File Changes for hiram

v497_preview to v497_preview2 (2026-04-06 to 2026-04-13) v497

• src/hg/hgTracks/hgTracks.c
  • lines changed 27, context: html, text, full: html, text
    16113a55a853321b5251989c64f6c995f8ed583b Mon Apr 6 14:05:40 2026 -0700
    restore the hg.conf switches to control the gcOnFly track - lost in later edits
• src/hg/hubApi/apiUtils.c
  • lines changed 20, context: html, text, full: html, text
    a62a60916a2ae4aebf9452d0f005f2ad2213ed94 Mon Apr 6 16:21:57 2026 -0700
    remove the gcOnFly track from consideration - do not see it at all anywhere refs #35958
• src/hg/makeDb/doc/evaSnp8.txt
  • lines changed 3, context: html, text, full: html, text
    d02449d1394960b2bc3e6f0de73ad6ae32458456 Wed Apr 8 14:09:17 2026 -0700
    minor issues noted from claude code review refs #36957
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    908132d6c2e74753a8c44df8d97a8557fbb331d0 Wed Apr 8 14:19:21 2026 -0700
    correct spelling Andian -> Andean correction found by claude code review
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    92d94309df312d21e49178f9b682bfb7147582d6 Mon Apr 6 21:31:26 2026 -0700
    differentiate between great and intermediate fruit-eating bat refs #29545
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 0, context: html, text, full: html, text
    0a566da9105da8a5434482c3b5df14e983a8073f Wed Apr 8 14:14:59 2026 -0700
    fixup minor errors found by claude review
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 7, context: html, text, full: html, text
    0a566da9105da8a5434482c3b5df14e983a8073f Wed Apr 8 14:14:59 2026 -0700
    fixup minor errors found by claude review
• src/hg/makeDb/doc/vgpAsmHub/vgp.legacy.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    908132d6c2e74753a8c44df8d97a8557fbb331d0 Wed Apr 8 14:19:21 2026 -0700
    correct spelling Andian -> Andean correction found by claude code review
• src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    92d94309df312d21e49178f9b682bfb7147582d6 Mon Apr 6 21:31:26 2026 -0700
    differentiate between great and intermediate fruit-eating bat refs #29545
  • lines changed 1, context: html, text, full: html, text
    908132d6c2e74753a8c44df8d97a8557fbb331d0 Wed Apr 8 14:19:21 2026 -0700
    correct spelling Andian -> Andean correction found by claude code review
• src/hg/makeDb/trackDb/betaGenArk.txt
  • lines changed 1, context: html, text, full: html, text
    e36763d9058bbd555e6c0be3987c4dbdf8ca8c31 Mon Apr 6 23:40:46 2026 -0700
    begin experiment with vgp577way alignment first on on GCF_037176765.1
• src/hg/makeDb/trackDb/human/hg38/hprcV2.trackDb.txt
  • lines changed 44, context: html, text, full: html, text
    cd2739b2490649fcaab39f8acb015c815e8945d2 Fri Apr 10 11:11:18 2026 -0700
    initial test of two HPRC V2 chain tracks refs #35415
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    cd2739b2490649fcaab39f8acb015c815e8945d2 Fri Apr 10 11:11:18 2026 -0700
    initial test of two HPRC V2 chain tracks refs #35415
  • lines changed 1, context: html, text, full: html, text
    77a40437a3d14dfc86d46500b0c3efbd5640aba1 Fri Apr 10 11:19:12 2026 -0700
    initial test of two HPRC V2 chain tracks refs #35415
• src/hg/ratStuff/mafAddIRows/makefile
  • lines changed 3, context: html, text, full: html, text
    e8258c11259af202782b3c2bb62198cc55a3e2f1 Tue Apr 7 12:59:16 2026 -0700
    add testing in preparation for a new program to replace this one - these tests are the same for the new command, as suggested by claude refs #34370
• src/hg/ratStuff/mafAddIRows/tests/expected/expected.maf
  • lines changed 31, context: html, text, full: html, text
    e8258c11259af202782b3c2bb62198cc55a3e2f1 Tue Apr 7 12:59:16 2026 -0700
    add testing in preparation for a new program to replace this one - these tests are the same for the new command, as suggested by claude refs #34370
• src/hg/ratStuff/mafAddIRows/tests/expected/expectedGC.maf
  • lines changed 31, context: html, text, full: html, text
    e8258c11259af202782b3c2bb62198cc55a3e2f1 Tue Apr 7 12:59:16 2026 -0700
    add testing in preparation for a new program to replace this one - these tests are the same for the new command, as suggested by claude refs #34370
• src/hg/ratStuff/mafAddIRows/tests/input/input.2bit
  • lines changed 0, context: html, text, full: html, text
    e8258c11259af202782b3c2bb62198cc55a3e2f1 Tue Apr 7 12:59:16 2026 -0700
    add testing in preparation for a new program to replace this one - these tests are the same for the new command, as suggested by claude refs #34370
