All File Changes

v405_base to v406_preview (2020-10-05 to 2020-10-12) v406

• confs/hgwbeta.hg.conf
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    8d639b25cf1b90a9380222c1b392bdd3c4dec1ed Sun Oct 11 01:11:41 2020 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 3, context: html, text, full: html, text
    8d639b25cf1b90a9380222c1b392bdd3c4dec1ed Sun Oct 11 01:11:41 2020 -0700
    Installing updated hg.conf files from UCSC servers
• src/blat/version.doc
  • lines changed 1, context: html, text, full: html, text
    2aa9a5801154010a033d3cdc760a8c3e296e835a Fri Oct 9 02:30:57 2020 -0700
    Changed default -timeout to 90 seconds instead of 10. Improved handling skips further sending on socket after failure to avoid multiple long timeouts. refs #26285
• src/gfServer/gfServer.c
  • lines changed 53, context: html, text, full: html, text
    2aa9a5801154010a033d3cdc760a8c3e296e835a Fri Oct 9 02:30:57 2020 -0700
    Changed default -timeout to 90 seconds instead of 10. Improved handling skips further sending on socket after failure to avoid multiple long timeouts. refs #26285
• src/hg/geneBounds/clusterGenes/clusterGenes.c
  • lines changed 113, context: html, text, full: html, text
    dddc3258aec53ba33f27a2233816cc02a42b940d Wed Sep 30 12:41:38 2020 -0700
    refactor to simplified code in prep for fixing minOverlapping functionality
  • lines changed 154, context: html, text, full: html, text
    f0b2eab01fa6d080c92c0444ef84d482b75afec9 Mon Oct 5 17:31:06 2020 -0700
    replaced the -minOverlappingBases option with -ignoreBases; -minOverlappingBases did not work correctly and would have requred major restructing of the code. The -ignoreBases directly address the issue of minor overlap at the ends of transcripts
  • lines changed 8, context: html, text, full: html, text
    9debf7ab57d1bccb620f13fa1ba81a0a9434211c Mon Oct 5 17:40:32 2020 -0700
    remove -minOverlappingBases rather than map it to the new option, since the behavior is significantly different enough than the intended old behavior that is is better to fail
• src/hg/geneBounds/clusterGenes/tests/expected/ignoreBasesCdsTest.gl
  • lines changed 5, context: html, text, full: html, text
    f0b2eab01fa6d080c92c0444ef84d482b75afec9 Mon Oct 5 17:31:06 2020 -0700
    replaced the -minOverlappingBases option with -ignoreBases; -minOverlappingBases did not work correctly and would have requred major restructing of the code. The -ignoreBases directly address the issue of minor overlap at the ends of transcripts
• src/hg/geneBounds/clusterGenes/tests/expected/ignoreBasesTest.gl
  • lines changed 5, context: html, text, full: html, text
    f0b2eab01fa6d080c92c0444ef84d482b75afec9 Mon Oct 5 17:31:06 2020 -0700
    replaced the -minOverlappingBases option with -ignoreBases; -minOverlappingBases did not work correctly and would have requred major restructing of the code. The -ignoreBases directly address the issue of minor overlap at the ends of transcripts
• src/hg/geneBounds/clusterGenes/tests/expected/minOverlappingBasesTest.gl
  • lines changed 2, context: html, text, full: html, text
    dddc3258aec53ba33f27a2233816cc02a42b940d Wed Sep 30 12:41:38 2020 -0700
    refactor to simplified code in prep for fixing minOverlapping functionality
  • lines changed 3, context: html, text, full: html, text
    f0b2eab01fa6d080c92c0444ef84d482b75afec9 Mon Oct 5 17:31:06 2020 -0700
    replaced the -minOverlappingBases option with -ignoreBases; -minOverlappingBases did not work correctly and would have requred major restructing of the code. The -ignoreBases directly address the issue of minor overlap at the ends of transcripts
