All File Changes

v389_preview to v389_preview2 (2019-09-30 to 2019-10-07) v389

• src/hg/hgTrackUi/hgTrackUi.c
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    d76fc3bb23fc5e6082e3787cc7c26d1204f47c8e Thu Oct 3 12:14:29 2019 -0700
    Fix bug with bigNarrowPeak packability. refs #24249
• src/hg/hgTracks/bedTrack.c
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    11c964b7808489b442a7f1efbd7581a6bc3b685d Tue Oct 1 12:39:48 2019 -0700
    add "filtered" label for bigBed tracks that aren't bed12.
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    0f0590f5eb6254ddd039868aa5f09f60e44f64b9 Thu Oct 3 13:48:03 2019 -0700
    Append 'filter activated' notice to composites hiding empty subtracks. refs #23365
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    9275ee8d88f2f0b40c9331a2c5139b13f617421d Thu Oct 3 14:46:24 2019 -0700
    Fixes to filter activated labeling. refs #23365
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    56f851c10e07b46bb5c033f871aa7885743739b7 Thu Oct 3 15:33:01 2019 -0700
    Fix bug with bigNarrowPeak packability. refs #24249
• src/hg/hgTracks/bigBedTrack.c
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    d18b793186d29af399659630096721baefbb21b2 Thu Oct 3 09:54:59 2019 -0700
    make default score filters work on bigBeds
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    0f0590f5eb6254ddd039868aa5f09f60e44f64b9 Thu Oct 3 13:48:03 2019 -0700
    Append 'filter activated' notice to composites hiding empty subtracks. refs #23365
  • lines changed 8, context: html, text, full: html, text
    9275ee8d88f2f0b40c9331a2c5139b13f617421d Thu Oct 3 14:46:24 2019 -0700
    Fixes to filter activated labeling. refs #23365
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    56f851c10e07b46bb5c033f871aa7885743739b7 Thu Oct 3 15:33:01 2019 -0700
    Fix bug with bigNarrowPeak packability. refs #24249
• src/hg/hgTracks/hgTracks.c
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    41c714552893985429bfd6c988dd257046e8e6d3 Thu Oct 3 11:49:46 2019 -0700
    keep proper track of y coordinate in predraw routine #24247
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    d76fc3bb23fc5e6082e3787cc7c26d1204f47c8e Thu Oct 3 12:14:29 2019 -0700
    Fix bug with bigNarrowPeak packability. refs #24249
  • lines changed 8, context: html, text, full: html, text
    8954b57b721661b897012362dd8eb14452c9be01 Thu Oct 3 13:18:57 2019 -0700
    Add filter activated to composite track center labels. refs #24252
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    0f0590f5eb6254ddd039868aa5f09f60e44f64b9 Thu Oct 3 13:48:03 2019 -0700
    Append 'filter activated' notice to composites hiding empty subtracks. refs #23365
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    9275ee8d88f2f0b40c9331a2c5139b13f617421d Thu Oct 3 14:46:24 2019 -0700
    Fixes to filter activated labeling. refs #23365
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
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    d16f1d2a074202e1f33da56801c87d401a7de6ce Wed Oct 2 15:49:25 2019 -0700
    Linking searchable track hub guide to other docs #20881
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
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    d16f1d2a074202e1f33da56801c87d401a7de6ce Wed Oct 2 15:49:25 2019 -0700
    Linking searchable track hub guide to other docs #20881
• src/hg/htdocs/goldenPath/help/hubQuickStart.html
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    d16f1d2a074202e1f33da56801c87d401a7de6ce Wed Oct 2 15:49:25 2019 -0700
    Linking searchable track hub guide to other docs #20881
• src/hg/htdocs/goldenPath/help/hubQuickStartSearch.html
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    ee834122adef9f9a07a301ea536892b4232bfd8a Wed Oct 2 15:13:26 2019 -0700
    Making code review minor edits #24231
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
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    b568111cde4c11852f720e950f76a170101d84bd Wed Oct 2 09:57:19 2019 -0700
