File Changes for hiram

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v434_base to v435_preview (2022-07-18 to 2022-07-25) v435

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src/hg/makeDb/doc/asmHubs/commonHtml.pm
- lines changed 4, context: html, text, full: html, text
  2862b2a8ea3a56805265df693bf94a4ed7d07cca Thu Jul 21 18:04:51 2022 -0700
  adding the viral group to the index page footer table and special sets of columns for virus index pages refs #29545
src/hg/makeDb/doc/asmHubs/lastzRuns.txt
- lines changed 79, context: html, text, full: html, text
  6428d3411111567658e7496a9d131dcbe85034f6 Tue Jul 19 11:36:26 2022 -0700
  platypus to platypus per user request refs #29753
src/hg/makeDb/doc/asmHubs/master.run.list
- lines changed 150, context: html, text, full: html, text
  38596ae2e82cc2e3d6e7b037aaa5bfc609e03177 Wed Jul 20 17:24:33 2022 -0700
  adding 150 human virus genome builds refs #29484
- lines changed 101, context: html, text, full: html, text
  e027227ddfc859d20fdf629f9ea606b5a578861e Fri Jul 22 22:31:34 2022 -0700
  adding another set of viruses related to human diseases refs #29484
src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
- lines changed 29, context: html, text, full: html, text
  2862b2a8ea3a56805265df693bf94a4ed7d07cca Thu Jul 21 18:04:51 2022 -0700
  adding the viral group to the index page footer table and special sets of columns for virus index pages refs #29545
src/hg/makeDb/doc/asmHubs/trackData.pl
- lines changed 18, context: html, text, full: html, text
  2862b2a8ea3a56805265df693bf94a4ed7d07cca Thu Jul 21 18:04:51 2022 -0700
  adding the viral group to the index page footer table and special sets of columns for virus index pages refs #29545
- lines changed 2, context: html, text, full: html, text
  7a68602b325c40864c6937bc5803c4afd606bc9d Thu Jul 21 20:19:43 2022 -0700
  customize the track table for viral genomes refs #29545
src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh
- lines changed 7, context: html, text, full: html, text
  8f226d9ae51d5aa0907e717fb310cab91a54cf87 Wed Jul 20 17:21:05 2022 -0700
  better choice of common names and manage lower valid track count for viruses refs #29484
src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
- lines changed 1, context: html, text, full: html, text
  3ceca135069039ba2ce2290cc909128f3777dcc4 Fri Jul 22 23:40:38 2022 -0700
  this one GCF_000951615.1_common_carp_genome is in legacy refs #29545
src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
- lines changed 222, context: html, text, full: html, text
  a15d57f02b4b49c9e3dbceaad6234e340ec96bbd Thu Jul 21 17:04:25 2022 -0700
  improve the legacy index page with a GenArk clade indication refs #29545
src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
- lines changed 10, context: html, text, full: html, text
  fe31f12c7713e5cfa4612a64f70752388646c424 Thu Jul 21 09:25:50 2022 -0700
  catch up listing with zoo241 genomes refs #29545
- lines changed 1, context: html, text, full: html, text
  5654588935d1aa4ea6cbc928d2b5706d275a6249 Fri Jul 22 23:41:56 2022 -0700
  this one GCA_000738955.1_M_pentadactyla-1.1.1 is in mammals not legacy yet refs #29545
src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
- lines changed 13, context: html, text, full: html, text
  d017527e4dddb716147a243efe2bb38d1acff329 Thu Jul 21 09:27:24 2022 -0700
  catch up listing with zoo241 genomes refs #29545
- lines changed 1, context: html, text, full: html, text
  41a463cd8f3d221e36fd583e4d58dd12993f0975 Fri Jul 22 23:40:10 2022 -0700
  this one GCA_004026985.1_MyoMyo_v1_BIUU is in legacy refs #29545
src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
- lines changed 2, context: html, text, full: html, text
  035f7ea1c057b4923fc64f7bea14b3bae513ea2e Thu Jul 21 09:24:08 2022 -0700
  catch up listing with zoo241 genomes refs #29545
src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
- lines changed 152, context: html, text, full: html, text
  6cb40b8c7c2d15cf867031a5039a1ed1f198d04f Wed Jul 20 17:18:42 2022 -0700
  adding all human viruses from refseq about 150 refs #29484