• src/hg/geneBounds/clusterGenes/tests/expected/minOverlappingCdsBasesTest.gl
  • lines changed 3, context: html, text, full: html, text
    dddc3258aec53ba33f27a2233816cc02a42b940d Wed Sep 30 12:41:38 2020 -0700
    refactor to simplified code in prep for fixing minOverlapping functionality
  • lines changed 3, context: html, text, full: html, text
    f0b2eab01fa6d080c92c0444ef84d482b75afec9 Mon Oct 5 17:31:06 2020 -0700
    replaced the -minOverlappingBases option with -ignoreBases; -minOverlappingBases did not work correctly and would have requred major restructing of the code. The -ignoreBases directly address the issue of minor overlap at the ends of transcripts
• src/hg/geneBounds/clusterGenes/tests/input/minOverlapCases.gp
  • lines changed 2, context: html, text, full: html, text
    dddc3258aec53ba33f27a2233816cc02a42b940d Wed Sep 30 12:41:38 2020 -0700
    refactor to simplified code in prep for fixing minOverlapping functionality
  • lines changed 2, context: html, text, full: html, text
    f0b2eab01fa6d080c92c0444ef84d482b75afec9 Mon Oct 5 17:31:06 2020 -0700
    replaced the -minOverlappingBases option with -ignoreBases; -minOverlappingBases did not work correctly and would have requred major restructing of the code. The -ignoreBases directly address the issue of minor overlap at the ends of transcripts
• src/hg/geneBounds/clusterGenes/tests/input/overlapCases.gp
  • lines changed 4, context: html, text, full: html, text
    f0b2eab01fa6d080c92c0444ef84d482b75afec9 Mon Oct 5 17:31:06 2020 -0700
    replaced the -minOverlappingBases option with -ignoreBases; -minOverlappingBases did not work correctly and would have requred major restructing of the code. The -ignoreBases directly address the issue of minor overlap at the ends of transcripts
• src/hg/geneBounds/clusterGenes/tests/input/smallOverlap.gp
  • lines changed 2, context: html, text, full: html, text
    f0b2eab01fa6d080c92c0444ef84d482b75afec9 Mon Oct 5 17:31:06 2020 -0700
    replaced the -minOverlappingBases option with -ignoreBases; -minOverlappingBases did not work correctly and would have requred major restructing of the code. The -ignoreBases directly address the issue of minor overlap at the ends of transcripts
• src/hg/geneBounds/clusterGenes/tests/makefile
  • lines changed 9, context: html, text, full: html, text
    dddc3258aec53ba33f27a2233816cc02a42b940d Wed Sep 30 12:41:38 2020 -0700
    refactor to simplified code in prep for fixing minOverlapping functionality
  • lines changed 9, context: html, text, full: html, text
    f0b2eab01fa6d080c92c0444ef84d482b75afec9 Mon Oct 5 17:31:06 2020 -0700
    replaced the -minOverlappingBases option with -ignoreBases; -minOverlappingBases did not work correctly and would have requred major restructing of the code. The -ignoreBases directly address the issue of minor overlap at the ends of transcripts
• src/hg/hgBlat/hgBlat.c
  • lines changed 3, context: html, text, full: html, text
    7bb6da83f4a5c8be7932c48c22eb6c917e222ba1 Tue Oct 6 11:38:32 2020 -0700
    oops, another little hgBlat bug with Blats Guess and SearchAllGenomes and only newline for intput. refs #26285
  • lines changed 67, context: html, text, full: html, text
    7d0af5fc6dbc224c4131e6d6a43b09a8f661502b Thu Oct 8 23:09:56 2020 -0700
    Improving hgBlat by moving the gfServer connect from being done up front to being done in the per-thread routine. This means it should use fewer connections in worse case scenarios, and also mean that gfServer will not have to wait as long.
