All File Changes

v404_base to v405_preview (2020-09-14 to 2020-09-21) v405

• confs/hgwbeta.hg.conf
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    7a9279988c8a570cf5c96dbca2f492e5c639a9fd Sun Sep 20 01:11:40 2020 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgTracks/hgTracks.c
  • lines changed 59, context: html, text, full: html, text
    cd3cb167196e74d31050cd822634a4529a1ebf01 Thu Sep 17 18:09:51 2020 -0700
    show chrom alias names on sequence display page refs #24396
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    cb8f8b8e1fa7a5e122b4e0e5c7fb84bf4027d008 Fri Sep 18 13:03:08 2020 -0700
    assembly hubs and now display alias names on sequence display page refs #24396
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    baca98f3366561495cb20ac6ecb41c8794daf34d Fri Sep 18 14:27:22 2020 -0700
    fix last row of table to correctly have three columns when required refs #24396
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    2631a6777054d51ebcaf26b5bccffc52e90fc047 Thu Sep 17 16:06:34 2020 -0700
    Rename decipher code paths to decipherOld for switch to bigBed, refs #25841
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    2631a6777054d51ebcaf26b5bccffc52e90fc047 Thu Sep 17 16:06:34 2020 -0700
    Rename decipher code paths to decipherOld for switch to bigBed, refs #25841
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 12, context: html, text, full: html, text
    eae19514329af9e929c1911a6a560a4eb8acb286 Fri Sep 11 16:14:09 2020 -0700
    Adding GTEx pub to page refs #26199
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    34d012f58ce1e9867ecb7e2ff6435deb83185347 Thu Sep 17 09:49:20 2020 -0700
    Addding PMID refs #26029
• src/hg/htdocs/inc/recTrackSets.hg19.tab
  • lines changed 2, context: html, text, full: html, text
    4fc15f02f8abeb474ddf3d25f9542e7c77eda273 Mon Sep 14 17:11:58 2020 -0700
    Adding final recommended track sets under the View user refs #25601
• src/hg/inc/trackHub.h
  • lines changed 6, context: html, text, full: html, text
    cb8f8b8e1fa7a5e122b4e0e5c7fb84bf4027d008 Fri Sep 18 13:03:08 2020 -0700
    assembly hubs and now display alias names on sequence display page refs #24396
• src/hg/lib/googleAnalytics.c
  • lines changed 16, context: html, text, full: html, text
    9f25e02aec426e8ae2cd2d67a66c218d51b03989 Mon Sep 21 08:06:01 2020 -0700
    adding outbound link tracking to google analytics code, refs #21916
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    44cb7640ca7a6e0c8c8e85a79d3954270f077417 Mon Sep 21 08:49:45 2020 -0700
    bugfix for link tracking, refs #21916
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    c4661cda019152764c73081214c662c709adc243 Mon Sep 21 08:51:54 2020 -0700
    another bugfix for link tracking, refs #21916
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    826a14eeb65fa9a877c362ded4de9d311f991a61 Thu Sep 17 16:25:15 2020 -0700
    Fix relatedTracks section breaking on trackHubs that was lost when merging development branch, refs #26203
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    0b94f3b834f98b8e0218a4fcd41c819adfd82184 Mon Sep 21 04:45:32 2020 -0700
    adding little grey borders around the filter boxes. With many filter dimensions, it's hard to see where they start and end now, refs #24850
• src/hg/lib/trackHub.c
  • lines changed 116, context: html, text, full: html, text
    cb8f8b8e1fa7a5e122b4e0e5c7fb84bf4027d008 Fri Sep 18 13:03:08 2020 -0700
    assembly hubs and now display alias names on sequence display page refs #24396
• src/hg/makeDb/doc/calJac4/initialBuild.txt
  • lines changed 224, context: html, text, full: html, text
    180734e3da31c25fecc1583231a29885abc1d18b Thu Sep 17 12:00:59 2020 -0700
    pretty close to done refs #24074
• src/hg/makeDb/doc/canFam5/initialBuild.txt
