All File Changes

v400_preview to v400_preview2 (2020-06-08 to 2020-06-15) v400

• confs/asia.hg.conf
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    a3f43d53cd55a8142087339f0294248e2932ab13 Sun Jun 14 01:11:40 2020 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
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    a3f43d53cd55a8142087339f0294248e2932ab13 Sun Jun 14 01:11:40 2020 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 1, context: html, text, full: html, text
    a3f43d53cd55a8142087339f0294248e2932ab13 Sun Jun 14 01:11:40 2020 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 6, context: html, text, full: html, text
    cdebb4d04806710cd984f9501568d724a1b8e601 Thu Jun 11 09:58:03 2020 -0700
    Handle missing description page. refs #24948
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    ea1f7873f7fbb38c2acfce40982d5dd88e5d2478 Thu Jun 11 05:23:11 2020 -0700
    making autocomplete click the go button immediately, refs #25703
• src/hg/hgc/gencodeClick.c
  • lines changed 9, context: html, text, full: html, text
    fcdf5c401c80840d28c346409c4fbb527544fac7 Tue Jun 9 13:59:33 2020 -0700
    make gencode hgc robust against metadata that is sometimes not mapped in the backmap releases
• src/hg/htdocs/goldenPath/help/geneSearchBox.html
  • lines changed 9, context: html, text, full: html, text
    26e6a4bf36de8ad6b82e737daac654077721a7cb Thu Jun 11 10:49:55 2020 -0700
    Documenting auto-complete click suggestion feature ref #25703
• src/hg/htdocs/goldenPath/help/hubQuickStartSearch.html
  • lines changed 9, context: html, text, full: html, text
    0336ab0d15416a66c9eece5091e726c381d55c53 Fri Jun 12 15:53:55 2020 -0700
    Fixing doc No RM
• src/hg/htdocs/goldenPath/help/query.html
  • lines changed 9, context: html, text, full: html, text
    26e6a4bf36de8ad6b82e737daac654077721a7cb Thu Jun 11 10:49:55 2020 -0700
    Documenting auto-complete click suggestion feature ref #25703
• src/hg/htdocs/goldenPath/help/trackDbIndexBb.html
  • lines changed 50, context: html, text, full: html, text
    3a5356e5e0d64e331f9639b86b712506f58e251d Mon Jun 8 17:33:44 2020 -0700
    Making changes in response to CR, refs #25695
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 1, context: html, text, full: html, text
    3a5356e5e0d64e331f9639b86b712506f58e251d Mon Jun 8 17:33:44 2020 -0700
    Making changes in response to CR, refs #25695
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    7fef04a14e3f37e2be923d3c885c585d321aa52b Fri Jun 12 14:33:05 2020 -0700
    Removing hg19 from the MANE announcement at the request of EBI/NCBI refs #24787
• src/hg/htdocs/inc/gbFooter.html
  • lines changed 1, context: html, text, full: html, text
    e6b82252f0bad705e635ab97bdce5769b537e78b Wed Jun 10 11:14:25 2020 -0700
    updating data of copyright statement
• src/hg/htdocs/inc/gbFooterHardcoded.html
  • lines changed 1, context: html, text, full: html, text
    e6b82252f0bad705e635ab97bdce5769b537e78b Wed Jun 10 11:14:25 2020 -0700
    updating data of copyright statement
• src/hg/htdocs/inc/gbsFooter.html
  • lines changed 1, context: html, text, full: html, text
    e6b82252f0bad705e635ab97bdce5769b537e78b Wed Jun 10 11:14:25 2020 -0700
    updating data of copyright statement
• src/hg/htdocs/inc/jWestFooter.html
  • lines changed 1, context: html, text, full: html, text
    e6b82252f0bad705e635ab97bdce5769b537e78b Wed Jun 10 11:14:25 2020 -0700
    updating data of copyright statement
• src/hg/js/hgTracks.js
  • lines changed 2, context: html, text, full: html, text
    ea1f7873f7fbb38c2acfce40982d5dd88e5d2478 Thu Jun 11 05:23:11 2020 -0700