• src/hg/hgCustom/hgCustom.c
  • lines changed 1, context: html, text, full: html, text
    7fede59d2f44a75de07669204558815a12d6766f Thu Oct 8 13:40:54 2020 -0700
    Adding note about hic format to hgCustom page, no ticket (Thanks b0b)
• src/hg/hgSession/hgSession.c
  • lines changed 1, context: html, text, full: html, text
    8096016592d2f0e41b77c1203adc29119f7d5dc3 Mon Oct 5 11:05:16 2020 -0700
    Sorting sessions by creation date, by default refs #26075
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 1, context: html, text, full: html, text
    584d0d429e9fa7beb1213e9ece961b3a58d5d413 Thu Oct 8 08:07:26 2020 -0700
    making refseq default to showing accessions. refs #26089
• src/hg/hgTracks/barChartTrack.c
  • lines changed 1, context: html, text, full: html, text
    264a2ffcc41a3a622bdf65a46314f242917506a4 Mon Oct 12 05:43:02 2020 -0700
    small improvement to a barchart warning message. Email with Jim, no redmine (change is too small)
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 4, context: html, text, full: html, text
    e5d963606c378c0f08cb946c3a9393847dd6ce22 Wed Oct 7 15:23:41 2020 -0700
    Add bigBed to GeneReviews to support mouseOver with diseases. refs #19841
• src/hg/hgTracks/lollyTrack.c
  • lines changed 3, context: html, text, full: html, text
    e5d963606c378c0f08cb946c3a9393847dd6ce22 Wed Oct 7 15:23:41 2020 -0700
    Add bigBed to GeneReviews to support mouseOver with diseases. refs #19841
• src/hg/hgTracks/simpleTracks.c
  • lines changed 3, context: html, text, full: html, text
    584d0d429e9fa7beb1213e9ece961b3a58d5d413 Thu Oct 8 08:07:26 2020 -0700
    making refseq default to showing accessions. refs #26089
• src/hg/hgc/clinvarSubLolly.c
  • lines changed 133, context: html, text, full: html, text
    7355201a77e934e6e7f28242d4beb15d694e7c8d Sun Oct 11 13:21:05 2020 -0700
    initial work on Clinvar Submissions track #26330
• src/hg/hgc/clinvarSubLolly.h
  • lines changed 2, context: html, text, full: html, text
    7355201a77e934e6e7f28242d4beb15d694e7c8d Sun Oct 11 13:21:05 2020 -0700
    initial work on Clinvar Submissions track #26330
• src/hg/hgc/geneReviewsClick.c
  • lines changed 20, context: html, text, full: html, text
    e5d963606c378c0f08cb946c3a9393847dd6ce22 Wed Oct 7 15:23:41 2020 -0700
    Add bigBed to GeneReviews to support mouseOver with diseases. refs #19841
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    e5d963606c378c0f08cb946c3a9393847dd6ce22 Wed Oct 7 15:23:41 2020 -0700
    Add bigBed to GeneReviews to support mouseOver with diseases. refs #19841
  • lines changed 5, context: html, text, full: html, text
    7355201a77e934e6e7f28242d4beb15d694e7c8d Sun Oct 11 13:21:05 2020 -0700
    initial work on Clinvar Submissions track #26330
• src/hg/hgc/makefile
  • lines changed 1, context: html, text, full: html, text
    7355201a77e934e6e7f28242d4beb15d694e7c8d Sun Oct 11 13:21:05 2020 -0700
    initial work on Clinvar Submissions track #26330
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 4, context: html, text, full: html, text
    a9e45767d1ff8899bed32ff418e2ff20f29b4457 Wed Oct 7 11:36:31 2020 -0700
    Adding references to hgdowload2 refs #25778
• src/hg/htdocs/contacts.html
  • lines changed 1, context: html, text, full: html, text