  • lines changed 193, context: html, text, full: html, text
    2986dc8f9e9b8e1d276f8dbc981309fba29d9016 Mon Sep 14 16:39:05 2020 -0700
    completed marked QA Ready refs #25917
• src/hg/makeDb/doc/covid/covidHgiGwas.txt
  • lines changed 13, context: html, text, full: html, text
    b62b289568697d98f019a4bd82bb910b044cbeb7 Tue Sep 15 15:27:20 2020 -0700
    Support for use of lolly size, and pvalue displayed as E notation. refs #26129
  • lines changed 39, context: html, text, full: html, text
    ca4516b7f5442f06d7eca5bffd7a82d18ef18a3b Wed Sep 16 11:18:35 2020 -0700
    Interim check-in for exploratory work with COVID GWAS V2 track (moving to branch). refs #26129
• src/hg/makeDb/doc/hg19.txt
  • lines changed 41, context: html, text, full: html, text
    87d5b93cb522e7bfa4a66ae41f93e94394d2e1d1 Fri Sep 18 14:34:02 2020 -0700
    Stagin gnomad pext track, refs #25869
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 28, context: html, text, full: html, text
    17748af09f0add98009e2c4c181cb4e75d068d26 Wed Sep 16 14:17:15 2020 -0700
    modified procedure to make a new style LRG transcript track refs #24672
• src/hg/makeDb/gnomad/buildPext.py
  • lines changed 171, context: html, text, full: html, text
    87d5b93cb522e7bfa4a66ae41f93e94394d2e1d1 Fri Sep 18 14:34:02 2020 -0700
    Stagin gnomad pext track, refs #25869
• src/hg/makeDb/outside/covid/covidHgiGwas.as
  • lines changed 7, context: html, text, full: html, text
    007a3bff22438077c95cf425e22877644704c23a Tue Sep 15 15:25:10 2020 -0700
    1. Size lollies based on #studies. 2. Display p-value in E notation (request from Juha). refs #26129
• src/hg/makeDb/outside/covid/makeCovidHgiGwas.pl
  • lines changed 11, context: html, text, full: html, text
    007a3bff22438077c95cf425e22877644704c23a Tue Sep 15 15:25:10 2020 -0700
    1. Size lollies based on #studies. 2. Display p-value in E notation (request from Juha). refs #26129
• src/hg/makeDb/schema/all.joiner
  • lines changed 2, context: html, text, full: html, text
    411acf92db70f5f7a8584cb3cad643b88d4aeabc Mon Sep 14 15:04:51 2020 -0700
    additional rules for canFam5 refs #25917
• src/hg/makeDb/trackDb/chicken/galGal6/refSeqComposite.ra
  • lines changed 1, context: html, text, full: html, text
    fb16f066927defaf0c6a29849717967572be916e Mon Sep 14 15:23:16 2020 -0700
    Sqashing stale pennantIcons, no RM
• src/hg/makeDb/trackDb/human/clinGen.html
  • lines changed 3, context: html, text, full: html, text
    eb302eb9bf4446136c7a81a9839688de53241206 Tue Sep 15 14:46:19 2020 -0700
    Staging new clinGen composite on beta, and touching up desc page refs #24818
  • lines changed 23, context: html, text, full: html, text
    a355c10495e00dfed6f7c7cc3294d7bc5f323efd Tue Sep 15 15:20:35 2020 -0700
    Removing mentions of the clinGen CNVs track since it was consolidated to clinVar refs #24818
  • lines changed 111, context: html, text, full: html, text
    14023d97345829f14154773c87712ed9550a0638 Wed Sep 16 08:17:42 2020 -0700
    added validity track descriptions refs #24818
  • lines changed 1, context: html, text, full: html, text
    12e8636480a0a6d0be0f116f8319a0a352fc2975 Wed Sep 16 08:28:37 2020 -0700
    added Lou to Credits refs #24818
  • lines changed 9, context: html, text, full: html, text
    149a70c694fe71916a96dda3afeb6139ea764d08 Thu Sep 17 09:00:05 2020 -0700
    Final touches to desc page, and adding new track pennantIcon refs #24818
• src/hg/makeDb/trackDb/human/covidHgiGwas.html
  • lines changed 26, context: html, text, full: html, text
    0506b5e5664de6618ba073285e0f9bc561c5e959 Tue Sep 15 01:57:52 2020 -0700
    improved desc page after covid19 HGI folks feedback refs #26129
  • lines changed 5, context: html, text, full: html, text
    021de8301f32cdd5576b80baa7db03a8edc8d60a Wed Sep 16 01:19:33 2020 -0700