• src/hg/ratStuff/mafAddIRows/tests/input/input.maf
  • lines changed 16, context: html, text, full: html, text
    e8258c11259af202782b3c2bb62198cc55a3e2f1 Tue Apr 7 12:59:16 2026 -0700
    add testing in preparation for a new program to replace this one - these tests are the same for the new command, as suggested by claude refs #34370
• src/hg/ratStuff/mafAddIRows/tests/input/inputGC.maf
  • lines changed 16, context: html, text, full: html, text
    e8258c11259af202782b3c2bb62198cc55a3e2f1 Tue Apr 7 12:59:16 2026 -0700
    add testing in preparation for a new program to replace this one - these tests are the same for the new command, as suggested by claude refs #34370
• src/hg/ratStuff/mafAddIRows/tests/makefile
  • lines changed 20, context: html, text, full: html, text
    e8258c11259af202782b3c2bb62198cc55a3e2f1 Tue Apr 7 12:59:16 2026 -0700
    add testing in preparation for a new program to replace this one - these tests are the same for the new command, as suggested by claude refs #34370
• src/hg/ratStuff/mafAddIRowsStream/makefile
  • lines changed 3, context: html, text, full: html, text
    1b7d4ae05dffff0eeb67deac21f445816ad4e21d Tue Apr 7 13:02:32 2026 -0700
    add testing for this new program to replace mafAddIRows - this has been exhaustedly tested with full runs on hs1 and hg38 Tb of data input and output, identical to mafAddIRows - these tests are the same for the new and previous command, as suggested by claude refs #34370
• src/hg/ratStuff/mafAddIRowsStream/tests/expected/expected.maf
  • lines changed 31, context: html, text, full: html, text
    1b7d4ae05dffff0eeb67deac21f445816ad4e21d Tue Apr 7 13:02:32 2026 -0700
    add testing for this new program to replace mafAddIRows - this has been exhaustedly tested with full runs on hs1 and hg38 Tb of data input and output, identical to mafAddIRows - these tests are the same for the new and previous command, as suggested by claude refs #34370
• src/hg/ratStuff/mafAddIRowsStream/tests/expected/expectedGC.maf
  • lines changed 31, context: html, text, full: html, text
    1b7d4ae05dffff0eeb67deac21f445816ad4e21d Tue Apr 7 13:02:32 2026 -0700
    add testing for this new program to replace mafAddIRows - this has been exhaustedly tested with full runs on hs1 and hg38 Tb of data input and output, identical to mafAddIRows - these tests are the same for the new and previous command, as suggested by claude refs #34370
• src/hg/ratStuff/mafAddIRowsStream/tests/input/input.2bit
  • lines changed 0, context: html, text, full: html, text
    1b7d4ae05dffff0eeb67deac21f445816ad4e21d Tue Apr 7 13:02:32 2026 -0700
    add testing for this new program to replace mafAddIRows - this has been exhaustedly tested with full runs on hs1 and hg38 Tb of data input and output, identical to mafAddIRows - these tests are the same for the new and previous command, as suggested by claude refs #34370
• src/hg/ratStuff/mafAddIRowsStream/tests/input/input.maf
  • lines changed 16, context: html, text, full: html, text
    1b7d4ae05dffff0eeb67deac21f445816ad4e21d Tue Apr 7 13:02:32 2026 -0700
    add testing for this new program to replace mafAddIRows - this has been exhaustedly tested with full runs on hs1 and hg38 Tb of data input and output, identical to mafAddIRows - these tests are the same for the new and previous command, as suggested by claude refs #34370
• src/hg/ratStuff/mafAddIRowsStream/tests/input/inputGC.maf
  • lines changed 16, context: html, text, full: html, text
    1b7d4ae05dffff0eeb67deac21f445816ad4e21d Tue Apr 7 13:02:32 2026 -0700
    add testing for this new program to replace mafAddIRows - this has been exhaustedly tested with full runs on hs1 and hg38 Tb of data input and output, identical to mafAddIRows - these tests are the same for the new and previous command, as suggested by claude refs #34370
• src/hg/ratStuff/mafAddIRowsStream/tests/makefile
  • lines changed 20, context: html, text, full: html, text
    1b7d4ae05dffff0eeb67deac21f445816ad4e21d Tue Apr 7 13:02:32 2026 -0700
    add testing for this new program to replace mafAddIRows - this has been exhaustedly tested with full runs on hs1 and hg38 Tb of data input and output, identical to mafAddIRows - these tests are the same for the new and previous command, as suggested by claude refs #34370
• src/hg/ratStuff/makefile
  • lines changed 1, context: html, text, full: html, text
    94b4f059748ac6676cac1a7c9096b4d9cc138142 Tue Apr 7 13:04:32 2026 -0700
    adding mafAddIRowsStream to the utils output - more efficient version of mafAddIRows - refs #34370