File Changes for hiram

v503_preview to v503_preview2 (2026-08-17 to 2026-08-24) v503

• src/hg/inc/asmAlias.h
  • lines changed 6, context: html, text, full: html, text
    8d662255bea829d680d17220a0b049f5f9c02f16 Fri Aug 21 22:32:26 2026 -0700
    finalize asmAlias selection issue - if a given GenArk assembly is requested and it exists then use it, otherwise look for an alias refs #38082
• src/hg/lib/asmAlias.c
  • lines changed 18, context: html, text, full: html, text
    8d662255bea829d680d17220a0b049f5f9c02f16 Fri Aug 21 22:32:26 2026 -0700
    finalize asmAlias selection issue - if a given GenArk assembly is requested and it exists then use it, otherwise look for an alias refs #38082
• src/hg/lib/hubConnect.c
  • lines changed 3, context: html, text, full: html, text
    8d662255bea829d680d17220a0b049f5f9c02f16 Fri Aug 21 22:32:26 2026 -0700
    finalize asmAlias selection issue - if a given GenArk assembly is requested and it exists then use it, otherwise look for an alias refs #38082
• src/hg/lib/web.c
  • lines changed 2, context: html, text, full: html, text
    8d662255bea829d680d17220a0b049f5f9c02f16 Fri Aug 21 22:32:26 2026 -0700
    finalize asmAlias selection issue - if a given GenArk assembly is requested and it exists then use it, otherwise look for an alias refs #38082
• src/hg/liftRequest/liftRequest.c
  • lines changed 49, context: html, text, full: html, text
    8edca3cf0a86dfbcd71116bcd117ecd2aa29aac7 Fri Aug 21 22:45:23 2026 -0700
    remove temporary experiment that never went anywhere
• src/hg/liftRequest/makefile
  • lines changed 18, context: html, text, full: html, text
    8edca3cf0a86dfbcd71116bcd117ecd2aa29aac7 Fri Aug 21 22:45:23 2026 -0700
    remove temporary experiment that never went anywhere
• src/hg/makeDb/doc/archaeaAsmHub/archaea.orderList.tsv
  • lines changed 155, context: html, text, full: html, text
    2b477adcbd343ade24789ebb6c4629e57e45222f Tue Aug 18 07:27:52 2026 -0700
    RefSeq update refs @29545
• src/hg/makeDb/doc/asmHubs/asmHubs.mk
  • lines changed 15, context: html, text, full: html, text
    25ea393c310876076793bbad0e093f83161e9d78 Tue Aug 18 14:39:58 2026 -0700
    improve efficiency of the trackData.pl an now using faSize to get sizes out of the 2bit files no redmine
• src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
  • lines changed 2, context: html, text, full: html, text
    25ea393c310876076793bbad0e093f83161e9d78 Tue Aug 18 14:39:58 2026 -0700
    improve efficiency of the trackData.pl an now using faSize to get sizes out of the 2bit files no redmine
• src/hg/makeDb/doc/asmHubs/runBuild
  • lines changed 11, context: html, text, full: html, text
    90552b46adcb6b1641a0e027e1cf722e411c9664 Mon Aug 17 10:23:57 2026 -0700
    now running the oneLftp.sh to fetch the NCBI files for the build of the assembly refs #32596
• src/hg/makeDb/doc/asmHubs/trackData.pl
  • lines changed 416, context: html, text, full: html, text
    25ea393c310876076793bbad0e093f83161e9d78 Tue Aug 18 14:39:58 2026 -0700
    improve efficiency of the trackData.pl an now using faSize to get sizes out of the 2bit files no redmine
  • lines changed 1, context: html, text, full: html, text
    f3707c75a44a765397fd2c7f9144dc5dfd61f3c7 Wed Aug 19 09:46:50 2026 -0700
    restore the backslash r character which was lost in edits since it used to be an explicit control-M literal character found by claude code review no redmine
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 1322, context: html, text, full: html, text
    2b477adcbd343ade24789ebb6c4629e57e45222f Tue Aug 18 07:27:52 2026 -0700
    RefSeq update refs @29545
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 11, context: html, text, full: html, text
    2b477adcbd343ade24789ebb6c4629e57e45222f Tue Aug 18 07:27:52 2026 -0700
    RefSeq update refs @29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 13, context: html, text, full: html, text
    2b477adcbd343ade24789ebb6c4629e57e45222f Tue Aug 18 07:27:52 2026 -0700
    RefSeq update refs @29545
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 8, context: html, text, full: html, text
    2b477adcbd343ade24789ebb6c4629e57e45222f Tue Aug 18 07:27:52 2026 -0700
    RefSeq update refs @29545
  • lines changed 1, context: html, text, full: html, text
    0fa586e6489d2862fb499024ee66702b33056f55 Tue Aug 18 07:36:33 2026 -0700
    incorrectly identified as a fungi GCF_056827815.1 it is a bacteria refs #29545
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 18, context: html, text, full: html, text
    2b477adcbd343ade24789ebb6c4629e57e45222f Tue Aug 18 07:27:52 2026 -0700
