All File Changes

v368_base to v369_preview (2018-07-09 to 2018-07-16) v369

• src/hg/hgBlat/hgBlat.c
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    cbb1262183e62300d8b02b003f1ff0b0e602f8ba Mon Jul 9 09:31:59 2018 -0700
    allow maximum sequence count to be defined in hg.conf hgBlat.maxSequenceCount no redmine
• src/hg/hgMirror/hgMirror
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    3e3ffae1074ba80346bf2521780ca65f3c670fd5 Wed Jul 11 15:38:46 2018 -0700
    prevent hgMirror from dieing when trackDb contains valid 'superTrack on hide' lines, refs #21667
• src/hg/hgTracks/interactTrack.c
  • lines changed 15, context: html, text, full: html, text
    2c464560785805c684850c1bb05421fb72f0e994 Thu Jul 5 15:51:30 2018 -0700
    Make grab points more visible and easier to click. refs #21109
• src/hg/hgc/hgc.c
  • lines changed 67, context: html, text, full: html, text
    038c31ecb2bd9e59311bb3009646ddc5374fa9d6 Fri Jul 13 23:06:35 2018 -0700
    hgc functions using framesets and a few other odd places that make their own html head were tweaked to include the CSP header. Thisis also helpful with early errors. refs #21729
• src/hg/hgc/hgc.h
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    038c31ecb2bd9e59311bb3009646ddc5374fa9d6 Fri Jul 13 23:06:35 2018 -0700
    hgc functions using framesets and a few other odd places that make their own html head were tweaked to include the CSP header. Thisis also helpful with early errors. refs #21729
• src/hg/hgc/lowelab.c
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    038c31ecb2bd9e59311bb3009646ddc5374fa9d6 Fri Jul 13 23:06:35 2018 -0700
    hgc functions using framesets and a few other odd places that make their own html head were tweaked to include the CSP header. Thisis also helpful with early errors. refs #21729
• src/hg/hgc/pubs.c
  • lines changed 4, context: html, text, full: html, text
    038c31ecb2bd9e59311bb3009646ddc5374fa9d6 Fri Jul 13 23:06:35 2018 -0700
    hgc functions using framesets and a few other odd places that make their own html head were tweaked to include the CSP header. Thisis also helpful with early errors. refs #21729
• src/hg/hgc/retroClick.c
  • lines changed 4, context: html, text, full: html, text
    038c31ecb2bd9e59311bb3009646ddc5374fa9d6 Fri Jul 13 23:06:35 2018 -0700
    hgc functions using framesets and a few other odd places that make their own html head were tweaked to include the CSP header. Thisis also helpful with early errors. refs #21729
• src/hg/hgc/transMapClick.c
  • lines changed 3, context: html, text, full: html, text
    038c31ecb2bd9e59311bb3009646ddc5374fa9d6 Fri Jul 13 23:06:35 2018 -0700
    hgc functions using framesets and a few other odd places that make their own html head were tweaked to include the CSP header. Thisis also helpful with early errors. refs #21729
• src/hg/htdocs/goldenPath/newsarch.html
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    a36453699783ee0b2cae73a4ab913d531077030f Thu Jul 12 03:18:45 2018 -0700
    a bit late, but announcement never actually named gnomAD
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    a54c25609ad8acf353bc7fc68bd04c49757c9efd Thu Jul 12 13:37:37 2018 -0700
    Staging the DECIPHER SNVs track announcement until the v368 CGI release, refs #21104
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    56fee824c185a7ae383b6839d8ccc9e987acb9e8 Thu Jul 12 13:57:25 2018 -0700
    Adding common names to previous assembly announcements, no Redmine.