    changed P value to p-value refs #26129
  • lines changed 28, context: html, text, full: html, text
    0bce97ce16cc532f8a1792925e299ff2f2e1828c Fri Sep 18 12:50:18 2020 -0700
    added methods to desc page refs #26129
• src/hg/makeDb/trackDb/human/covidHgiGwas.ra
  • lines changed 9, context: html, text, full: html, text
    ddcb89a9cfc669f8a951f944049780de47402df5 Tue Sep 15 15:26:31 2020 -0700
    1. Add size as lolly variable. 2. Add filter for minimum effect size (abs value). refs #26129
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    ca4516b7f5442f06d7eca5bffd7a82d18ef18a3b Wed Sep 16 11:18:35 2020 -0700
    Interim check-in for exploratory work with COVID GWAS V2 track (moving to branch). refs #26129
  • lines changed 7, context: html, text, full: html, text
    762d9c9e10aaf5b6d5ac094cd4dfca8ec3b8b39d Wed Sep 16 12:13:51 2020 -0700
    Back out lollySize feature (deferring to V2). refs #26219
  • lines changed 1, context: html, text, full: html, text
    d7b990f72921f805401313fe5356d758bab8f95d Wed Sep 16 12:21:00 2020 -0700
    Tweak default size. refs #26129
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
  • lines changed 388, context: html, text, full: html, text
    87d5b93cb522e7bfa4a66ae41f93e94394d2e1d1 Fri Sep 18 14:34:02 2020 -0700
    Stagin gnomad pext track, refs #25869
  • lines changed 54, context: html, text, full: html, text
    7ce8e94968132c39c86928db146df911bee20197 Fri Sep 18 15:16:58 2020 -0700
    Add colors to gnomad pext wiggles, refs #25869
  • lines changed 110, context: html, text, full: html, text
    a46e9028d7f1e1cad0d3cf0838e9dc3a1e28b64c Mon Sep 21 07:49:45 2020 -0700
    Making some requested changes to gnomad PEXT track, refs #25869
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    fb16f066927defaf0c6a29849717967572be916e Mon Sep 14 15:23:16 2020 -0700
    Sqashing stale pennantIcons, no RM
  • lines changed 6, context: html, text, full: html, text
    ca4516b7f5442f06d7eca5bffd7a82d18ef18a3b Wed Sep 16 11:18:35 2020 -0700
    Interim check-in for exploratory work with COVID GWAS V2 track (moving to branch). refs #26129
  • lines changed 5, context: html, text, full: html, text
    762d9c9e10aaf5b6d5ac094cd4dfca8ec3b8b39d Wed Sep 16 12:13:51 2020 -0700
    Back out lollySize feature (deferring to V2). refs #26219
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    ca4516b7f5442f06d7eca5bffd7a82d18ef18a3b Wed Sep 16 11:18:35 2020 -0700
    Interim check-in for exploratory work with COVID GWAS V2 track (moving to branch). refs #26129
  • lines changed 6, context: html, text, full: html, text
    762d9c9e10aaf5b6d5ac094cd4dfca8ec3b8b39d Wed Sep 16 12:13:51 2020 -0700
    Back out lollySize feature (deferring to V2). refs #26219
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV34.ra
  • lines changed 1, context: html, text, full: html, text
    fb16f066927defaf0c6a29849717967572be916e Mon Sep 14 15:23:16 2020 -0700
    Sqashing stale pennantIcons, no RM
• src/hg/makeDb/trackDb/human/trackDb.clinGen.ra
  • lines changed 23, context: html, text, full: html, text
    579d4220eec5e357b78dc0deb459db6d1858af20 Mon Sep 14 12:06:57 2020 -0700
    Add ClinGen Gene Disease validity track to new clingen composite, refs Ana email
  • lines changed 2, context: html, text, full: html, text
    fff5eb057ce25327a375aa653ebbfb4d77b032f7 Tue Sep 15 15:39:44 2020 -0700
    Warning that old clinGen track is outdated and fixing config visibility for new clingen, refs #24818
  • lines changed 1, context: html, text, full: html, text
    149a70c694fe71916a96dda3afeb6139ea764d08 Thu Sep 17 09:00:05 2020 -0700
    Final touches to desc page, and adding new track pennantIcon refs #24818
• src/hg/makeDb/trackDb/human/trackDb.gtex.ra
  • lines changed 1, context: html, text, full: html, text