    Document new setting, hideEmptySubtracks. refs #23365
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    8c4619e50c1ca34fc534220c387658b7c35ff0af Thu Oct 3 09:11:24 2019 -0700
    Documenting three new Filters refs #20227
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    91b1afd308080b6da1f74653a777bcc65bdc5fb4 Thu Oct 3 12:18:58 2019 -0700
    Documenting three new Filter options for beds refs #20227
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    769e12f1ae87a1f6067cbae28b7005e059081424 Fri Oct 4 16:28:14 2019 -0700
    Further adding to trackDbDoc of the three new Filters refs #20227
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html
  • lines changed 5, context: html, text, full: html, text
    b568111cde4c11852f720e950f76a170101d84bd Wed Oct 2 09:57:19 2019 -0700
    Document new setting, hideEmptySubtracks. refs #23365
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    91b1afd308080b6da1f74653a777bcc65bdc5fb4 Thu Oct 3 12:18:58 2019 -0700
    Documenting three new Filter options for beds refs #20227
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 1, context: html, text, full: html, text
    dbfafcdbde09eb957c73db7064bb5bd5558ff2d8 Tue Oct 1 10:44:56 2019 -0700
    Fixing typo in barChartMaxSize documentation for #23691
  • lines changed 16, context: html, text, full: html, text
    b568111cde4c11852f720e950f76a170101d84bd Wed Oct 2 09:57:19 2019 -0700
    Document new setting, hideEmptySubtracks. refs #23365
  • lines changed 116, context: html, text, full: html, text
    8c4619e50c1ca34fc534220c387658b7c35ff0af Thu Oct 3 09:11:24 2019 -0700
    Documenting three new Filters refs #20227
  • lines changed 16, context: html, text, full: html, text
    91b1afd308080b6da1f74653a777bcc65bdc5fb4 Thu Oct 3 12:18:58 2019 -0700
    Documenting three new Filter options for beds refs #20227
  • lines changed 54, context: html, text, full: html, text
    769e12f1ae87a1f6067cbae28b7005e059081424 Fri Oct 4 16:28:14 2019 -0700
    Further adding to trackDbDoc of the three new Filters refs #20227
• src/hg/htdocs/goldenPath/help/trix.html
  • lines changed 6, context: html, text, full: html, text
    caba141a549362bfd5a24f8bf25a060b9595aa75 Wed Oct 2 16:01:03 2019 -0700
    Adding reference to searchable track hub #20881
• src/hg/htdocs/images/david_cluster.jpg
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    907aa2134408270dd89e30032e3a56abb7b37e69 Mon Sep 30 10:26:15 2019 -0700
    Adding more images for the history page, refs #20314
• src/hg/htdocs/images/genome_cd.jpg
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    907aa2134408270dd89e30032e3a56abb7b37e69 Mon Sep 30 10:26:15 2019 -0700
    Adding more images for the history page, refs #20314
• src/hg/htdocs/images/jim-in-garage.jpg
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    907aa2134408270dd89e30032e3a56abb7b37e69 Mon Sep 30 10:26:15 2019 -0700
    Adding more images for the history page, refs #20314
• src/hg/htdocs/training/index.html
  • lines changed 1, context: html, text, full: html, text
    30e3f9c5f7ffcea306902f61cfa96809a8ebddb0 Mon Sep 30 10:02:33 2019 -0700
    updated link to rotterdam workshop
• src/hg/inc/bigDbSnp.h
  • lines changed 104, context: html, text, full: html, text
    b7cb97d2942575d92f6385055e172dcbd979ee05 Tue Oct 1 13:09:29 2019 -0700
    Adding new data type bigDbSnp.as with associated dbSnpDetails.as, for a track based on the new "dbSNP 2.0" schema and JSON downloads. refs #23283
• src/hg/inc/dbSnpDetails.h
  • lines changed 71, context: html, text, full: html, text
    b7cb97d2942575d92f6385055e172dcbd979ee05 Tue Oct 1 13:09:29 2019 -0700
    Adding new data type bigDbSnp.as with associated dbSnpDetails.as, for a track based on the new "dbSNP 2.0" schema and JSON downloads. refs #23283
• src/hg/inc/hui.h
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    b63cfe435df3906e0638a0ce70d71bae530767d3 Tue Oct 1 12:37:14 2019 -0700