    RefSeq update refs @29545
  • lines changed 1, context: html, text, full: html, text
    b6d0ccc9abb33be090cbe30e5e8c1438b832ec35 Wed Aug 19 09:48:14 2026 -0700
    remove trailing dot on spider. name GCF_044657685.1 found by claude code review no redmine
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 5, context: html, text, full: html, text
    2b477adcbd343ade24789ebb6c4629e57e45222f Tue Aug 18 07:27:52 2026 -0700
    RefSeq update refs @29545
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 10, context: html, text, full: html, text
    2b477adcbd343ade24789ebb6c4629e57e45222f Tue Aug 18 07:27:52 2026 -0700
    RefSeq update refs @29545
  • lines changed 1, context: html, text, full: html, text
    2a36871abda76518c9bfdc555355e6c8c5294c34 Tue Aug 18 20:04:05 2026 -0700
    adding one per user lift over request refs #29545
  • lines changed 1, context: html, text, full: html, text
    28fbabb3b0f5dc9c9d2cc410138b07d550ec760f Wed Aug 19 10:09:13 2026 -0700
    missing (parens) around meta data for grain cowpea GCF_037176805.1 found by claude code review no redmine
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    2b477adcbd343ade24789ebb6c4629e57e45222f Tue Aug 18 07:27:52 2026 -0700
    RefSeq update refs @29545
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    2b477adcbd343ade24789ebb6c4629e57e45222f Tue Aug 18 07:27:52 2026 -0700
    RefSeq update refs @29545
• src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
  • lines changed 50, context: html, text, full: html, text
    049f3d331685a598d3fb2ee688b0599256fc3e0a Fri Aug 21 23:22:38 2026 -0700
    RefSeq update refs #29545
• src/hg/utils/automation/AsmHub.pm
  • lines changed 7, context: html, text, full: html, text
    62e62c6404011a058ce40b13b5d6a2a4d5724f29 Fri Aug 21 22:39:45 2026 -0700
    corresponding fix for updates to doNcbiGene.pl better indexing for ncbiGene refs #34917
• src/hg/utils/automation/HgAutomate.pm
  • lines changed 1, context: html, text, full: html, text
    902997abc3d6d90a569c219d1305e00535d2ef47 Tue Aug 18 13:42:07 2026 -0700
    just following orders refs #38021
  • lines changed 25, context: html, text, full: html, text
    2656c7a9162e938d9f9ae923985234a1561f480b Wed Aug 19 10:00:12 2026 -0700
    fixup nfsNoodge correctly to test filesystem gpfs/nfs refs #38021
  • lines changed 2, context: html, text, full: html, text
    75570fb95674659964f2488baffae618ba1de49c Thu Aug 20 09:38:11 2026 -0700
    nodge should check for file has contents not just exists claude review recommendation refs #38021
• src/hg/utils/automation/kmerPairs.pl
  • lines changed 65, context: html, text, full: html, text
    8709f15407b3ad4fdc8643cef50f65621a344a67 Wed Aug 19 14:28:29 2026 -0700
    4X speed improvement via claude analysis and rewrite - exact same inputs and outputs as before no redmine
• src/hg/utils/hubClone/hubClone.c
  • lines changed 50, context: html, text, full: html, text
    0afbe51b59a42ea8fd8e008b35dcb49159e8fcc6 Tue Aug 18 13:48:14 2026 -0700
    efficiency for hubClone to avoid reloading files repeatedly and fix error in reading include statements with trailing # comments refs #38147
• src/hg/utils/otto/genArk/asmAlias/runUpdate.sh
  • lines changed 5, context: html, text, full: html, text
    fa9b7f8c38f8fcb9972330f886d0655b44dc0404 Wed Aug 19 23:30:22 2026 -0700
    need to get the message about about the disable refs #38082
• src/hg/utils/otto/genArk/ncbiMirror/fetch.sh
  • lines changed 48, context: html, text, full: html, text
    4b13d1c5636bf6f7d87a554787a7ccc79c1dccf7 Mon Aug 17 10:16:17 2026 -0700
    updated script to eliminate the obsolete rsync commands refs #32596
• src/hg/utils/otto/genArk/ncbiMirror/ncbiRsync.sh
  • lines changed 3, context: html, text, full: html, text
    881817e2d9a77d5df168ae466beb23c8e6415c78 Mon Aug 17 10:19:49 2026 -0700
    updated script to eliminate the obsolete rsync commands refs #32596
• src/hg/utils/otto/genArk/ncbiMirror/oneLftp.sh
  • lines changed 83, context: html, text, full: html, text
    4bb151f462489071d5ae8eac563e5ce212b8fe6e Mon Aug 17 10:21:34 2026 -0700
    updated script to eliminate the obsolete rsync commands refs #32596
• src/hg/utils/otto/userRequests/ottoLib.py
  • lines changed 29, context: html, text, full: html, text
    6b237159a15cc8957bc40b802ebfe1116e06b9e7 Fri Aug 21 15:17:28 2026 -0700
    quite output on the git source tree update refs #31811
• src/lib/mailViaPipe.c
  • lines changed 1, context: html, text, full: html, text
    13790903b05424044d822006bf13c6b9a9f16e21 Fri Aug 21 22:42:31 2026 -0700
    correct email bounce receiver address no redmine