• src/hg/htdocs/indexNews.html
  • lines changed 1, context: html, text, full: html, text
    a36453699783ee0b2cae73a4ab913d531077030f Thu Jul 12 03:18:45 2018 -0700
    a bit late, but announcement never actually named gnomAD
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    a54c25609ad8acf353bc7fc68bd04c49757c9efd Thu Jul 12 13:37:37 2018 -0700
    Staging the DECIPHER SNVs track announcement until the v368 CGI release, refs #21104
• src/hg/logCrawl/dbTrackAndSearchUsage/README.txt
  • lines changed 20, context: html, text, full: html, text
    96fafe24284cb88f63dc8602e76c4b483b71638b Wed Jul 11 15:12:08 2018 -0700
    Adding scripts for generating search, db and track usage stats as well as a helper script for both. Also adding a README for all of three. refs #20225
• src/hg/logCrawl/dbTrackAndSearchUsage/generateSearchUse.py
  • lines changed 140, context: html, text, full: html, text
    96fafe24284cb88f63dc8602e76c4b483b71638b Wed Jul 11 15:12:08 2018 -0700
    Adding scripts for generating search, db and track usage stats as well as a helper script for both. Also adding a README for all of three. refs #20225
• src/hg/logCrawl/dbTrackAndSearchUsage/generateUsageStats.py
  • lines changed 467, context: html, text, full: html, text
    96fafe24284cb88f63dc8602e76c4b483b71638b Wed Jul 11 15:12:08 2018 -0700
    Adding scripts for generating search, db and track usage stats as well as a helper script for both. Also adding a README for all of three. refs #20225
• src/hg/logCrawl/dbTrackAndSearchUsage/makeLogSymLinks.sh
  • lines changed 73, context: html, text, full: html, text
    96fafe24284cb88f63dc8602e76c4b483b71638b Wed Jul 11 15:12:08 2018 -0700
    Adding scripts for generating search, db and track usage stats as well as a helper script for both. Also adding a README for all of three. refs #20225
• src/hg/makeDb/doc/ambMex1/initialBuild.txt
  • lines changed 439, context: html, text, full: html, text
    74425b74c2d4cd28a8ef90a5748e9c6f92b25a62 Tue Jul 10 11:34:08 2018 -0700
    added genbank definitions running up mm10 lastz chainNet refs #21715
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    d069f32c28cd22141e4ba10e9eedd63db9c0e13c Tue Jul 10 11:44:20 2018 -0700
    turning on signal for genbank to run refs #21715
  • lines changed 35, context: html, text, full: html, text
    b812219ab79f0f6ae871974803764dc6f885cd7a Wed Jul 11 09:41:06 2018 -0700
    lastz chain net swaps from hg38 and mm10 refs #21715
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    9332df756fb318c4bd7c3fc4a031b718f8b668ba Fri Jul 13 09:32:40 2018 -0700
    QA Ready with no blat server refs #21715
• src/hg/makeDb/doc/ambMex1/twoGbChunks.pl
  • lines changed 68, context: html, text, full: html, text
    62ea85fa943b018907c42aff118199b80fee20f5 Tue Jul 10 11:35:07 2018 -0700
    script to manage to this gigantic genome refs #21715
• src/hg/makeDb/doc/hg38/lastzRuns.txt
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    89f62bfd8aee9fabba868d186fe9bb38acafd678 Tue Jul 10 13:17:11 2018 -0700
    lastz chain net run to ambMex1 refs #21715
• src/hg/makeDb/doc/mm10.txt
  • lines changed 83, context: html, text, full: html, text
    075e7086a8c68293fc7cb05cc2fd64f7108f47cd Wed Jul 11 09:37:49 2018 -0700
    lastz chain net to ambMex1 refs #21715
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    68edf4def88d67a6728778c61172135af46edfe6 Tue Jul 10 11:42:50 2018 -0700
    adding ambMex1/axolotl refs #21715
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 24, context: html, text, full: html, text
    511e00386c784f37a43aca45a5367c068a2dccc4 Tue Jul 10 11:03:23 2018 -0700
    adding ambMex1 Axolotl - Ambystoma mexicanum
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    68edf4def88d67a6728778c61172135af46edfe6 Tue Jul 10 11:42:50 2018 -0700
    adding ambMex1/axolotl refs #21715
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 2, context: html, text, full: html, text
    511e00386c784f37a43aca45a5367c068a2dccc4 Tue Jul 10 11:03:23 2018 -0700
    adding ambMex1 Axolotl - Ambystoma mexicanum
• src/hg/makeDb/schema/all.joiner
  • lines changed 9, context: html, text, full: html, text
    dfe26d626345b785d82a952ae9e61984e9949222 Wed Jul 11 09:49:47 2018 -0700
    adding ambMex1 rules refs #21715
• src/hg/makeDb/trackDb/axolotl/ambMex1/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    b7a925d39b4755947047aaf047c94c957a13cb36 Tue Jul 10 11:32:51 2018 -0700
    adding gold table assembly track search rule refs #21715
  • lines changed 34, context: html, text, full: html, text
    15bbec7f5dca3361b54d138109f240dc178b8eb5 Thu Jul 12 16:21:13 2018 -0700
    default viz on tracks to make an interesting display at default position on PAX7 gene refs #21715
  • lines changed 7, context: html, text, full: html, text
    f71f3e5656f50a221cfe8dba528480db1c34c35e Thu Jul 12 17:14:53 2018 -0700
    override cpgIslanSuper visibilities refs #21715
• src/hg/makeDb/trackDb/crispr10K.html
  • lines changed 3, context: html, text, full: html, text
    ac59e261fc1f34972d61ee0bf2d786f5c8dc0455 Mon Jul 9 13:26:06 2018 -0700
    Adding a note that the 10K crispr tracks were built with financial support from Regeneron, refs #19874
• src/hg/makeDb/trackDb/human/chainNetVertebrate.ra
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    8265e44093ad21c6366b8260b8f5a7f6ed7ad50a Tue Jul 10 13:48:39 2018 -0700
    adding definitions for chainNet to Axolotl refs #21715
• src/hg/makeDb/trackDb/human/cosmicRegions.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
    Updating redirected links for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg19/allHg19RS_BW.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
    Updating redirected links for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg19/chainSelf.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
