File Changes for hiram

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v408_preview2 to v408_base (2020-11-30 to 2020-12-07) v408

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src/hg/hgTracks/wigTrack.c
- lines changed 2, context: html, text, full: html, text
  c1a9283f4164879abb6d6eb36a7ae39537706c73 Fri Dec 4 15:19:37 2020 -0800
  restore two lines which were thought to be dead code. Resurrected from the dead. refs #26637
src/hg/makeDb/doc/asmHubs/asmHubs.mk
- lines changed 3, context: html, text, full: html, text
  86b6f856f6131c16ac920d1604a1c1fe3ef9845f Fri Dec 4 16:40:35 2020 -0800
  adding legacy hub and correct links in trackData refs #23891
src/hg/makeDb/doc/asmHubs/commonHtml.pm
- lines changed 4, context: html, text, full: html, text
  86b6f856f6131c16ac920d1604a1c1fe3ef9845f Fri Dec 4 16:40:35 2020 -0800
  adding legacy hub and correct links in trackData refs #23891
src/hg/makeDb/doc/asmHubs/master.run.list
- lines changed 449, context: html, text, full: html, text
  04e6795d4c5c364da07a3d2c1e73585310e5ad41 Mon Nov 30 16:22:52 2020 -0800
  keeping track of the assembly hub production, this is a list of hubs completed refs #23891
- lines changed 44, context: html, text, full: html, text
  16b6442ca6e05286dae290d65ca4508734143a33 Tue Dec 1 12:35:04 2020 -0800
  catching up with updated build list refs #23891
- lines changed 17, context: html, text, full: html, text
  a7c4f2e7ca8a5d7f1bc28c43f6e243206b58ac51 Sun Dec 6 12:01:29 2020 -0800
  catching up more vertebrates refs #23891
src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
- lines changed 1, context: html, text, full: html, text
  7b56acab5e13b635fa964e8ef6707cccaf0e640c Fri Dec 4 16:34:28 2020 -0800
  better information on what is missing refs #23891
src/hg/makeDb/doc/asmHubs/runBuild
- lines changed 153, context: html, text, full: html, text
  76cb5f9fd7108a71a14b834d8e5a9def0fdd2150 Sat Dec 5 22:53:37 2020 -0800
  capture current build script refs #23891
src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
- lines changed 1, context: html, text, full: html, text
  00dd865686fa361f20b8750606d3607a977ca3ef Fri Dec 4 16:33:29 2020 -0800
  catching up with new assembly hubs refs #23891
src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
- lines changed 11, context: html, text, full: html, text
  00dd865686fa361f20b8750606d3607a977ca3ef Fri Dec 4 16:33:29 2020 -0800
  catching up with new assembly hubs refs #23891
src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
- lines changed 6, context: html, text, full: html, text
  00dd865686fa361f20b8750606d3607a977ca3ef Fri Dec 4 16:33:29 2020 -0800
  catching up with new assembly hubs refs #23891
src/hg/makeDb/doc/legacyAsmHub/hub.txt
- lines changed 6, context: html, text, full: html, text
  47f51f1afeb71f16b2a29cabfc5e81b4615d2966 Mon Nov 30 13:03:36 2020 -0800
  beginning to move out of date hubs to this legacy group refs #23891
src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
- lines changed 7, context: html, text, full: html, text
  47f51f1afeb71f16b2a29cabfc5e81b4615d2966 Mon Nov 30 13:03:36 2020 -0800
  beginning to move out of date hubs to this legacy group refs #23891
- lines changed 4, context: html, text, full: html, text
  00dd865686fa361f20b8750606d3607a977ca3ef Fri Dec 4 16:33:29 2020 -0800
  catching up with new assembly hubs refs #23891
src/hg/makeDb/doc/legacyAsmHub/makefile
- lines changed 26, context: html, text, full: html, text
  47f51f1afeb71f16b2a29cabfc5e81b4615d2966 Mon Nov 30 13:03:36 2020 -0800
  beginning to move out of date hubs to this legacy group refs #23891
src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
- lines changed 11, context: html, text, full: html, text
  00dd865686fa361f20b8750606d3607a977ca3ef Fri Dec 4 16:33:29 2020 -0800
  catching up with new assembly hubs refs #23891
