File Changes for hiram

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v487_base to v488_preview (2025-09-01 to 2025-09-08) v488

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src/hg/lib/genomePriority.as
- lines changed 5, context: html, text, full: html, text
  f6c778facb8d507287c93ae2c4027cd09e1e7b8b Mon Sep 1 23:31:40 2025 -0700
  improved priority business refs #32897
src/hg/lib/genomePriority.c
- lines changed 116, context: html, text, full: html, text
  f6c778facb8d507287c93ae2c4027cd09e1e7b8b Mon Sep 1 23:31:40 2025 -0700
  improved priority business refs #32897
src/hg/lib/genomePriority.sql
- lines changed 11, context: html, text, full: html, text
  f6c778facb8d507287c93ae2c4027cd09e1e7b8b Mon Sep 1 23:31:40 2025 -0700
  improved priority business refs #32897
src/hg/makeDb/doc/asmHubs/compareJsonLists.py
- lines changed 47, context: html, text, full: html, text
  eaa0b77b060608e37c70bbc22f6aaa75aeb91c75 Mon Sep 1 22:54:28 2025 -0700
  helper script for minimalBuild.sh refs #29545
src/hg/makeDb/doc/asmHubs/dynaBlatLinks.sh
- lines changed 33, context: html, text, full: html, text
  911babaa75518844e606fa2e29ab92caaedaf377 Mon Sep 1 23:01:12 2025 -0700
  improved procedure
src/hg/makeDb/doc/asmHubs/findEquiv.py
- lines changed 14, context: html, text, full: html, text
  168c7a7081021c0656d309e61e00e070c66bfd2d Mon Sep 1 22:57:04 2025 -0700
  improved procedure refs #34917
src/hg/makeDb/doc/asmHubs/master.run.list
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  6fa70b95c35a30c56deef04db5297b04740ff776 Mon Sep 1 22:11:56 2025 -0700
  move list out of source tree
src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
- lines changed 6, context: html, text, full: html, text
  d8388d5ea3fcd84481a3ac81633ef927dc40679c Mon Sep 1 22:55:17 2025 -0700
  adding the quickLift links refs #29545
src/hg/makeDb/doc/asmHubs/updateLiftOverChain.pl
- lines changed 13, context: html, text, full: html, text
  e1db15e52f8b00f85ecd45ea54f68f9a8949f8c2 Mon Sep 1 22:59:47 2025 -0700
  refine the check refs #35575
src/hg/makeDb/doc/assemblyEquivalence/createNearMissRunList.pl
- lines changed 8, context: html, text, full: html, text
  0a3f8c738cfc06e5f7154258dd8a19dbc471c8d7 Mon Sep 1 23:41:56 2025 -0700
  improvements
src/hg/makeDb/doc/assemblyEquivalence/exact.sh
- lines changed 28, context: html, text, full: html, text
  0a3f8c738cfc06e5f7154258dd8a19dbc471c8d7 Mon Sep 1 23:41:56 2025 -0700
  improvements
src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
- lines changed 2, context: html, text, full: html, text
  99ec03901d84f8b2af5c0ca1e9956f6110291ab9 Mon Sep 1 22:03:31 2025 -0700
  adding a couple per user request refs #29545
src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
- lines changed 1, context: html, text, full: html, text
  99ec03901d84f8b2af5c0ca1e9956f6110291ab9 Mon Sep 1 22:03:31 2025 -0700
  adding a couple per user request refs #29545
src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
- lines changed 1, context: html, text, full: html, text
  99ec03901d84f8b2af5c0ca1e9956f6110291ab9 Mon Sep 1 22:03:31 2025 -0700
  adding a couple per user request refs #29545
src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
- lines changed 1, context: html, text, full: html, text
  99ec03901d84f8b2af5c0ca1e9956f6110291ab9 Mon Sep 1 22:03:31 2025 -0700
  adding a couple per user request refs #29545
