Commits for hiram

v400_preview2 to v400_base (2020-06-15 to 2020-06-22) v400

a35f450f1d4f1f128460141ab8e8faea28980fe6 Mon Jun 15 10:35:08 2020 -0700

• adding rules for panPan3 refs #25720
  • src/hg/makeDb/schema/all.joiner - lines changed 8, context: html, text, full: html, text

86543de97fd1c1f6d8c3c34e23109ffc3703cf82 Mon Jun 15 10:39:41 2020 -0700

• starting lastz chain net to panPan3 refs #25720
  • src/hg/makeDb/doc/mm10.txt - lines changed 66, context: html, text, full: html, text

9d279d553cfcde698a092b45550c8a1d5341b62f Mon Jun 15 10:40:15 2020 -0700

• starting crispr run refs #25720
  • src/hg/makeDb/doc/panPan3/initialBuild.txt - lines changed 30, context: html, text, full: html, text

4e7d82cb16cd4cea93698834b637815cd74c7960 Mon Jun 15 17:35:53 2020 -0700

• adding definitions for panPan3 chainNet refs #25720
  • src/hg/makeDb/trackDb/human/chainNetPrimate.ra - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.chainNet.primates.ra - lines changed 54, context: html, text, full: html, text

76fba02a1a3d0f8a66beebaafce75b2770407522 Tue Jun 16 12:54:12 2020 -0700

• liftOvers to panPan3 refs #25720
  • src/hg/makeDb/doc/panPan1.txt - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/doc/panPan2/initialBuild.txt - lines changed 19, context: html, text, full: html, text

6a31a3cb05530a6c630b865796b58d4406f3ea0e Tue Jun 16 13:21:58 2020 -0700

• lastz chain Net to panPan3 refs #25720
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 82, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm10.txt - lines changed 16, context: html, text, full: html, text

f3de53bf75b2281935c4635b661b44413dcd8d78 Tue Jun 16 15:56:47 2020 -0700

• new asmEquivalent loaded refs #25744
  • src/hg/makeDb/doc/assemblyEquivalence/update.2020-06-15.txt - lines changed 157, context: html, text, full: html, text

982d69ac4a666c4ff32f7ed167f788b81d960285 Wed Jun 17 12:30:05 2020 -0700

• reduce the vertical space consumed by options and explanations refs #25555
  • src/hg/makeDb/doc/asmHubs/mkAsmStats.pl - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/mkHubIndex.pl - lines changed 25, context: html, text, full: html, text

ec085390d79da88eac31afc7e9b4efb40c5e554b Wed Jun 17 12:32:56 2020 -0700

• the VGP class is sharks not snakes refs #25555
  • src/hg/makeDb/doc/vgpAsmHub/altMakefile - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/legacyMakefile - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/makefile - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/trioMakefile - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/userDataMakefile - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt - lines changed 5, context: html, text, full: html, text

76c6e48fa890a9ccb5c25798fe0bccffc814fc63 Wed Jun 17 12:35:00 2020 -0700

• one off tracks for Arang.s data refs #25555
  • src/hg/makeDb/doc/vgpAsmHub/vgp.userTracks.tsv - lines changed 17, context: html, text, full: html, text

0c6145f99f76da49d5bbed9d2e775bb5a619c2ab Wed Jun 17 14:08:34 2020 -0700

• no need to sed names now that commonHtml.pm is used refs #25555
  • src/hg/makeDb/doc/asmHubs/asmHubs.mk - lines changed 4, context: html, text, full: html, text

c1652ce0c3eb547b499bb530f27228b6cbd4607b Wed Jun 17 14:23:22 2020 -0700

• eliminate useless views and references to phyloP phastCons mostConserved refs #25569
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.7way.ra - lines changed 90, context: html, text, full: html, text

d1779bfd20329fc0fac2f2fef3fdb43d519ca402 Wed Jun 17 16:17:32 2020 -0700

• line break request refs #25555
  • src/hg/makeDb/doc/asmHubs/mkHubIndex.pl - lines changed 1, context: html, text, full: html, text

1a40e3021a59b8139fd74aa9aa6cc0146e6273d8 Fri Jun 19 09:06:35 2020 -0700

• now using unique hub.txt files for each subset refs #25555
  • src/hg/makeDb/doc/asmHubs/asmHubs.mk - lines changed 2, context: html, text, full: html, text

ca4529ed736df2bff629dcbfcaaef4b1c1a24160 Fri Jun 19 09:07:55 2020 -0700

• now using unique hub.txt files for each subset refs #25555
  • src/hg/makeDb/doc/vgpAsmHub/altMakefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/legacyMakefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/trioMakefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/userDataMakefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgpAltHub.txt - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgpLegacyHub.txt - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgpTrioHub.txt - lines changed 6, context: html, text, full: html, text

e406546091f3ce7fd7677a1ca86f08b3bf23d2c3 Fri Jun 19 09:58:08 2020 -0700

• unique short and long label for this primary set refs #25555
  • src/hg/makeDb/doc/vgpAsmHub/hub.txt - lines changed 2, context: html, text, full: html, text

c15d38611d858377a05366fd11f507f4dbf90cac Fri Jun 19 10:51:55 2020 -0700

• trying to get masking done with a special library refs #23367
  • src/hg/makeDb/doc/ambMex2/initialBuild.txt - lines changed 974, context: html, text, full: html, text

de697f3424320f0679649fcba305e3b8641d3cad Fri Jun 19 12:19:07 2020 -0700

• attempt to work without an NCBI lift file and issue warning refs #23367
  • src/hg/utils/automation/doRepeatMasker.pl - lines changed 14, context: html, text, full: html, text