    making autocomplete click the go button immediately, refs #25703
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    c8fe24dffc3894a4832016750093533c68ca8388 Thu Jun 11 10:45:29 2020 -0700
    Fix for trackUi crash when obsolete setting, dividers, is used improperly. Public hub Cotney tack rep_cf_segments had this issue. refs #25713
• src/hg/makeDb/doc/codisHub/codis.html
  • lines changed 129, context: html, text, full: html, text
    c3410576391423b865b4014a849c8dfc7c25bea0 Tue Jun 9 13:42:14 2020 -0700
    files for Codis hub and sessions refs #21399
• src/hg/makeDb/doc/codisHub/codisMarkers.bb
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    c3410576391423b865b4014a849c8dfc7c25bea0 Tue Jun 9 13:42:14 2020 -0700
    files for Codis hub and sessions refs #21399
• src/hg/makeDb/doc/codisHub/codisMarkers.bed
  • lines changed 22, context: html, text, full: html, text
    c3410576391423b865b4014a849c8dfc7c25bea0 Tue Jun 9 13:42:14 2020 -0700
    files for Codis hub and sessions refs #21399
• src/hg/makeDb/doc/codisHub/codisPrimers.bb
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    c3410576391423b865b4014a849c8dfc7c25bea0 Tue Jun 9 13:42:14 2020 -0700
    files for Codis hub and sessions refs #21399
• src/hg/makeDb/doc/codisHub/codisPrimers.bed
  • lines changed 53, context: html, text, full: html, text
    c3410576391423b865b4014a849c8dfc7c25bea0 Tue Jun 9 13:42:14 2020 -0700
    files for Codis hub and sessions refs #21399
• src/hg/makeDb/doc/codisHub/codisRepeats.bb
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    c3410576391423b865b4014a849c8dfc7c25bea0 Tue Jun 9 13:42:14 2020 -0700
    files for Codis hub and sessions refs #21399
• src/hg/makeDb/doc/codisHub/codisRepeats.bed
  • lines changed 477, context: html, text, full: html, text
    c3410576391423b865b4014a849c8dfc7c25bea0 Tue Jun 9 13:42:14 2020 -0700
    files for Codis hub and sessions refs #21399
• src/hg/makeDb/doc/codisHub/hubComposite.txt
  • lines changed 55, context: html, text, full: html, text
    c3410576391423b865b4014a849c8dfc7c25bea0 Tue Jun 9 13:42:14 2020 -0700
    files for Codis hub and sessions refs #21399
• src/hg/makeDb/doc/codisHub/primerRange.bb
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    c3410576391423b865b4014a849c8dfc7c25bea0 Tue Jun 9 13:42:14 2020 -0700
    files for Codis hub and sessions refs #21399
• src/hg/makeDb/doc/codisHub/primerRange.bed
  • lines changed 22, context: html, text, full: html, text
    c3410576391423b865b4014a849c8dfc7c25bea0 Tue Jun 9 13:42:14 2020 -0700
    files for Codis hub and sessions refs #21399
• src/hg/makeDb/doc/hg19.gencode.txt
  • lines changed 29, context: html, text, full: html, text
    fcdf5c401c80840d28c346409c4fbb527544fac7 Tue Jun 9 13:59:33 2020 -0700
    make gencode hgc robust against metadata that is sometimes not mapped in the backmap releases
• src/hg/makeDb/doc/hg38/gencode.txt
  • lines changed 34, context: html, text, full: html, text
    938e268e16bbcd34a1c98b98919df7d9869f588b Fri Jun 5 18:57:32 2020 -0700
    imported GENCODE V35 pre-release
• src/hg/makeDb/doc/panPan3/initialBuild.txt
  • lines changed 1054, context: html, text, full: html, text
    4b6cb56f6b3515084b0e04b184e2e27d99114cba Fri Jun 12 10:35:43 2020 -0700
    beginning panPan3 build refs #25720
  • lines changed 46, context: html, text, full: html, text
    c5dc7044d76420830c68a063b195599f655e8e5d Fri Jun 12 12:03:39 2020 -0700
    running repeat masker refs #25720
  • lines changed 232, context: html, text, full: html, text
    812466da062023d89e3a27b7b3bb8e4413be46c5 Mon Jun 15 09:25:21 2020 -0700
    continuing build after masking done refs #25720