src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
- lines changed 4, context: html, text, full: html, text
  00dd865686fa361f20b8750606d3607a977ca3ef Fri Dec 4 16:33:29 2020 -0800
  catching up with new assembly hubs refs #23891
src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
- lines changed 2, context: html, text, full: html, text
  00dd865686fa361f20b8750606d3607a977ca3ef Fri Dec 4 16:33:29 2020 -0800
  catching up with new assembly hubs refs #23891
src/hg/makeDb/doc/vgpAsmHub/vgp.legacy.orderList.tsv
- lines changed 4, context: html, text, full: html, text
  f93e98fc9967bd790a6155e82cc7d2409139b2f9 Mon Nov 30 17:01:26 2020 -0800
  catching up with new assemblies refs #23734
- lines changed 1, context: html, text, full: html, text
  00dd865686fa361f20b8750606d3607a977ca3ef Fri Dec 4 16:33:29 2020 -0800
  catching up with new assembly hubs refs #23891
src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv
- lines changed 16, context: html, text, full: html, text
  f93e98fc9967bd790a6155e82cc7d2409139b2f9 Mon Nov 30 17:01:26 2020 -0800
  catching up with new assemblies refs #23734
- lines changed 1, context: html, text, full: html, text
  00dd865686fa361f20b8750606d3607a977ca3ef Fri Dec 4 16:33:29 2020 -0800
  catching up with new assembly hubs refs #23891
src/hg/makeDb/doc/vgpAsmHub/vgp.taxId,asmId.class.txt
- lines changed 166, context: html, text, full: html, text
  bc8e1eda6f35a3b241241b30ca5b5028f802e86f Mon Nov 30 17:04:05 2020 -0800
  incorrect file name refs #23734
src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt
- lines changed 8, context: html, text, full: html, text
  f93e98fc9967bd790a6155e82cc7d2409139b2f9 Mon Nov 30 17:01:26 2020 -0800
  catching up with new assemblies refs #23734
- lines changed 2, context: html, text, full: html, text
  eb6ffba6a690073514ca8977c6e0410f8657e20d Fri Dec 4 16:49:49 2020 -0800
  catching up with new assembly hubs refs #23891
src/hg/makeDb/doc/vgpAsmHub/vgp.trio.orderList.tsv
- lines changed 1, context: html, text, full: html, text
  00dd865686fa361f20b8750606d3607a977ca3ef Fri Dec 4 16:33:29 2020 -0800
  catching up with new assembly hubs refs #23891
src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra
- lines changed 56, context: html, text, full: html, text
  1596652e312cb81a414ccbd0f393bfb0921d5f90 Wed Dec 2 12:56:30 2020 -0800
  trying a chainNet with dot names refs #26584
- lines changed 1, context: html, text, full: html, text
  8583c65794346572e48e118f4854f7980256a458 Wed Dec 2 13:03:47 2020 -0800
  type bigChain needs a database name refs #26584
src/hg/utils/automation/doAssemblyHub.pl
- lines changed 9, context: html, text, full: html, text
  9a693302d1b139fb9e045ac1032345ccbef293a3 Mon Nov 30 15:48:45 2020 -0800
  correct order of names file for fakeAgp refs #24396
src/hg/utils/automation/doIdKeys.pl
- lines changed 2, context: html, text, full: html, text
  71839b5c94882709f10f982ff4d91b8da3e23ec4 Fri Dec 4 23:34:55 2020 -0800
  twoBitDup has been improved can now run up very large contig counts in one go refs #23891
src/hg/utils/automation/doNcbiRefSeq.pl
- lines changed 12, context: html, text, full: html, text
  06be530f59c8628ccc70d7087528b2d78eaca226 Mon Nov 30 15:49:52 2020 -0800
  correctly removing duplicate names refs #24396
src/utils/twoBitDup/twoBitDup.c
- lines changed 17, context: html, text, full: html, text
  469949aeb805fd5ad78395c248fe62bc583ccbf9 Fri Dec 4 23:28:46 2020 -0800
  use MD5() from openssl instead of md5HexForString() hundreds of times faster refs #23891
- lines changed 3, context: html, text, full: html, text
  8a2514bdfd594490e0a459fa72364af995a56ddb Sat Dec 5 23:07:19 2020 -0800
  no longer need the warning about excessive time with the keyList option refs #23891

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