    1d9cf4096b66dda11cc008e56daf89eb9bcb0a57 Tue Oct 6 15:45:19 2020 -0700
    Removing low volume email phrase No RM
• src/hg/htdocs/goldenPath/help/cutters.html
  • lines changed 1, context: html, text, full: html, text
    43a8b1be29d4e0aa6215c91711bdb56296a8e470 Wed Oct 7 16:02:52 2020 -0700
    Fixed broken URLs refs #9677
• src/hg/htdocs/goldenPath/help/hgCnvColoring.html
  • lines changed 1, context: html, text, full: html, text
    f1944b9c04bb45c304c1bfa917141a50b0d2a6d6 Fri Oct 9 14:41:16 2020 -0700
    CR typo fixes #26295
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 5, context: html, text, full: html, text
    a9e45767d1ff8899bed32ff418e2ff20f29b4457 Wed Oct 7 11:36:31 2020 -0700
    Adding references to hgdowload2 refs #25778
• src/hg/htdocs/goldenPath/help/mirror.html
  • lines changed 3, context: html, text, full: html, text
    a9e45767d1ff8899bed32ff418e2ff20f29b4457 Wed Oct 7 11:36:31 2020 -0700
    Adding references to hgdowload2 refs #25778
• src/hg/htdocs/goldenPath/help/oligoMatch.html
  • lines changed 1, context: html, text, full: html, text
    43a8b1be29d4e0aa6215c91711bdb56296a8e470 Wed Oct 7 16:02:52 2020 -0700
    Fixed broken URLs refs #9677
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 22, context: html, text, full: html, text
    33a50a1b48d704712ce4e723ec3b7e8cd271d381 Mon Oct 5 16:54:29 2020 -0700
    Announcing dbVar track #25424
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    d28f6abf35134407909c039b8f083f0cd699125b Tue Oct 6 15:44:47 2020 -0700
    Typo fixes for dbVar refs #26241
• src/hg/htdocs/indexNews.html
  • lines changed 14, context: html, text, full: html, text
    33a50a1b48d704712ce4e723ec3b7e8cd271d381 Mon Oct 5 16:54:29 2020 -0700
    Announcing dbVar track #25424
  • lines changed 1, context: html, text, full: html, text
    d28f6abf35134407909c039b8f083f0cd699125b Tue Oct 6 15:44:47 2020 -0700
    Typo fixes for dbVar refs #26241
• src/hg/inc/clinvarSub.h
  • lines changed 75, context: html, text, full: html, text
    7355201a77e934e6e7f28242d4beb15d694e7c8d Sun Oct 11 13:21:05 2020 -0700
    initial work on Clinvar Submissions track #26330
• src/hg/lib/clinvarSub.as
  • lines changed 17, context: html, text, full: html, text
    7355201a77e934e6e7f28242d4beb15d694e7c8d Sun Oct 11 13:21:05 2020 -0700
    initial work on Clinvar Submissions track #26330
• src/hg/lib/clinvarSub.c
  • lines changed 211, context: html, text, full: html, text
    7355201a77e934e6e7f28242d4beb15d694e7c8d Sun Oct 11 13:21:05 2020 -0700
    initial work on Clinvar Submissions track #26330
• src/hg/lib/clinvarSub.sql
  • lines changed 23, context: html, text, full: html, text
    7355201a77e934e6e7f28242d4beb15d694e7c8d Sun Oct 11 13:21:05 2020 -0700
    initial work on Clinvar Submissions track #26330
• src/hg/lib/clinvarSubLolly.as
  • lines changed 21, context: html, text, full: html, text
    7355201a77e934e6e7f28242d4beb15d694e7c8d Sun Oct 11 13:21:05 2020 -0700
    initial work on Clinvar Submissions track #26330
• src/hg/lib/googleAnalytics.c
  • lines changed 14, context: html, text, full: html, text
    9b67cdea994aadecdacbdac6fc9a521b94d84d71 Wed Sep 30 07:08:31 2020 -0700
    applying fixes to analytics click handler found by Jonathan, refs #21916, many thanks to Jonathan for finding these!