    fb16f066927defaf0c6a29849717967572be916e Mon Sep 14 15:23:16 2020 -0700
    Sqashing stale pennantIcons, no RM
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    486c312a04bb6eaacc345af466b52304bc2fa516 Tue Sep 15 08:48:23 2020 -0700
    Change LOVD and DECIPHER release tags for testing on hgwbeta, refs #25841
  • lines changed 1, context: html, text, full: html, text
    eb302eb9bf4446136c7a81a9839688de53241206 Tue Sep 15 14:46:19 2020 -0700
    Staging new clinGen composite on beta, and touching up desc page refs #24818
  • lines changed 1, context: html, text, full: html, text
    fff5eb057ce25327a375aa653ebbfb4d77b032f7 Tue Sep 15 15:39:44 2020 -0700
    Warning that old clinGen track is outdated and fixing config visibility for new clingen, refs #24818
  • lines changed 26, context: html, text, full: html, text
    27e330737ba88fc3682f401974d8cab1b2fa841b Wed Sep 16 14:02:58 2020 -0700
    prototype for new style LRG Fixed Transcript Annotations refs #24672
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    2e4a8cbfa1318e57f930fd42f0efa84b49a27fec Wed Sep 16 16:49:43 2020 -0700
    Adding release tags #26129
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    3af218d47412cedb69a0cf92e6484f38c059a224 Thu Sep 17 08:29:29 2020 -0700
    Adding pennantIcon to no longer updated clinGen CNVs track refs #24818
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    7ec003fc7ae8f5bb327037388ac9ce1031286b01 Thu Sep 17 12:32:59 2020 -0700
    Making lovd long variants a bigBed 9 + so mergeSpannedItems works , refs #25841
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    1c4b864cb6c2799aadb8babc49c5dd1246199a05 Thu Sep 17 15:59:40 2020 -0700
    Fix mismatched search rules on decipher track. Track has release tags public but search rule still present on dev/beta, refs #25841
  • lines changed 3, context: html, text, full: html, text
    2631a6777054d51ebcaf26b5bccffc52e90fc047 Thu Sep 17 16:06:34 2020 -0700
    Rename decipher code paths to decipherOld for switch to bigBed, refs #25841
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    cf2be0080798ae72a1711a7affd0d5d06e10c719 Thu Sep 17 16:23:49 2020 -0700
    Woops forgot to also switch decipher bigBed search stanza release tags too
• src/hg/makeDb/trackDb/marmoset/calJac4/trackDb.ra
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    02b770de07c1c9f575406b32ea3ce241fbefaeb1 Thu Sep 17 11:21:35 2020 -0700
    now with NCBI RefSeq track refs #24074
• src/hg/makeDb/trackDb/seal/neoSch1/trackDb.ra
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    63491544e7dc3ee27e910ed05897f1610d1b8a0f Mon Sep 14 10:55:46 2020 -0700
    turn gap track to pack by default (young genome)
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 3, context: html, text, full: html, text
    5736c27ba84cabf7298c075d3eb915de415cb2a7 Wed Sep 16 14:05:37 2020 -0700
    prototype for new style LRG Fixed Transcript Annotations refs #24672
• src/hg/makeDb/trackDb/trackDb.encode3.ra
  • lines changed 1, context: html, text, full: html, text
    fb16f066927defaf0c6a29849717967572be916e Mon Sep 14 15:23:16 2020 -0700
    Sqashing stale pennantIcons, no RM
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    fb16f066927defaf0c6a29849717967572be916e Mon Sep 14 15:23:16 2020 -0700
    Sqashing stale pennantIcons, no RM
• src/hg/makeDb/trackDb/virus/wuhCor1/kim2020.ra
  • lines changed 1, context: html, text, full: html, text
    09f6433ede6b3c480074be38c12af7379c5eb268 Wed Sep 16 05:28:57 2020 -0700
    wuhCor1 kim shortlabel change, email from David, no redmine
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
  • lines changed 52, context: html, text, full: html, text
    907da4f0560c7ad75597a1111e6cf6e0cca042c4 Mon Sep 14 16:36:16 2020 -0700
    Updated dataVersion, pennantIcon and hapClusterMethod for all releases of sarsCov2Phylo (refs #26177)