- lines changed 1, context: html, text, full: html, text
  837e1e89d23da949d16c0f9e6cd00eed3788642c Wed Jul 20 19:10:24 2022 -0700
  no need to have SARS-CoV-2 on this list refs #29484
- lines changed 236, context: html, text, full: html, text
  50060dece064d88d993690dfbb67a802c7d3578e Fri Jul 22 22:51:33 2022 -0700
  adding another set of viruses related to human diseases refs #29484
src/hg/makeDb/trackDb/human/hs1/assembly.trackDb.ra
- lines changed 16, context: html, text, full: html, text
  d1c7d424a88170e9153809be96213b4a30259187 Tue Jul 19 13:48:36 2022 -0700
  split of sections of trackDb to individual track includes refs #29762trackDb.ra
src/hg/makeDb/trackDb/human/hs1/cpgIslands.trackDb.ra
- lines changed 25, context: html, text, full: html, text
  d1c7d424a88170e9153809be96213b4a30259187 Tue Jul 19 13:48:36 2022 -0700
  split of sections of trackDb to individual track includes refs #29762trackDb.ra
src/hg/makeDb/trackDb/human/hs1/gc5Base.trackDb.ra
- lines changed 17, context: html, text, full: html, text
  d1c7d424a88170e9153809be96213b4a30259187 Tue Jul 19 13:48:36 2022 -0700
  split of sections of trackDb to individual track includes refs #29762trackDb.ra
src/hg/makeDb/trackDb/human/hs1/humanChainNet.trackDb.ra
- lines changed 415, context: html, text, full: html, text
  3e88efb3cf44c9e58c3297c0aeb2a2c36bd27dfe Tue Jul 19 13:58:02 2022 -0700
  split off sections of trackDb to individual track includes refs #29762
src/hg/makeDb/trackDb/human/hs1/ncbiRefSeq.trackDb.ra
- lines changed 93, context: html, text, full: html, text
  3e88efb3cf44c9e58c3297c0aeb2a2c36bd27dfe Tue Jul 19 13:58:02 2022 -0700
  split off sections of trackDb to individual track includes refs #29762
src/hg/makeDb/trackDb/human/hs1/simpleRepeat.trackDb.ra
- lines changed 9, context: html, text, full: html, text
  d1c7d424a88170e9153809be96213b4a30259187 Tue Jul 19 13:48:36 2022 -0700
  split of sections of trackDb to individual track includes refs #29762trackDb.ra
src/hg/makeDb/trackDb/human/hs1/trackDb.ra
- lines changed 596, context: html, text, full: html, text
  3e88efb3cf44c9e58c3297c0aeb2a2c36bd27dfe Tue Jul 19 13:58:02 2022 -0700
  split off sections of trackDb to individual track includes refs #29762
src/hg/makeDb/trackDb/human/hs1/windowMasker.trackDb.ra
- lines changed 9, context: html, text, full: html, text
  3e88efb3cf44c9e58c3297c0aeb2a2c36bd27dfe Tue Jul 19 13:58:02 2022 -0700
  split off sections of trackDb to individual track includes refs #29762
src/hg/makeDb/trackDb/human/hs1/xenoRefGene.trackDb.ra
- lines changed 13, context: html, text, full: html, text
  3e88efb3cf44c9e58c3297c0aeb2a2c36bd27dfe Tue Jul 19 13:58:02 2022 -0700
  split off sections of trackDb to individual track includes refs #29762
src/hg/utils/automation/asmHubRepeatMasker.sh
- lines changed 24, context: html, text, full: html, text
  3c8ffb11a3e0a8830f64c3e19ca7f7ff8b167f33 Wed Jul 20 17:19:51 2022 -0700
  handle cases where there is no result from RepeatMasker or TRF simple repeats for virus browser building refs #29484
src/hg/utils/automation/asmHubTrackDb.sh
- lines changed 3, context: html, text, full: html, text
  3c8ffb11a3e0a8830f64c3e19ca7f7ff8b167f33 Wed Jul 20 17:19:51 2022 -0700
  handle cases where there is no result from RepeatMasker or TRF simple repeats for virus browser building refs #29484
- lines changed 20, context: html, text, full: html, text
  5b5a242f38f695c23bc52e5388b941b8335307df Thu Jul 21 20:18:42 2022 -0700
  properly eliminate rmsk from trackDb when there are no items in the track refs #29545
src/hg/utils/automation/doAssemblyHub.pl
- lines changed 32, context: html, text, full: html, text
  3c8ffb11a3e0a8830f64c3e19ca7f7ff8b167f33 Wed Jul 20 17:19:51 2022 -0700
  handle cases where there is no result from RepeatMasker or TRF simple repeats for virus browser building refs #29484
src/utils/bedSingleCover.pl
- lines changed 2, context: html, text, full: html, text
  75fb410e4222543ccdc30335f02247649e0d7186 Wed Jul 20 12:51:15 2022 -0700
  output nothing when nothing to output no redmine

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