  • lines changed 11, context: html, text, full: html, text
    c3410649af2d12dcfdb396a403b25524eb3d4291 Wed Oct 7 05:15:24 2020 -0700
    fixing analytics link tracking breaking hgBlat, refs #21916
  • lines changed 9, context: html, text, full: html, text
    091025a3f66bf4635fe4d7c5b457160e78914af3 Wed Oct 7 05:33:42 2020 -0700
    making analytics link tracking a bit more careful, by only modifying external inks, also fixing the indentation, refs #21916
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    7355201a77e934e6e7f28242d4beb15d694e7c8d Sun Oct 11 13:21:05 2020 -0700
    initial work on Clinvar Submissions track #26330
• src/hg/makeDb/doc/hg19.txt
  • lines changed 13, context: html, text, full: html, text
    7355201a77e934e6e7f28242d4beb15d694e7c8d Sun Oct 11 13:21:05 2020 -0700
    initial work on Clinvar Submissions track #26330
• src/hg/makeDb/doc/wuhCor1/iedb.txt
  • lines changed 2, context: html, text, full: html, text
    5b094ce0cd511545e4cc07ffcdfa81a1c10da032 Tue Oct 6 07:56:07 2020 -0700
    addding iedb validated track, refs #26305
• src/hg/makeDb/doc/wuhCor1/phylogenetics.txt
  • lines changed 2, context: html, text, full: html, text
    efad2e8e6baab58bf98fae7b1041d3794b4ba3a9 Tue Oct 6 11:36:46 2020 -0700
    Adding note for next time about recent changes to usher program.
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 2, context: html, text, full: html, text
    6742a481fabe8de636cae39f4f2ba230b09e53a7 Mon Oct 5 13:37:51 2020 -0700
    Moving mm39 to the urgent databases section, refs #22271
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 1, context: html, text, full: html, text
    1f69d9c0e783e5628ba79200f30f41ed8d2137ef Fri Oct 9 15:31:45 2020 -0700
    Turning on Genbank updates for mm39, refs #22271
• src/hg/makeDb/trackDb/human/chainNetPlacental.ra
  • lines changed 55, context: html, text, full: html, text
    08b3b394e57c1ca8a8b31ad773e2e7506c32b56b Wed Oct 7 15:06:28 2020 -0700
    package in mm39 chainNet properly and a couple others refs #22271
  • lines changed 55, context: html, text, full: html, text
    c036ff920227730eb81df27d750ce6af006d92a5 Wed Oct 7 16:32:54 2020 -0700
    cleaning up stray chainNet tracks outside composites refs #22271
• src/hg/makeDb/trackDb/human/chainNetPrimate.ra
  • lines changed 21, context: html, text, full: html, text
    08b3b394e57c1ca8a8b31ad773e2e7506c32b56b Wed Oct 7 15:06:28 2020 -0700
    package in mm39 chainNet properly and a couple others refs #22271
  • lines changed 37, context: html, text, full: html, text
    c036ff920227730eb81df27d750ce6af006d92a5 Wed Oct 7 16:32:54 2020 -0700
    cleaning up stray chainNet tracks outside composites refs #22271
• src/hg/makeDb/trackDb/human/chainNetRheMac10.ra
  • lines changed 15, context: html, text, full: html, text
    08b3b394e57c1ca8a8b31ad773e2e7506c32b56b Wed Oct 7 15:06:28 2020 -0700
    package in mm39 chainNet properly and a couple others refs #22271
• src/hg/makeDb/trackDb/human/chainNetRheMac8.ra
  • lines changed 16, context: html, text, full: html, text
    08b3b394e57c1ca8a8b31ad773e2e7506c32b56b Wed Oct 7 15:06:28 2020 -0700
    package in mm39 chainNet properly and a couple others refs #22271
• src/hg/makeDb/trackDb/human/chainNetVertebrate.ra
  • lines changed 37, context: html, text, full: html, text
    c036ff920227730eb81df27d750ce6af006d92a5 Wed Oct 7 16:32:54 2020 -0700
    cleaning up stray chainNet tracks outside composites refs #22271