• src/hg/makeDb/doc/wuhCor1/kimIvtCov.txt
  • lines changed 7, context: html, text, full: html, text
    05173ea10950d4e314d3cb7131121a94356fcda2 Thu Jun 11 06:34:46 2020 -0700
    adding Kim 2020 IVT cov tracks, refs #25708
  • lines changed 7, context: html, text, full: html, text
    52e2d7f833d8e1e27abce67b1535a423176427cd Fri Jun 12 05:08:48 2020 -0700
    updating makedoc for kim cov tracks, refs #25708
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    149b7811896b9a06abbd2765db41e772bdba113c Mon Jun 15 09:24:31 2020 -0700
    Added panPan3 - bonobo refs #25720
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 17, context: html, text, full: html, text
    f439762a10b2c2aa841b2550c484469364f2ec31 Mon Jun 15 09:23:27 2020 -0700
    Added panPan3 bonobo; refs #25720
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 2, context: html, text, full: html, text
    149b7811896b9a06abbd2765db41e772bdba113c Mon Jun 15 09:24:31 2020 -0700
    Added panPan3 - bonobo refs #25720
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 10, context: html, text, full: html, text
    938e268e16bbcd34a1c98b98919df7d9869f588b Fri Jun 5 18:57:32 2020 -0700
    imported GENCODE V35 pre-release
  • lines changed 9, context: html, text, full: html, text
    fcdf5c401c80840d28c346409c4fbb527544fac7 Tue Jun 9 13:59:33 2020 -0700
    make gencode hgc robust against metadata that is sometimes not mapped in the backmap releases
• src/hg/makeDb/schema/all.joiner
  • lines changed 96, context: html, text, full: html, text
    938e268e16bbcd34a1c98b98919df7d9869f588b Fri Jun 5 18:57:32 2020 -0700
    imported GENCODE V35 pre-release
  • lines changed 92, context: html, text, full: html, text
    fcdf5c401c80840d28c346409c4fbb527544fac7 Tue Jun 9 13:59:33 2020 -0700
    make gencode hgc robust against metadata that is sometimes not mapped in the backmap releases
• src/hg/makeDb/trackDb/bonobo/panPan3/description.html
  • lines changed 64, context: html, text, full: html, text
    d56a04cc5955922be29a8cb71e82a1efb09eedfb Fri Jun 12 11:27:39 2020 -0700
    adding panPan3 to the build refs #25720
• src/hg/makeDb/trackDb/bonobo/panPan3/gap.html
  • lines changed 31, context: html, text, full: html, text
    d56a04cc5955922be29a8cb71e82a1efb09eedfb Fri Jun 12 11:27:39 2020 -0700
    adding panPan3 to the build refs #25720
• src/hg/makeDb/trackDb/bonobo/panPan3/gold.html
  • lines changed 34, context: html, text, full: html, text
    d56a04cc5955922be29a8cb71e82a1efb09eedfb Fri Jun 12 11:27:39 2020 -0700
    adding panPan3 to the build refs #25720
• src/hg/makeDb/trackDb/bonobo/panPan3/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    d56a04cc5955922be29a8cb71e82a1efb09eedfb Fri Jun 12 11:27:39 2020 -0700
    adding panPan3 to the build refs #25720
  • lines changed 7, context: html, text, full: html, text
    c9ee6ffe7ecbb5b6e673b590859b45db0d76cd1e Sat Jun 13 14:59:56 2020 -0700
    with proper search specs for assembly track and turn on NCBI RefSeq gene track refs #25720
• src/hg/makeDb/trackDb/human/clinGen.html
  • lines changed 124, context: html, text, full: html, text
    88f8aab41e092f1ee56d50cc7743281bbca5f6b7 Tue Jun 9 15:36:54 2020 -0700
    added description pages to new ClinGen tracks refs #24817
• src/hg/makeDb/trackDb/human/clinGenDosage.html
  • lines changed 133, context: html, text, full: html, text
    88f8aab41e092f1ee56d50cc7743281bbca5f6b7 Tue Jun 9 15:36:54 2020 -0700
    added description pages to new ClinGen tracks refs #24817
• src/hg/makeDb/trackDb/human/clinGenSv.html
  • lines changed 104, context: html, text, full: html, text
    88f8aab41e092f1ee56d50cc7743281bbca5f6b7 Tue Jun 9 15:36:54 2020 -0700