src/hg/phyloPng/makefile
- lines changed 1, context: html, text, full: html, text
  455a0b2500ffc2c3b4c2c11733d3103c3d3fb53e Mon Sep 1 23:34:56 2025 -0700
  do not need the -lm specification on the library link
src/hg/utils/automation/asmHubChainNetTrackDb.pl
- lines changed 12, context: html, text, full: html, text
  87f551dfb14925f9e7e1d6f23d798fef313fd73c Mon Sep 1 23:25:33 2025 -0700
  new chain net construction and update genePred names
src/hg/utils/automation/asmHubChainNetTrackDb.sh
- lines changed 12, context: html, text, full: html, text
  87f551dfb14925f9e7e1d6f23d798fef313fd73c Mon Sep 1 23:25:33 2025 -0700
  new chain net construction and update genePred names
src/hg/utils/automation/asmHubChromAlias.pl
- lines changed 37, context: html, text, full: html, text
  87f551dfb14925f9e7e1d6f23d798fef313fd73c Mon Sep 1 23:25:33 2025 -0700
  new chain net construction and update genePred names
src/hg/utils/automation/asmHubTrackDb.sh
- lines changed 18, context: html, text, full: html, text
  87f551dfb14925f9e7e1d6f23d798fef313fd73c Mon Sep 1 23:25:33 2025 -0700
  new chain net construction and update genePred names
- lines changed 9, context: html, text, full: html, text
  5acd42ee6f0f2031ce020ff60a2fd1ffa9d7940a Tue Sep 2 13:49:47 2025 -0700
  reset default gene name display on RefSeq gene tracks refs #36206
src/hg/utils/automation/doIdKeys.pl
- lines changed 1, context: html, text, full: html, text
  87f551dfb14925f9e7e1d6f23d798fef313fd73c Mon Sep 1 23:25:33 2025 -0700
  new chain net construction and update genePred names
src/hg/utils/automation/doRepeatMasker.pl
- lines changed 3, context: html, text, full: html, text
  07239334f514fc80e68aba6968335e56853e3177 Tue Sep 2 11:23:25 2025 -0700
  upgrade to version 4.2.1
src/hg/utils/automation/doRepeatModeler.pl
- lines changed 3, context: html, text, full: html, text
  a7d8fc835322d9017fdd5d932c22aaf2b3f5c56e Tue Sep 2 11:12:17 2025 -0700
  updated to version 2.0.7
src/hg/utils/automation/doXenoRefGene.pl
- lines changed 14, context: html, text, full: html, text
  87f551dfb14925f9e7e1d6f23d798fef313fd73c Mon Sep 1 23:25:33 2025 -0700
  new chain net construction and update genePred names
src/hg/utils/automation/gpToIx.pl
- lines changed 1, context: html, text, full: html, text
  87f551dfb14925f9e7e1d6f23d798fef313fd73c Mon Sep 1 23:25:33 2025 -0700
  new chain net construction and update genePred names
src/hg/utils/automation/makeGenomeDb.pl
- lines changed 2, context: html, text, full: html, text
  87f551dfb14925f9e7e1d6f23d798fef313fd73c Mon Sep 1 23:25:33 2025 -0700
  new chain net construction and update genePred names
src/hg/utils/otto/genArk/README
- lines changed 4, context: html, text, full: html, text
  a20c0e1ae1ef0957b267321b78e43e1dbd91092c Mon Sep 1 23:43:36 2025 -0700
  mention the alphaBetaPush.pl procedure
src/hg/utils/phyloTrees/asciiTree.pl
- lines changed 9, context: html, text, full: html, text
  56aff44eacee07bc3679dd18fe70ad621f6142d5 Mon Sep 1 23:45:50 2025 -0700
  allow stdin as argument to asciiTree and updated perl issues for binaryTree
src/hg/utils/phyloTrees/binaryTree.pl
- lines changed 2, context: html, text, full: html, text
  56aff44eacee07bc3679dd18fe70ad621f6142d5 Mon Sep 1 23:45:50 2025 -0700
  allow stdin as argument to asciiTree and updated perl issues for binaryTree

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