• src/hg/makeDb/trackDb/human/clinvar.html
  • lines changed 2, context: html, text, full: html, text
    8a144988470f693d6618c13ba5fe364b56b428d2 Fri Oct 9 14:36:38 2020 -0700
    Correcting relative links for #25207
• src/hg/makeDb/trackDb/human/clinvarSubLolly.ra
  • lines changed 20, context: html, text, full: html, text
    7355201a77e934e6e7f28242d4beb15d694e7c8d Sun Oct 11 13:21:05 2020 -0700
    initial work on Clinvar Submissions track #26330
• src/hg/makeDb/trackDb/human/dbVarCommon.html
  • lines changed 21, context: html, text, full: html, text
    dc28e7eaba410716bba6a5f86c78a11b9e817a61 Mon Oct 5 15:04:15 2020 -0700
    Small link fixes for dbVar refs #25423
• src/hg/makeDb/trackDb/human/dbVarConflict.html
  • lines changed 21, context: html, text, full: html, text
    dc28e7eaba410716bba6a5f86c78a11b9e817a61 Mon Oct 5 15:04:15 2020 -0700
    Small link fixes for dbVar refs #25423
• src/hg/makeDb/trackDb/human/dbVarCurated.html
  • lines changed 23, context: html, text, full: html, text
    dc28e7eaba410716bba6a5f86c78a11b9e817a61 Mon Oct 5 15:04:15 2020 -0700
    Small link fixes for dbVar refs #25423
• src/hg/makeDb/trackDb/human/decipher.html
  • lines changed 1, context: html, text, full: html, text
    8a144988470f693d6618c13ba5fe364b56b428d2 Fri Oct 9 14:36:38 2020 -0700
    Correcting relative links for #25207
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    f1944b9c04bb45c304c1bfa917141a50b0d2a6d6 Fri Oct 9 14:41:16 2020 -0700
    CR typo fixes #26295
• src/hg/makeDb/trackDb/human/geneReviews.html
  • lines changed 2, context: html, text, full: html, text
    92a2cc316ffc835ad7e3b8e1514ce93320b6d5b5 Fri Oct 9 00:17:52 2020 -0700
    added mouseover sentence in desc page refs#26321
• src/hg/makeDb/trackDb/human/hg19/clinsub.ra
  • lines changed 19, context: html, text, full: html, text
    7355201a77e934e6e7f28242d4beb15d694e7c8d Sun Oct 11 13:21:05 2020 -0700
    initial work on Clinvar Submissions track #26330
• src/hg/makeDb/trackDb/human/hg19/gnomadPext.html
  • lines changed 71, context: html, text, full: html, text
    0af64c7b47c77df906475f326121baf2fd43b79b Mon Oct 12 08:52:20 2020 -0700
    new html track description page refs #25869
• src/hg/makeDb/trackDb/human/hg19/gnomadSv.html
  • lines changed 1, context: html, text, full: html, text
    8a144988470f693d6618c13ba5fe364b56b428d2 Fri Oct 9 14:36:38 2020 -0700
    Correcting relative links for #25207
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
  • lines changed 1, context: html, text, full: html, text
    0af64c7b47c77df906475f326121baf2fd43b79b Mon Oct 12 08:52:20 2020 -0700
    new html track description page refs #25869
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    7355201a77e934e6e7f28242d4beb15d694e7c8d Sun Oct 11 13:21:05 2020 -0700
    initial work on Clinvar Submissions track #26330
• src/hg/makeDb/trackDb/human/hg38/gencodeV35.html
  • lines changed 3, context: html, text, full: html, text
    c76012f505f97bb5e7736ae9122df3bb5e9edc80 Fri Oct 9 17:34:11 2020 -0700
    Fixing typos #25704
• src/hg/makeDb/trackDb/human/omimGene2.html
  • lines changed 1, context: html, text, full: html, text
    1f0c31eb2d7c7c6528e7414cf804e969e4185324 Fri Oct 9 01:15:22 2020 -0700
    corrected table browser output results description refs #18419
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 14, context: html, text, full: html, text
    e5d963606c378c0f08cb946c3a9393847dd6ce22 Wed Oct 7 15:23:41 2020 -0700