    added description pages to new ClinGen tracks refs #24817
  • lines changed 1, context: html, text, full: html, text
    ed2cdfc5f35ab5b5636cfacb8777ea1839e05dc2 Tue Jun 9 15:47:40 2020 -0700
    corrected red color sentence refs #24817
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    fcdf5c401c80840d28c346409c4fbb527544fac7 Tue Jun 9 13:59:33 2020 -0700
    make gencode hgc robust against metadata that is sometimes not mapped in the backmap releases
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
  • lines changed 28, context: html, text, full: html, text
    76bc1fdc2a3fffef076de17e4ba7b11ee06feb7d Tue Jun 9 15:14:20 2020 -0700
    Changing gnomAD trackDb release tags to allow new linkouts to gnomAD site, CGI release change that went out in v399 refs #25600
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 15, context: html, text, full: html, text
    76bc1fdc2a3fffef076de17e4ba7b11ee06feb7d Tue Jun 9 15:14:20 2020 -0700
    Changing gnomAD trackDb release tags to allow new linkouts to gnomAD site, CGI release change that went out in v399 refs #25600
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
  • lines changed 4, context: html, text, full: html, text
    fcdf5c401c80840d28c346409c4fbb527544fac7 Tue Jun 9 13:59:33 2020 -0700
    make gencode hgc robust against metadata that is sometimes not mapped in the backmap releases
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV35lift37.html
  • lines changed 32, context: html, text, full: html, text
    fcdf5c401c80840d28c346409c4fbb527544fac7 Tue Jun 9 13:59:33 2020 -0700
    make gencode hgc robust against metadata that is sometimes not mapped in the backmap releases
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV35lift37.ra
  • lines changed 224, context: html, text, full: html, text
    fcdf5c401c80840d28c346409c4fbb527544fac7 Tue Jun 9 13:59:33 2020 -0700
    make gencode hgc robust against metadata that is sometimes not mapped in the backmap releases
• src/hg/makeDb/trackDb/human/hg38/encodeCcreCombined.html
  • lines changed 1, context: html, text, full: html, text
    7d70f159eac27e53b4d8fbeb3b1458b198b4c670 Sun Jun 14 19:34:35 2020 -0700
    Fix HTML syntax err. refs #24668
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 16, context: html, text, full: html, text
    76bc1fdc2a3fffef076de17e4ba7b11ee06feb7d Tue Jun 9 15:14:20 2020 -0700
    Changing gnomAD trackDb release tags to allow new linkouts to gnomAD site, CGI release change that went out in v399 refs #25600
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeSuper.html
  • lines changed 4, context: html, text, full: html, text
    938e268e16bbcd34a1c98b98919df7d9869f588b Fri Jun 5 18:57:32 2020 -0700
    imported GENCODE V35 pre-release
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV35.html
  • lines changed 47, context: html, text, full: html, text
    938e268e16bbcd34a1c98b98919df7d9869f588b Fri Jun 5 18:57:32 2020 -0700
    imported GENCODE V35 pre-release
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV35.ra
  • lines changed 286, context: html, text, full: html, text
    938e268e16bbcd34a1c98b98919df7d9869f588b Fri Jun 5 18:57:32 2020 -0700
    imported GENCODE V35 pre-release
• src/hg/makeDb/trackDb/human/trackDb.clinGen.ra
  • lines changed 3, context: html, text, full: html, text
    ea4c7a498b1828d64c1448a36c42abb7197c73f0 Tue Jun 9 15:28:28 2020 -0700
    added html to tracks refs #24817
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    d56a04cc5955922be29a8cb71e82a1efb09eedfb Fri Jun 12 11:27:39 2020 -0700
    adding panPan3 to the build refs #25720
• src/hg/makeDb/trackDb/trackDb.encode3.ra