    Updating redirected links for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg19/cons100way.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
    Updating redirected links for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg19/cons46way.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
    Updating redirected links for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg19/evoCpg.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
    Updating redirected links for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg19/evsEsp6500.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
    Updating redirected links for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg19/exoniphy.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
    Updating redirected links for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg19/genomicSuperDups.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
    Updating redirected links for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg19/genotypeArrays.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
    Updating redirected links for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg19/gwipsvizRiboseq.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
    Updating redirected links for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg19/hg19Patch13.ra
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    3b39629cbdd305534f553640ce6b711280477058 Mon Jul 9 10:38:41 2018 -0700
    Adding pennantIcon for the GRCh37.p13 release, refs #9869
• src/hg/makeDb/trackDb/human/hg19/knownGene.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
    Updating redirected links for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg19/pgSnp.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
    Updating redirected links for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg19/pseudoYale60.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
    Updating redirected links for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg19/targetScanS.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
    Updating redirected links for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg19/tgpPhase1Accessibility.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
    Updating redirected links for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg19/ucscRetroAli5.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
    Updating redirected links for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg19/vegaGeneComposite.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
    Updating redirected links for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBuOrchid.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
    Updating redirected links for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliChip.release2.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
    Updating redirected links for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV14.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV17.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV19.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV24lift37.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
    Updating redirected links for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV27lift37.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV28lift37.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV7.html
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release3.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTfbsClustered.release2.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTfbsClusteredV3.html
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release4.html
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunySwitchgear.html
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhRnaSeq.patch.html
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release3.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
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• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProtGenc.html
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• src/hg/makeDb/trackDb/human/hg19/wgRna.html
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• src/hg/makeDb/trackDb/human/hg38/description.html
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    fe960c47b792f629dc0bfb71051fb6914b1828b0 Mon Jul 9 14:30:05 2018 -0700
    Correction of hg19 mito sequence accession in response to user report in MLQ, refs #21731
• src/hg/makeDb/trackDb/human/hg38/hoffMap.ra
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    04fe0e276324a01597ad04572787323b6f46dab8 Wed Jul 11 15:39:24 2018 -0700
    Removing hide from 'superTrack on hide' as it was causing issues with hgMirror, no Redmine.
• src/hg/makeDb/trackDb/human/hgIkmc.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
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• src/hg/makeDb/trackDb/human/lovd.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
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• src/hg/makeDb/trackDb/human/lrg.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
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• src/hg/makeDb/trackDb/human/lrgTranscriptAli.html
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• src/hg/makeDb/trackDb/human/placentalChainNet.html
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• src/hg/makeDb/trackDb/human/primateChainNet.html
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• src/hg/makeDb/trackDb/human/snp150Common.html
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    e3960c409f105aaaa00976d0d72811487d6cb4d7 Tue Jul 10 14:29:53 2018 -0700
    Adding note about dbSNP's different method for determining a subset of common variants.