    Add bigBed to GeneReviews to support mouseOver with diseases. refs #19841
  • lines changed 14, context: html, text, full: html, text
    669a81f7278f0dc4dde1a0680b64eb0457bd65f7 Fri Oct 9 04:24:39 2020 -0700
    adding search to bigified OMIM track, refs #26221
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    63f50212c4c3be6f94ed5eed5c1c1df9f75f4b6e Fri Oct 9 17:31:04 2020 -0700
    Add noScore filter to geneReviews #26231
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    7355201a77e934e6e7f28242d4beb15d694e7c8d Sun Oct 11 13:21:05 2020 -0700
    initial work on Clinvar Submissions track #26330
• src/hg/makeDb/trackDb/tagTypes.tab
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    7355201a77e934e6e7f28242d4beb15d694e7c8d Sun Oct 11 13:21:05 2020 -0700
    initial work on Clinvar Submissions track #26330
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
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    11d9f18b340dd6eef227973d70d962c9e60be109 Mon Sep 28 10:09:18 2020 -0700
    forgot a file in last commit, refs #26216
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    5b094ce0cd511545e4cc07ffcdfa81a1c10da032 Tue Oct 6 07:56:07 2020 -0700
    addding iedb validated track, refs #26305
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    3cf6ac8b10f4f26ce14c4797ea07981d33cb266c Wed Oct 7 12:08:13 2020 -0700
    Beta testing #26265
• src/hg/utils/otto/clinvarSubLolly/assignColors
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    7355201a77e934e6e7f28242d4beb15d694e7c8d Sun Oct 11 13:21:05 2020 -0700
    initial work on Clinvar Submissions track #26330
• src/hg/utils/otto/clinvarSubLolly/makeFranklin
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    7355201a77e934e6e7f28242d4beb15d694e7c8d Sun Oct 11 13:21:05 2020 -0700
    initial work on Clinvar Submissions track #26330
• src/hg/utils/otto/geneReviews/buildGeneReviews.sh
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    e5d963606c378c0f08cb946c3a9393847dd6ce22 Wed Oct 7 15:23:41 2020 -0700
    Add bigBed to GeneReviews to support mouseOver with diseases. refs #19841
• src/hg/utils/otto/geneReviews/geneReviews.as
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    e5d963606c378c0f08cb946c3a9393847dd6ce22 Wed Oct 7 15:23:41 2020 -0700
    Add bigBed to GeneReviews to support mouseOver with diseases. refs #19841
• src/hg/utils/otto/geneReviews/geneReviewsWrapper.sh
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    b184d01c4cf9cfc3dd132567ed0809cba0389ca4 Thu Oct 8 16:39:49 2020 -0700
    Biggified to add diseases to GeneReviews mouseover. refs #19841
• src/hg/utils/otto/geneReviews/geneRevsAddDiseases.pl
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    e5d963606c378c0f08cb946c3a9393847dd6ce22 Wed Oct 7 15:23:41 2020 -0700
    Add bigBed to GeneReviews to support mouseOver with diseases. refs #19841
• src/hg/utils/otto/geneReviews/geneRevsListDiseases.pl
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    e5d963606c378c0f08cb946c3a9393847dd6ce22 Wed Oct 7 15:23:41 2020 -0700
    Add bigBed to GeneReviews to support mouseOver with diseases. refs #19841
• src/hg/utils/otto/geneReviews/makefile
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    e5d963606c378c0f08cb946c3a9393847dd6ce22 Wed Oct 7 15:23:41 2020 -0700
    Add bigBed to GeneReviews to support mouseOver with diseases. refs #19841
• src/hg/utils/otto/geneReviews/test/testBuildBb.sh
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    e5d963606c378c0f08cb946c3a9393847dd6ce22 Wed Oct 7 15:23:41 2020 -0700