    More memorable name. refs #23365
• src/hg/inc/trackDb.h
  • lines changed 4, context: html, text, full: html, text
    9275ee8d88f2f0b40c9331a2c5139b13f617421d Thu Oct 3 14:46:24 2019 -0700
    Fixes to filter activated labeling. refs #23365
• src/hg/lib/bigDbSnp.as
  • lines changed 21, context: html, text, full: html, text
    b7cb97d2942575d92f6385055e172dcbd979ee05 Tue Oct 1 13:09:29 2019 -0700
    Adding new data type bigDbSnp.as with associated dbSnpDetails.as, for a track based on the new "dbSNP 2.0" schema and JSON downloads. refs #23283
• src/hg/lib/bigDbSnp.c
  • lines changed 299, context: html, text, full: html, text
    b7cb97d2942575d92f6385055e172dcbd979ee05 Tue Oct 1 13:09:29 2019 -0700
    Adding new data type bigDbSnp.as with associated dbSnpDetails.as, for a track based on the new "dbSNP 2.0" schema and JSON downloads. refs #23283
• src/hg/lib/dbSnpDetails.as
  • lines changed 17, context: html, text, full: html, text
    b7cb97d2942575d92f6385055e172dcbd979ee05 Tue Oct 1 13:09:29 2019 -0700
    Adding new data type bigDbSnp.as with associated dbSnpDetails.as, for a track based on the new "dbSNP 2.0" schema and JSON downloads. refs #23283
• src/hg/lib/dbSnpDetails.c
  • lines changed 346, context: html, text, full: html, text
    b7cb97d2942575d92f6385055e172dcbd979ee05 Tue Oct 1 13:09:29 2019 -0700
    Adding new data type bigDbSnp.as with associated dbSnpDetails.as, for a track based on the new "dbSNP 2.0" schema and JSON downloads. refs #23283
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    550fe72fc67d9683003817fa862edb530d757c2b Tue Oct 1 11:46:06 2019 -0700
    fix bug in number filtering when float is specified in tdb, but the actual field is an integer
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    b63cfe435df3906e0638a0ce70d71bae530767d3 Tue Oct 1 12:37:14 2019 -0700
    More memorable name. refs #23365
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    bc4a273280414037d4428364d577928261d2c234 Tue Oct 1 14:17:33 2019 -0700
    Fix hideEmptySubtracks checkbox init. refs #23365
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    c53b02b2abf43cd974ffbfb7a6a9dd9f1d8bb32a Tue Oct 1 14:33:49 2019 -0700
    Fixing path issue noted in code review (tnx Angie!). refs #23365
• src/hg/lib/makefile
  • lines changed 2, context: html, text, full: html, text
    b7cb97d2942575d92f6385055e172dcbd979ee05 Tue Oct 1 13:09:29 2019 -0700
    Adding new data type bigDbSnp.as with associated dbSnpDetails.as, for a track based on the new "dbSNP 2.0" schema and JSON downloads. refs #23283
• src/hg/lib/trackDbCustom.c
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    9275ee8d88f2f0b40c9331a2c5139b13f617421d Thu Oct 3 14:46:24 2019 -0700
    Fixes to filter activated labeling. refs #23365
• src/hg/makeDb/doc/bigDbSnp.txt
  • lines changed 279, context: html, text, full: html, text
    122806164798753fbfbce3cc77411c911a4d9d1e Tue Oct 1 13:15:36 2019 -0700
    Adding automation script doBigDbSnp.pl that downloads dbSNP JSON files, does a cluster run of dbSnpJsonToTab, aggregates results, runs checkBigDbSnp & installs track files. refs #23283
• src/hg/makeDb/doc/hg19.txt
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    a8a5aadd1e6a8d5faf9625f4b51ab4bbc5134000 Tue Oct 1 12:10:54 2019 -0700
    import of gencode V32lift37 release
• src/hg/makeDb/doc/hg38/gencode.txt
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    46a0545522c321cc4774ae6e1fdafcefefaa03b9 Thu Sep 26 11:46:39 2019 -0700
    import of GENCODE VM23
• src/hg/makeDb/doc/mm10.txt
  • lines changed 20, context: html, text, full: html, text
    46a0545522c321cc4774ae6e1fdafcefefaa03b9 Thu Sep 26 11:46:39 2019 -0700
    import of GENCODE VM23
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    1501c6b2ee52ef133b74150ebb88ced8e65ca50a Thu Sep 26 11:46:55 2019 -0700
    import of GENCODE VM23
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
