.pl output for easier extraction of IDs to ping submitters / NCBI about. Watch out for duplicated sequences in fasta.
• src/hg/utils/otto/sarscov2phylo/gisaidNameToCountry.pl
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    dcdb342ff4f255973940339af65b1b7266684ef9 Thu Sep 2 17:45:48 2021 -0700
    Add DRC -> Democratic Republic of the Congo.
• src/hg/utils/otto/sarscov2phylo/publicCredits.sh
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    78a15f21fb3bfad23eac7217e6d831810558304e Thu Sep 2 17:50:15 2021 -0700
    Adding note about COG-UK credits in BioSample text (although I should repeat with the new biosample.jsonl file).
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
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    1f64522294183ac3613b48b2d937fa8a666c9afa Thu Sep 2 17:55:45 2021 -0700
    Move the --max-parsimony post-filtering into usher's new --max-parsimony-per-sample option. Add mechanism to exclude sequences that sneak past quality filters by faking reference alleles where they should have Ns.
• src/inc/srcVersion.h
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    4069de964171b015cdf61e9a4cdb7cd2c4bf8a3b Tue Sep 7 10:08:34 2021 -0700
    New version number v420
• src/lib/pipeline.c
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    8943b642b61d368bbd4833fe55a39207ec4ecaa8 Tue Aug 31 16:26:16 2021 -0700
    forked pipeline() process shouldn't call the atexit() routines, so call _exit() rather than exit()
• src/utils/qa/hubPublicAutoUpdate
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    c638753eb8b699b35d0e795403b3f6481ed40198 Tue Aug 31 12:10:04 2021 -0700
    Adding util to automatically update hubPublic table refs #28008
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    558157a5068cd07e44e84538fb706184324633a4 Tue Aug 31 12:12:08 2021 -0700
    Improving formatting of help statement refs #28008
• src/utils/qa/makefile
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    c638753eb8b699b35d0e795403b3f6481ed40198 Tue Aug 31 12:10:04 2021 -0700
    Adding util to automatically update hubPublic table refs #28008
• src/utils/qa/weeklybld/buildEnv.csh
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    c365f2fc17d39433ae97e347a4fd16c8dc00b75d Tue Sep 7 10:07:27 2021 -0700
    v420 final build, refs #28041

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