• src/hg/makeDb/trackDb/human/snp151Common.html
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    7f43d805474b52bfbb2a19da8ed8e9559a64f1b9 Tue Jul 10 14:22:09 2018 -0700
    Adding note about dbSNP's different method for determining a subset of common variants.
• src/hg/makeDb/trackDb/human/switchDbTss.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
    Updating redirected links for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/trackDb.ra
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    dbb0d64dff975019a02bcacad978659ded8b4d20 Mon Jul 9 15:42:50 2018 -0700
    Adding beta release tag for the DECIPHER SNV track now that the hgc fix is on the v368 final build, refs #21104
• src/hg/makeDb/trackDb/human/vertebrateChainNet.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
    Updating redirected links for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
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    059158b0f5ece7a6dd45c115fd8aa98fd23dca2d Mon Jul 9 13:45:51 2018 -0700
    Staging on hgwbeta and adding beta release tag, ref #19874
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    af560fad874cb1be6c26a057a3a6a3d4b0d320ba Mon Jul 9 16:13:25 2018 -0700
    Removing release tags to stage on the RR, refs #19874
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.vertebrateChainNet.ra
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    8265e44093ad21c6366b8260b8f5a7f6ed7ad50a Tue Jul 10 13:48:39 2018 -0700
    adding definitions for chainNet to Axolotl refs #21715
• src/hg/makeDb/trackDb/patSeq.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
    Updating redirected links for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/spAnnot.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
    Updating redirected links for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/spMut.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
    Updating redirected links for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/spUniprot.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
    Updating redirected links for hg19, uiLinks cronjob.
• src/hg/makeDb/trackDb/trackDb.chainNet.sarcopterygii.ra
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    8265e44093ad21c6366b8260b8f5a7f6ed7ad50a Tue Jul 10 13:48:39 2018 -0700
    adding definitions for chainNet to Axolotl refs #21715
• src/hg/makeDb/trackDb/trackDb.ra
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    b199702ea2e5425fe84d4d1f47ee9ba26424a361 Thu Jul 12 17:17:23 2018 -0700
    visibility on a super track is meaningless refs #21715
• src/hg/makeDb/trackDb/uniprot.html
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    024af5fc96313d62eadb2758e7e1ee9bd2e35656 Mon Jul 9 10:49:06 2018 -0700
    Updating redirected links for hg19, uiLinks cronjob.
• src/hg/mouseStuff/chainBridge/tests/expected/awful.bridged.chain
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    122bc264524b1dd6efc9dea3d59812c3da3529a1 Fri Jul 13 16:50:19 2018 -0700
    Adding test cases for chainBridge. refs #21660
• src/hg/mouseStuff/chainBridge/tests/expected/noChange.bridged.chain
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    122bc264524b1dd6efc9dea3d59812c3da3529a1 Fri Jul 13 16:50:19 2018 -0700
    Adding test cases for chainBridge. refs #21660
• src/hg/mouseStuff/chainBridge/tests/expected/someChange.bridged.chain
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    122bc264524b1dd6efc9dea3d59812c3da3529a1 Fri Jul 13 16:50:19 2018 -0700
    Adding test cases for chainBridge. refs #21660
• src/hg/mouseStuff/chainBridge/tests/input/hg19ToHg38.awful.chain
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    122bc264524b1dd6efc9dea3d59812c3da3529a1 Fri Jul 13 16:50:19 2018 -0700
    Adding test cases for chainBridge. refs #21660
• src/hg/mouseStuff/chainBridge/tests/input/hg19ToHg38.noChange.chain
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    122bc264524b1dd6efc9dea3d59812c3da3529a1 Fri Jul 13 16:50:19 2018 -0700
    Adding test cases for chainBridge. refs #21660
• src/hg/mouseStuff/chainBridge/tests/input/hg19ToHg38.someChange.chain
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    122bc264524b1dd6efc9dea3d59812c3da3529a1 Fri Jul 13 16:50:19 2018 -0700
    Adding test cases for chainBridge. refs #21660