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    46a0545522c321cc4774ae6e1fdafcefefaa03b9 Thu Sep 26 11:46:39 2019 -0700
    import of GENCODE VM23
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    a8a5aadd1e6a8d5faf9625f4b51ab4bbc5134000 Tue Oct 1 12:10:54 2019 -0700
    import of gencode V32lift37 release
• src/hg/makeDb/trackDb/human/geneHancer.html
  • lines changed 1, context: html, text, full: html, text
    7324d595d6a645c91238b9ab40c752eb8272660c Mon Sep 30 11:32:15 2019 -0700
    Making some changes from CR refs #24232
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    012c668d540195a35f0171307648355d1837833d Tue Oct 1 08:34:13 2019 -0700
    Removing crispr10k.ra mention from both hg19 & hg38 trackDb.ra files, refs #24172
• src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.html
  • lines changed 92, context: html, text, full: html, text
    863fdfb6a101ce9fef7df1cc7d71e0bada997d7d Fri Oct 4 16:12:51 2019 -0700
    Adding sections that were on the current GENCODE track from the live server to the alpha version. Adding GENCODE v32 stats from the GENCODE website. refs #24032
• src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra
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    d9146ad7adce0c2ecc23c7b2256b430ed82cf995 Fri Oct 4 16:18:38 2019 -0700
    Adding missing pennantIcon, refs #24032
• src/hg/makeDb/trackDb/human/hg38/knownGeneOld11.html
  • lines changed 25, context: html, text, full: html, text
    738a6aaab01eb7052e70d0e057f73b399d3035e7 Fri Oct 4 11:29:57 2019 -0700
    Creating an HTML page for the Old UCSC Genes track, refs #24032
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    14b7b1f68d52489ba38bfae62ad7bc78f29e78bf Mon Sep 30 11:25:09 2019 -0700
    Staging the GENCODE V32 track on hgwbeta for hg38, refs #24032
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    012c668d540195a35f0171307648355d1837833d Tue Oct 1 08:34:13 2019 -0700
    Removing crispr10k.ra mention from both hg19 & hg38 trackDb.ra files, refs #24172
• src/hg/makeDb/trackDb/human/mastermind.html
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    7324d595d6a645c91238b9ab40c752eb8272660c Mon Sep 30 11:32:15 2019 -0700
    Making some changes from CR refs #24232
• src/hg/makeDb/trackDb/human/trackDb.geneHancer.ra
  • lines changed 4, context: html, text, full: html, text
    020977dd4affb45bfc6e22c6f500f3cafcaec7ef Tue Oct 1 15:01:55 2019 -0700
    Removing release tags for interact multi-region #24037
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    c7a70c4c3c4cab2845a2f695c81808936107fa0b Tue Oct 1 15:07:05 2019 -0700
    Removing redundant stanzas for interact multi-region #24037
• src/hg/makeDb/trackDb/mouse/mm10/encode3.atac.ra
  • lines changed 1, context: html, text, full: html, text
    f89032d77a5b5cc8bc294f2ee243bc65c38bf637 Tue Oct 1 12:36:11 2019 -0700
    Keeping tracks working while filtering morphs. refs #20227
• src/hg/makeDb/trackDb/mouse/mm10/encode3.histone.ra
  • lines changed 1, context: html, text, full: html, text
    f89032d77a5b5cc8bc294f2ee243bc65c38bf637 Tue Oct 1 12:36:11 2019 -0700
    Keeping tracks working while filtering morphs. refs #20227
• src/hg/makeDb/trackDb/mouse/mm10/knownGene.html
  • lines changed 8, context: html, text, full: html, text
    40f3ee310fb276c164e39e623728ef65dbec6dc9 Tue Oct 1 11:49:44 2019 -0700
    Updating mm10 knownGene.html for the Gencode VM23 release, refs #24212
• src/hg/makeDb/trackDb/mouse/mm10/tabulamuris.ra
  • lines changed 2, context: html, text, full: html, text
    7c67b000f11cde0d57ad1b254c69af89fc723ce6 Fri Oct 4 08:54:23 2019 -0700
    adding link to cell browser to track, refs #21811
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    beabeca271240569ab12c46e2037c47fe19e353e Fri Oct 4 09:01:57 2019 -0700
    tiny trackDb change, refs #21811
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    159898c8ba688b6181d0bb605716e7e0efb12bfa Fri Oct 4 09:03:52 2019 -0700
    Adding a colon to match the style of the other entries on the details page. refs #21811