  • lines changed 1, context: html, text, full: html, text
    869a56849c5d3d8f55f21b3cc623270442253135 Mon Jun 8 16:58:16 2020 -0700
    Adding the beta release tag, refs #24668
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    702f35fab84c9ddeae96f12da148f743e8af36da Thu Jun 11 13:50:54 2020 -0700
    Removing the release tags for the ENCODE cCREs track, refs #24668
• src/hg/makeDb/trackDb/virus/wuhCor1/epitopes.html
  • lines changed 4, context: html, text, full: html, text
    2de553b6fa6627cc9fa31f5f0ef7b72f3fc06a76 Mon Jun 8 10:08:47 2020 -0700
    add statement about the color range in the display refs #25295
• src/hg/makeDb/trackDb/virus/wuhCor1/kim2020.ra
  • lines changed 11, context: html, text, full: html, text
    05173ea10950d4e314d3cb7131121a94356fcda2 Thu Jun 11 06:34:46 2020 -0700
    adding Kim 2020 IVT cov tracks, refs #25708
• src/hg/makeDb/trackDb/virus/wuhCor1/kimIvtCov.html
  • lines changed 37, context: html, text, full: html, text
    05173ea10950d4e314d3cb7131121a94356fcda2 Thu Jun 11 06:34:46 2020 -0700
    adding Kim 2020 IVT cov tracks, refs #25708
• src/hg/pslStats/pslStats.c
  • lines changed 9, context: html, text, full: html, text
    2ffab4396193a716178dbf8b75c36633607d0bcb Sun Jun 14 14:38:26 2020 -0700
    fixed typo in header
• src/hg/pslStats/tests/expected/cdna2cdnaOverallTest.stats
  • lines changed 1, context: html, text, full: html, text
    2ffab4396193a716178dbf8b75c36633607d0bcb Sun Jun 14 14:38:26 2020 -0700
    fixed typo in header
• src/hg/pslStats/tests/expected/cdna2cdnaQueryTest.stats
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    2ffab4396193a716178dbf8b75c36633607d0bcb Sun Jun 14 14:38:26 2020 -0700
    fixed typo in header
• src/hg/pslStats/tests/expected/untransOverallTest.stats
  • lines changed 1, context: html, text, full: html, text
    2ffab4396193a716178dbf8b75c36633607d0bcb Sun Jun 14 14:38:26 2020 -0700
    fixed typo in header
• src/hg/pslStats/tests/expected/untransOverallUnalnTest.stats
  • lines changed 1, context: html, text, full: html, text
    2ffab4396193a716178dbf8b75c36633607d0bcb Sun Jun 14 14:38:26 2020 -0700
    fixed typo in header
• src/hg/pslStats/tests/expected/untransQueryTest.stats
  • lines changed 1, context: html, text, full: html, text
    2ffab4396193a716178dbf8b75c36633607d0bcb Sun Jun 14 14:38:26 2020 -0700
    fixed typo in header
• src/hg/pslStats/tests/expected/untransQueryUnalnTest.stats
  • lines changed 1, context: html, text, full: html, text
    2ffab4396193a716178dbf8b75c36633607d0bcb Sun Jun 14 14:38:26 2020 -0700
    fixed typo in header
• src/hg/utils/automation/doRepeatMasker.pl
  • lines changed 2, context: html, text, full: html, text
    85c0a7c33e839c9f6226dbcca902253df97692e5 Fri Jun 12 11:37:40 2020 -0700
    better method of getting the version of RM recommended per MarkDrefs #25720
• src/hg/utils/automation/makeGenomeDb.pl
  • lines changed 2, context: html, text, full: html, text
    94d9d0495ac3ff8446552a7ee48cf7bfd889be3d Fri Jun 12 11:04:38 2020 -0700
    catching up trackDb source tree files refs #25720
• src/lib/dlist.c
  • lines changed 10, context: html, text, full: html, text
    8e6806e280ba9ad2d95f6a33829aa7df6f8f5a24 Sat Jun 13 02:32:07 2020 -0700
    Adding Clang pragma to disable optimization only for function dlSort() in dlist.c so that BLAT on mac will give the same output as it does on linux. refs #25700
• src/utils/qa/weeklybld/buildEnv.csh
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    29f81cd4fe06fdd046fea4ac7bff607317116135 Mon Jun 15 09:58:39 2020 -0700
    v400 preview2

• lines changed: 3756
• files changed: 80