File Changes for hiram

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v392_preview2 to v392_base (2019-12-16 to 2020-01-06) v392

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src/hg/htdocs/images/phylo/regenCho1_7way.png
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  bbb2c537ecb4b7736ccd5b4d038e3158ba71e382 Thu Dec 19 13:57:22 2019 -0800
  regenCho1 7-way phylo tree refs #24568
src/hg/hubApi/apiUtils.c
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  e40ef673e43640059fa00f7ee103f12367152f3d Thu Jan 2 10:32:53 2020 -0800
  update restricted list for lovd tables Short Long and add redmine24666 test refs #24666
src/hg/hubApi/getData.c
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  487174a2ad313bc229c6733ce263fb6a4413d50f Wed Dec 18 14:26:41 2019 -0800
  start=end=0 does not work for NIB fetch sequence refs #24666
src/hg/hubApi/tests/expected/err45.gz
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  e40ef673e43640059fa00f7ee103f12367152f3d Thu Jan 2 10:32:53 2020 -0800
  update restricted list for lovd tables Short Long and add redmine24666 test refs #24666
src/hg/hubApi/tests/expected/err47.gz
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  e40ef673e43640059fa00f7ee103f12367152f3d Thu Jan 2 10:32:53 2020 -0800
  update restricted list for lovd tables Short Long and add redmine24666 test refs #24666
src/hg/hubApi/tests/expected/list03.gz
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  a294ea346dc9c75b388aee27be600aee90174c23 Thu Jan 2 11:20:14 2020 -0800
  fixup tests to eliminate differences between hgwdev test vs. RR site same test no redmine
src/hg/hubApi/tests/expected/list09.gz
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  a294ea346dc9c75b388aee27be600aee90174c23 Thu Jan 2 11:20:14 2020 -0800
  fixup tests to eliminate differences between hgwdev test vs. RR site same test no redmine
src/hg/hubApi/tests/expected/redmine24666.gz
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  e40ef673e43640059fa00f7ee103f12367152f3d Thu Jan 2 10:32:53 2020 -0800
  update restricted list for lovd tables Short Long and add redmine24666 test refs #24666
src/hg/hubApi/tests/makefile
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  e40ef673e43640059fa00f7ee103f12367152f3d Thu Jan 2 10:32:53 2020 -0800
  update restricted list for lovd tables Short Long and add redmine24666 test refs #24666
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  a294ea346dc9c75b388aee27be600aee90174c23 Thu Jan 2 11:20:14 2020 -0800
  fixup tests to eliminate differences between hgwdev test vs. RR site same test no redmine
src/hg/makeDb/doc/globalReference/README.txt
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  147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
  set of files for hub build refs @24354
src/hg/makeDb/doc/globalReference/accAsmId.list
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  147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
  set of files for hub build refs @24354
src/hg/makeDb/doc/globalReference/commonNameOrder.list
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  147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
  set of files for hub build refs @24354
src/hg/makeDb/doc/globalReference/commonNames.txt
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  147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
  set of files for hub build refs @24354
src/hg/makeDb/doc/globalReference/ethnicGroup.txt
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  147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
  set of files for hub build refs @24354
src/hg/makeDb/doc/globalReference/family.txt
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  147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
  set of files for hub build refs @24354
src/hg/makeDb/doc/globalReference/groups.txt
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  147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
  set of files for hub build refs @24354
src/hg/makeDb/doc/globalReference/hub.txt
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  147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
  set of files for hub build refs @24354
src/hg/makeDb/doc/globalReference/human.list
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  147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
  set of files for hub build refs @24354
src/hg/makeDb/doc/globalReference/isolate.txt
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  147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
  set of files for hub build refs @24354
src/hg/makeDb/doc/globalReference/makefile
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  147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
  set of files for hub build refs @24354
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  8bde61c3efd8828518d70bfc287c600b86683f68 Thu Jan 2 13:22:14 2020 -0800
  add hub.txt and groups.txt copies refs #24354
src/hg/makeDb/doc/globalReference/mkAsmStats.pl
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  147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
  set of files for hub build refs @24354
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  27228c7e494674469a64cdeb61d7c4e433102f24 Thu Jan 2 13:16:14 2020 -0800
  updated text to global reference wording refs #24534
src/hg/makeDb/doc/globalReference/mkGenomes.pl
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  147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
  set of files for hub build refs @24354
src/hg/makeDb/doc/globalReference/mkHubIndex.pl
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  147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
  set of files for hub build refs @24354
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  27228c7e494674469a64cdeb61d7c4e433102f24 Thu Jan 2 13:16:14 2020 -0800
  updated text to global reference wording refs #24534
src/hg/makeDb/doc/globalReference/mkSymLinks.sh
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  147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