• src/hg/utils/automation/doNcbiRefSeq.pl
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    531083fac3b99f775f940e7b124c88a0d41fc386 Thu Sep 17 11:20:04 2020 -0700
    recover function of local lift file when on db assembly refs #24074
• src/hg/utils/automation/parseLrgXml.pl
  • lines changed 28, context: html, text, full: html, text
    41ac5854aee6292610b1519e69d107116c8b9e22 Wed Sep 16 08:27:15 2020 -0700
    adding NCBI and Ensembl transcript and protein IDs to the genePred output refs #24672;
• src/hg/utils/otto/clinGen/checkClinGen.sh
  • lines changed 1, context: html, text, full: html, text
    579d4220eec5e357b78dc0deb459db6d1858af20 Mon Sep 14 12:06:57 2020 -0700
    Add ClinGen Gene Disease validity track to new clingen composite, refs Ana email
• src/hg/utils/otto/clinGen/makeGeneValidity.sh
  • lines changed 33, context: html, text, full: html, text
    579d4220eec5e357b78dc0deb459db6d1858af20 Mon Sep 14 12:06:57 2020 -0700
    Add ClinGen Gene Disease validity track to new clingen composite, refs Ana email
• src/hg/utils/otto/clinvar/clinVarToBed
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    70dea5ffaf352ada83e54b03aa0774bf515cbb65 Mon Sep 21 03:39:46 2020 -0700
    adding the Benet-Pages colorscheme to clinvar, fixing up the 'g.' names and auto-loading the clinvarSub table for Braney's new bigLolli clinvar submissions track. Also fixing the categorization of submissions. refs #25207, #25405 and emails with Chris/Braney.
• src/hg/utils/otto/lovd/checkAndLoad.sh
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    7ec003fc7ae8f5bb327037388ac9ce1031286b01 Thu Sep 17 12:32:59 2020 -0700
    Making lovd long variants a bigBed 9 + so mergeSpannedItems works , refs #25841
• src/hg/utils/otto/lovd/lovd.as
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    a08a57856cdee6e077684b0f8519a915e5fbdedd Mon Sep 21 07:53:05 2020 -0700
    Removing duplicated autoSql def for old version of lovd track, refs build email
• src/hg/utils/otto/lovd/lovd.long.as
  • lines changed 17, context: html, text, full: html, text
    7ec003fc7ae8f5bb327037388ac9ce1031286b01 Thu Sep 17 12:32:59 2020 -0700
    Making lovd long variants a bigBed 9 + so mergeSpannedItems works , refs #25841
• src/hg/utils/otto/lovd/lovd.short.as
  • lines changed 12, context: html, text, full: html, text
    7ec003fc7ae8f5bb327037388ac9ce1031286b01 Thu Sep 17 12:32:59 2020 -0700
    Making lovd long variants a bigBed 9 + so mergeSpannedItems works , refs #25841
• src/inc/linefile.h
  • lines changed 3, context: html, text, full: html, text
    7537b3246c147cc4d5de561cd8bed8014dbddf7b Thu Sep 17 01:59:41 2020 -0700
    Adding a hint to bedToBigBed when field count is not as expected. No redmine, just something that I keep forgetting myself and every Covid-track building student has asked about this until now.
• src/lib/linefile.c
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    7537b3246c147cc4d5de561cd8bed8014dbddf7b Thu Sep 17 01:59:41 2020 -0700
    Adding a hint to bedToBigBed when field count is not as expected. No redmine, just something that I keep forgetting myself and every Covid-track building student has asked about this until now.
• src/utils/bedToBigBed/bedToBigBed.c
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    7537b3246c147cc4d5de561cd8bed8014dbddf7b Thu Sep 17 01:59:41 2020 -0700
    Adding a hint to bedToBigBed when field count is not as expected. No redmine, just something that I keep forgetting myself and every Covid-track building student has asked about this until now.
• src/utils/qa/weeklybld/buildEnv.csh
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    b434602923e64c7dff8e1ef252b79da8c8a29675 Mon Sep 21 10:00:35 2020 -0700
    v405 preview1

• lines changed: 2308
• files changed: 82