• src/hg/pyLib/README.txt
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    e09b1b1dd5e9076155458418fc7161e3022690f1 Wed Oct 2 02:07:21 2019 -0700
    adding six to hgLib, refs #24240
• src/hg/pyLib/hgLib.py
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    e09b1b1dd5e9076155458418fc7161e3022690f1 Wed Oct 2 02:07:21 2019 -0700
    adding six to hgLib, refs #24240
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    a0eb070b36159223730af9309b35fbd3276733db Wed Oct 2 02:15:53 2019 -0700
    adding note about changed mysql library name, refs #24240
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    8b7d72a4470ec289780af7db00a364ba48b465b4 Wed Oct 2 02:17:18 2019 -0700
    avoiding line-length Kate comments, refs #24240
• src/hg/pyLib/makefile
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    e09b1b1dd5e9076155458418fc7161e3022690f1 Wed Oct 2 02:07:21 2019 -0700
    adding six to hgLib, refs #24240
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    aa9af906b6454f2787b0ae8a575b9e09b15b1fc8 Fri Oct 4 06:17:53 2019 -0700
    fixing build error
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    785577ea47d821c99b8baf55dbacbf365998d506 Fri Oct 4 09:15:09 2019 -0700
    fix copy paste error for alpha target
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    98e7759054399cd537317fbbc4338974063df3de Sat Oct 5 07:49:32 2019 -0700
    try this again... remove all the files we're copying into place
• src/hg/pyLib/six.py
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    e09b1b1dd5e9076155458418fc7161e3022690f1 Wed Oct 2 02:07:21 2019 -0700
    adding six to hgLib, refs #24240
• src/hg/snp/checkBigDbSnp/checkBigDbSnp.c
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    428a47dfc975f02f3c3a97b3273d7b95f9789ff4 Tue Oct 1 13:12:08 2019 -0700
    New util dbSnpJsonToTab converts JSON to bigDbSnp and dbSnpDetails files; checkBigDbSnp flags clustering anomalies. refs #23283
• src/hg/snp/checkBigDbSnp/makefile
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    428a47dfc975f02f3c3a97b3273d7b95f9789ff4 Tue Oct 1 13:12:08 2019 -0700
    New util dbSnpJsonToTab converts JSON to bigDbSnp and dbSnpDetails files; checkBigDbSnp flags clustering anomalies. refs #23283
• src/hg/snp/dbSnpJsonToTab/dbSnpJsonToTab.c
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    428a47dfc975f02f3c3a97b3273d7b95f9789ff4 Tue Oct 1 13:12:08 2019 -0700
    New util dbSnpJsonToTab converts JSON to bigDbSnp and dbSnpDetails files; checkBigDbSnp flags clustering anomalies. refs #23283
• src/hg/snp/dbSnpJsonToTab/makefile
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    428a47dfc975f02f3c3a97b3273d7b95f9789ff4 Tue Oct 1 13:12:08 2019 -0700
    New util dbSnpJsonToTab converts JSON to bigDbSnp and dbSnpDetails files; checkBigDbSnp flags clustering anomalies. refs #23283
• src/hg/snp/makefile
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    428a47dfc975f02f3c3a97b3273d7b95f9789ff4 Tue Oct 1 13:12:08 2019 -0700
    New util dbSnpJsonToTab converts JSON to bigDbSnp and dbSnpDetails files; checkBigDbSnp flags clustering anomalies. refs #23283
• src/hg/utils/automation/doBigDbSnp.pl
  • lines changed 644, context: html, text, full: html, text
    122806164798753fbfbce3cc77411c911a4d9d1e Tue Oct 1 13:15:36 2019 -0700
    Adding automation script doBigDbSnp.pl that downloads dbSNP JSON files, does a cluster run of dbSnpJsonToTab, aggregates results, runs checkBigDbSnp & installs track files. refs #23283
• src/hg/utils/hubCheck/hubCheck.c
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    082f54ce901345c6d0edd9992395acde932d642c Mon Sep 30 16:14:15 2019 -0700
    Fixing typo in hubCheck output, found by Lou
• src/utils/qa/weeklybld/buildEnv.csh
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    4f313e0914f40474a7bbd7be12fa5b725fe07dce Mon Oct 7 10:04:33 2019 -0700
    v389 preview2, refs #24238

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• files changed: 88