• src/hg/mouseStuff/chainBridge/tests/makefile
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    122bc264524b1dd6efc9dea3d59812c3da3529a1 Fri Jul 13 16:50:19 2018 -0700
    Adding test cases for chainBridge. refs #21660
• src/hg/utils/agpAlign/tests/expected/testHg19ToHg38.psl
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    205d4d9abc4262f430203184d1b62fe24250a33f Fri Jul 13 13:17:25 2018 -0700
    Adding test case for agpAlign. refs #21660
• src/hg/utils/agpAlign/tests/expected/testHg38ToHg19.psl
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    205d4d9abc4262f430203184d1b62fe24250a33f Fri Jul 13 13:17:25 2018 -0700
    Adding test case for agpAlign. refs #21660
• src/hg/utils/agpAlign/tests/input/test.hg19.chrom.sizes
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    205d4d9abc4262f430203184d1b62fe24250a33f Fri Jul 13 13:17:25 2018 -0700
    Adding test case for agpAlign. refs #21660
• src/hg/utils/agpAlign/tests/input/test.hg19.comp.agp
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    205d4d9abc4262f430203184d1b62fe24250a33f Fri Jul 13 13:17:25 2018 -0700
    Adding test case for agpAlign. refs #21660
• src/hg/utils/agpAlign/tests/input/test.hg38.chrom.sizes
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    205d4d9abc4262f430203184d1b62fe24250a33f Fri Jul 13 13:17:25 2018 -0700
    Adding test case for agpAlign. refs #21660
• src/hg/utils/agpAlign/tests/input/test.hg38.comp.agp
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    205d4d9abc4262f430203184d1b62fe24250a33f Fri Jul 13 13:17:25 2018 -0700
    Adding test case for agpAlign. refs #21660
• src/hg/utils/agpAlign/tests/makefile
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    205d4d9abc4262f430203184d1b62fe24250a33f Fri Jul 13 13:17:25 2018 -0700
    Adding test case for agpAlign. refs #21660
• src/hg/utils/automation/openStack/initParasol
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    881b58fb84858be273ecc0a0437f48531b8ac213 Thu Jul 12 11:23:37 2018 -0700
    correctly remove and add machines when resurrecting nodes refs #18874
• src/hg/utils/automation/openStack/paraHubSetup.sh
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    99bd950f66d2ab880841a0867d1ef883ac5c04fa Wed Jul 11 14:23:14 2018 -0700
    NFS exports needs to happen earlier refs #18874
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    5217655c0cbb3b72529f5d92ea4e37d1cf8a7618 Thu Jul 12 09:33:47 2018 -0700
    correctly setup /mnt/data/ refs #18874
• src/hg/utils/automation/openStack/paraNodeSetup.sh.template
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    56a3dccf5300faad732bb3a9f653112714e77a47 Wed Jul 11 10:22:40 2018 -0700
    updated to manage mnt and export from hub as mnt/data refs #18874
• src/hg/utils/gapToLift/gapToLift.c
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    cb473e9cc9f1013ca21d300b852873864f87e2aa Tue Jul 10 11:40:24 2018 -0700
    add allowBridged option refs #21715
• src/hg/utils/otto/geneReviews/checkGeneReviews.sh
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    c12e3b979e2d72f9b2f48a6f646a5b34c5ae6bed Wed Jul 11 10:21:58 2018 -0700
    Suppressing wget output in geneReviews otto build email, refs #18151
• src/hg/utils/phyloTrees/220.nh
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    bd81937d0a0aa0198bb47969902260ba29731e5d Tue Jul 10 10:29:57 2018 -0700
    adding ambMex1 Axolotl refs #21715
• src/utils/bedGraphToBigWig/bedGraphToBigWig.c
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    0ead254c2c73349eb7783877c5fc8a7fce94b233 Fri Jul 13 12:31:11 2018 -0700
    Making errAbort messages more explicit about being errors, following feedback from a user who didn't realize their partial output file was not a successful result (and didn't understand why it wasn't loading). No ticket.
• src/utils/qa/weeklybld/buildEnv.csh
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    6560d2ee6dec726908f1e230e7d75cec06d4c58a Mon Jul 16 10:06:33 2018 -0700
    v369 preview1, refs #21667
• src/utils/qa/weeklybld/makeUserApps.csh
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    5006160663afdcf527417df5cd98d5a3a983dd05 Thu Jul 12 18:56:48 2018 -0700
    hgdownload recognizes FOOTER.txt, but not FOOTER. Changing file name accordingly. No ticket.

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