Commits for hiram

v456_preview2 to v456_base (2023-10-23 to 2023-10-30) v456

0fb0515d36b58fbf20109d736e2c327e891430cd Tue Oct 24 11:17:50 2023 -0700

• VGP update adds 24 birds refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 33, context: html, text, full: html, text

da4f13a10991eeea650596371fd2879b99222a9b Tue Oct 24 21:12:47 2023 -0700

• Eurasian badger v3.1 has moved to legacy refs #29545
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 1, context: html, text, full: html, text

0b5a1f431e69714e84403c73c87ecfb48c78a553 Wed Oct 25 10:08:46 2023 -0700

• VGP update adding 23 fish refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 23, context: html, text, full: html, text
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 28, context: html, text, full: html, text

af46043499a829ab8e1bafcc2b37c761139e24a8 Wed Oct 25 10:26:46 2023 -0700

• VGP update adding 10 vertebrate refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 14, context: html, text, full: html, text

736710b4abb6ab631057f752e7a8e1b3411f1a36 Wed Oct 25 14:14:14 2023 -0700

• correct text description for query vs. target genomes for single line gap annotation meaning refs #32455
  • src/hg/makeDb/trackDb/chicken/galGal6/chainNet.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/hg19ChainNet.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/hg38primateChainNet.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/primateChainNet.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/t2tChain.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/placentalChainNet.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/primateChainNet.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/vertebrateChainNet.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/chainNet.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/vertebrateChainNet.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/mm39ChainNet.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn6/ratChainNet.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer7/danRer7multipleChainNet.html - lines changed 1, context: html, text, full: html, text

0f9e84d70ea5f9b94011729c486ca220be9bcfcb Wed Oct 25 14:21:14 2023 -0700

• there is no o_organism for these refs #32455
  • src/hg/makeDb/trackDb/mouse/mm10/chainNet.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/vertebrateChainNet.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/mm39ChainNet.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn6/ratChainNet.html - lines changed 1, context: html, text, full: html, text

75479452cf7a3eeeb3844e02cec904789d2bc14a Wed Oct 25 15:01:28 2023 -0700

• VGP update adding 9 mammal assemblies refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 14, context: html, text, full: html, text

f3b5d52f647e993599786170af8931721631259e Thu Oct 26 10:57:48 2023 -0700

• update adding 8 invertebrates refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 1, context: html, text, full: html, text

43e778085a841c112d25ff9d12da71083d1d99ec Thu Oct 26 12:05:46 2023 -0700

• illegal second copy of the same genome GCF_029834395.1 refs #29545
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 1, context: html, text, full: html, text

d0bcef580cd0c19bbe20a2c401e0baf62410790c Thu Oct 26 12:52:03 2023 -0700

• add sanityCheck to prevent duplicate accession IDs from leaking into the tsv orderList refs #29545
  • src/hg/makeDb/doc/asmHubs/asmHubs.mk - lines changed 10, context: html, text, full: html, text

c8cc281d9175f01aeda71372a49d3cd94b6eca90 Thu Oct 26 13:10:38 2023 -0700

• update adding 5 plants refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv - lines changed 7, context: html, text, full: html, text

6fd3a06eb1fdeb0992cead0af6ab3bb6bcd4024d Thu Oct 26 13:39:44 2023 -0700

• update adding 2 fish and 2 birds refs @29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 2, context: html, text, full: html, text

1b416ef57918a097a1da32249baa3fc7b675e18a Thu Oct 26 14:15:01 2023 -0700

• updated obsolte two birds refs #29545
  • src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 2, context: html, text, full: html, text

71c76a53f1894e0dcff810c06a35cc14fad66bde Thu Oct 26 19:40:25 2023 -0700

• update Atlantic stingray hap1 from genbank to refseq refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 2, context: html, text, full: html, text

e375c20d377485c5a56df45a9094833cb6738d54 Fri Oct 27 09:51:54 2023 -0700

• adding GCA_010365825.1_OtuSun1.0 Oriental scops-owl (oso-nibr-517 2020) per user request refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 1, context: html, text, full: html, text

411af8fc818febf61de8210a3cc05b019d9c8d2a Fri Oct 27 10:39:09 2023 -0700

• the missing files need to be marked as an error refs #29545
  • src/hg/makeDb/doc/asmHubs/mkSymLinks.pl - lines changed 3, context: html, text, full: html, text

9c779856e423e2f2030758080f93d8e1448b95b1 Fri Oct 27 10:44:05 2023 -0700

• do not need to do twoBitToFa twice in addMask, once is enough refs #29545
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 5, context: html, text, full: html, text

9db1c1b33a7d1db0f06783b71f81ed96a87ecb76 Fri Oct 27 15:01:53 2023 -0700

• VGP update to catch up with current listings refs #25555
  • src/hg/makeDb/doc/vgpAsmHub/vgp.alternate.orderList.tsv - lines changed 112, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv - lines changed 119, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt - lines changed 176, context: html, text, full: html, text