  set of files for hub build refs @24354
src/hg/makeDb/doc/globalReference/perlPara.pl
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  147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
  set of files for hub build refs @24354
src/hg/makeDb/doc/globalReference/run10.list
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  147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
  set of files for hub build refs @24354
src/hg/makeDb/doc/globalReference/runOne.sh
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  147dce6b6804f24a5396a7ccb0b3bee184d1f6a7 Thu Jan 2 11:47:50 2020 -0800
  set of files for hub build refs @24354
src/hg/makeDb/doc/primateAsmHub/groups.txt
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  2feb808479d0767a519a687c3948b1a21f1e8431 Fri Jan 3 13:31:23 2020 -0800
  initial set of files to create symlinks and index pages refs #20137
src/hg/makeDb/doc/primateAsmHub/hub.txt
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  2feb808479d0767a519a687c3948b1a21f1e8431 Fri Jan 3 13:31:23 2020 -0800
  initial set of files to create symlinks and index pages refs #20137
src/hg/makeDb/doc/primateAsmHub/makefile
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  2feb808479d0767a519a687c3948b1a21f1e8431 Fri Jan 3 13:31:23 2020 -0800
  initial set of files to create symlinks and index pages refs #20137
src/hg/makeDb/doc/primateAsmHub/mkAsmStats.pl
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  2feb808479d0767a519a687c3948b1a21f1e8431 Fri Jan 3 13:31:23 2020 -0800
  initial set of files to create symlinks and index pages refs #20137
src/hg/makeDb/doc/primateAsmHub/mkGenomes.pl
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  2feb808479d0767a519a687c3948b1a21f1e8431 Fri Jan 3 13:31:23 2020 -0800
  initial set of files to create symlinks and index pages refs #20137
src/hg/makeDb/doc/primateAsmHub/mkHubIndex.pl
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  2feb808479d0767a519a687c3948b1a21f1e8431 Fri Jan 3 13:31:23 2020 -0800
  initial set of files to create symlinks and index pages refs #20137
src/hg/makeDb/doc/primateAsmHub/mkList.sh
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  2feb808479d0767a519a687c3948b1a21f1e8431 Fri Jan 3 13:31:23 2020 -0800
  initial set of files to create symlinks and index pages refs #20137
src/hg/makeDb/doc/primateAsmHub/mkSymLinks.pl
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  2feb808479d0767a519a687c3948b1a21f1e8431 Fri Jan 3 13:31:23 2020 -0800
  initial set of files to create symlinks and index pages refs #20137
src/hg/makeDb/doc/primateAsmHub/primates.asmId.commonName.tsv
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  2feb808479d0767a519a687c3948b1a21f1e8431 Fri Jan 3 13:31:23 2020 -0800
  initial set of files to create symlinks and index pages refs #20137
src/hg/makeDb/doc/primateAsmHub/primates.commonName.asmId.orderList.tsv
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  2feb808479d0767a519a687c3948b1a21f1e8431 Fri Jan 3 13:31:23 2020 -0800
  initial set of files to create symlinks and index pages refs #20137
src/hg/makeDb/doc/rn6.txt
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  54c4f85da2fcff075df03bbce841043e0d5acc28 Tue Dec 17 08:31:41 2019 -0800
  lastz chainNet run regenCho1 vs. rn6 refs #24568
src/hg/makeDb/trackDb/criGri/regenCho1/cons7way.html
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  c1e99ae957ff7cd0b85aae8622779566054d4da0 Fri Dec 20 11:50:59 2019 -0800
  7-way multiz alignment refs #24524
src/hg/makeDb/trackDb/criGri/regenCho1/regenAGP.html
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  dc4b56b6156979617a0a79a99746f63c0090dcd2 Fri Dec 20 13:42:30 2019 -0800
  descriptions for AGP and gap definitions from the Regeneron AGP file refs #24524
src/hg/makeDb/trackDb/criGri/regenCho1/regenAGPGap.html
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  dc4b56b6156979617a0a79a99746f63c0090dcd2 Fri Dec 20 13:42:30 2019 -0800
  descriptions for AGP and gap definitions from the Regeneron AGP file refs #24524
src/hg/makeDb/trackDb/criGri/regenCho1/trackDb.7way.ra
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  c1e99ae957ff7cd0b85aae8622779566054d4da0 Fri Dec 20 11:50:59 2019 -0800
  7-way multiz alignment refs #24524
src/hg/makeDb/trackDb/criGri/regenCho1/trackDb.ra
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  c1e99ae957ff7cd0b85aae8622779566054d4da0 Fri Dec 20 11:50:59 2019 -0800
  7-way multiz alignment refs #24524
src/hg/makeDb/trackDb/rat/regenRn1/cons7way.html
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  9aa6bd8e92fd50cea40a4ac676493c9047ee03cd Fri Dec 20 13:15:54 2019 -0800
  documentation page for 7-way refs #21579
src/hg/utils/automation/asmHubGatewayPage.pl
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  d902053614e1eeeb5e84d4acf1dc4a2abb7120f8 Fri Jan 3 13:47:38 2020 -0800
  get the gateway page a bit more generic with argument to specify refs #20137
src/hg/utils/automation/asmHubTrackDb.sh
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  12b4622b8e00524ac3a6acd375fbf9a408ff41a6 Mon Dec 23 10:39:46 2019 -0800
  symlinks should be relative, not absolute refs #24354
src/hg/utils/automation/doAssemblyHub.pl
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  4ca6162650c6e0f213cf674642b7a2b6bcea9bc1 Fri Dec 27 00:50:12 2019 -0800
  now automatically eliminating duplicate sequences refs #24354
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  d902053614e1eeeb5e84d4acf1dc4a2abb7120f8 Fri Jan 3 13:47:38 2020 -0800
  get the gateway page a bit more generic with argument to specify refs #20137
src/hg/utils/automation/doXenoRefGene.pl
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  cb83116ca0be25e3e45c93468d951fe53cb2c1e4 Fri Dec 27 00:49:20 2019 -0800
  better partitioning of the target genome refs #24354
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  d902053614e1eeeb5e84d4acf1dc4a2abb7120f8 Fri Jan 3 13:47:38 2020 -0800
  get the gateway page a bit more generic with argument to specify refs #20137

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