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• src/hg/utils/otto/geneReviews/test/testCheck.sh
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    e5d963606c378c0f08cb946c3a9393847dd6ce22 Wed Oct 7 15:23:41 2020 -0700
    Add bigBed to GeneReviews to support mouseOver with diseases. refs #19841
• src/hg/utils/otto/geneReviews/test/testWrapper.sh
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    e5d963606c378c0f08cb946c3a9393847dd6ce22 Wed Oct 7 15:23:41 2020 -0700
    Add bigBed to GeneReviews to support mouseOver with diseases. refs #19841
• src/hg/utils/otto/omim/checkOmimUpload.sh
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    39e53d810c15fc0d58bc01e2ba11daa60f9632ef Mon Oct 5 11:19:39 2020 -0700
    Make the omim uploads if either omimGene2 or omimAvSnp changes, refs Jonathan email
• src/inc/common.mk
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    1a711580a80676e1fff181ccc13c4cccd38c9891 Mon Oct 12 04:13:08 2020 -0700
    adding a user log to cgi-alpha and cgi-beta targets. Email with Lou, after a problem on hgwdev possibly caused by myself. No redmine.
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    1a59145d5dd903ed9a6d8cc3279b4a2f0f637814 Mon Oct 12 05:42:04 2020 -0700
    fixing previous commit where I went about the makefile change in the wrong way. Email with Lou, no redmine.
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    3d6efad8b546f4976a34ceb268961c6d35fc972e Mon Oct 12 07:38:08 2020 -0700
    Allowing C99 syntax. OK'ed by Jim years ago and now again by the buildmeister. No redmine, as only build-related.
• src/inc/genoFind.h
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    2aa9a5801154010a033d3cdc760a8c3e296e835a Fri Oct 9 02:30:57 2020 -0700
    Changed default -timeout to 90 seconds instead of 10. Improved handling skips further sending on socket after failure to avoid multiple long timeouts. refs #26285
• src/inc/memgfx.h
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    make the background of freetype fonts be transparent
• src/lib/freeType.c
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    8b010980b84c625d264f46c77e74a79f96a5fe87 Sun Oct 11 13:36:42 2020 -0700
    make the background of freetype fonts be transparent
• src/lib/memgfx.c
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    0f3d2a3a5d7f1922711bedbfc5f8b63b425350b4 Tue Oct 6 15:58:40 2020 -0700
    fix problem with compiling memgfx.c if FREETYPE isn't defined
• src/makefile
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    1a711580a80676e1fff181ccc13c4cccd38c9891 Mon Oct 12 04:13:08 2020 -0700
    adding a user log to cgi-alpha and cgi-beta targets. Email with Lou, after a problem on hgwdev possibly caused by myself. No redmine.
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    1a59145d5dd903ed9a6d8cc3279b4a2f0f637814 Mon Oct 12 05:42:04 2020 -0700
    fixing previous commit where I went about the makefile change in the wrong way. Email with Lou, no redmine.
• src/product/installer/browserSetup.sh
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    1c23711ef09245b7f38f327200a7b5bebd10a4cc Thu Oct 8 03:38:48 2020 -0700
    fixing up GBIC installer for Centos 8, refs #26320
• src/utils/qa/weeklybld/buildEnv.csh
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    a455a195a72366eeb6bcabedb1c4f920430c0db5 Mon Oct 12 10:04:38 2020 -0700
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