File Changes for chmalee

v498_base to v499_preview (2026-05-11 to 2026-05-18) v499

• src/hg/hgCustom/hgCustom.c
  • lines changed 2, context: html, text, full: html, text
    e7264355c83a0d0875b372b7ad26162adb363f6c Tue May 12 13:20:28 2026 -0700
    myVariants v1 follow-ups: CT edit gate, anon-user button gate, hgc duplicate link, item-name synthesis from ref/alt or HGVS, refs #33808
  • lines changed 20, context: html, text, full: html, text
    d7dd4f55e28699bb783563b8bece5bf23f392995 Wed May 13 11:07:57 2026 -0700
    Adds hg.conf myVariantsDataDir for writing ctfiles outside trash/, per-db short/long label rename on hgTrackUi, and a shared removal helper so the hgTrackUi remove button, hgTracks trash icon, and hgCustom checkbox all function the same, refs #33808
  • lines changed 5, context: html, text, full: html, text
    80ab15c036bf35894b59df383c03c51cbeff30be Thu May 14 10:29:53 2026 -0700
    Stop myVariants from clobbering regular custom tracks by giving it its own cart variable (mvCtfile_<db>) instead of overloading ctfile_<db>, refs #37553
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 2, context: html, text, full: html, text
    3d006a7244d91a9d72260986a5741a5aa65787dc Tue May 12 15:01:28 2026 -0700
    Widen 'jump to position' dialog after creating a myVariants item via hgvs. Remove 'update custom track' button from hgTrackUi for myVariants tracks. Fix item clicks not working after item name update in last commit, refs #33808
  • lines changed 19, context: html, text, full: html, text
    d7dd4f55e28699bb783563b8bece5bf23f392995 Wed May 13 11:07:57 2026 -0700
    Adds hg.conf myVariantsDataDir for writing ctfiles outside trash/, per-db short/long label rename on hgTrackUi, and a shared removal helper so the hgTrackUi remove button, hgTracks trash icon, and hgCustom checkbox all function the same, refs #33808
  • lines changed 1, context: html, text, full: html, text
    80ab15c036bf35894b59df383c03c51cbeff30be Thu May 14 10:29:53 2026 -0700
    Stop myVariants from clobbering regular custom tracks by giving it its own cart variable (mvCtfile_<db>) instead of overloading ctfile_<db>, refs #37553
• src/hg/hgTracks/hgTracks.c
  • lines changed 2, context: html, text, full: html, text
    e7264355c83a0d0875b372b7ad26162adb363f6c Tue May 12 13:20:28 2026 -0700
    myVariants v1 follow-ups: CT edit gate, anon-user button gate, hgc duplicate link, item-name synthesis from ref/alt or HGVS, refs #33808
  • lines changed 1, context: html, text, full: html, text
    630eb30bc3695afcf73a19be6e3bc9a2829b365f Wed May 13 13:04:37 2026 -0700
    Make myVariants items bed12+ rather than bed9+, refs #33808
  • lines changed 7, context: html, text, full: html, text
    80ab15c036bf35894b59df383c03c51cbeff30be Thu May 14 10:29:53 2026 -0700
    Stop myVariants from clobbering regular custom tracks by giving it its own cart variable (mvCtfile_<db>) instead of overloading ctfile_<db>, refs #37553
• src/hg/hgTracks/myVariantsTrack.c
  • lines changed 7, context: html, text, full: html, text
    17fe5238421ff301f2b7360c96db92104e405094 Tue May 12 12:09:08 2026 -0700
    myVariants fixes: widen drag-select dialog a bit to fit the new button, save only the actual variant position, not the variant plus padding position when making a variant out of an hgvs term, refs #33808
  • lines changed 141, context: html, text, full: html, text
    e7264355c83a0d0875b372b7ad26162adb363f6c Tue May 12 13:20:28 2026 -0700
    myVariants v1 follow-ups: CT edit gate, anon-user button gate, hgc duplicate link, item-name synthesis from ref/alt or HGVS, refs #33808
  • lines changed 13, context: html, text, full: html, text
    3d006a7244d91a9d72260986a5741a5aa65787dc Tue May 12 15:01:28 2026 -0700
    Widen 'jump to position' dialog after creating a myVariants item via hgvs. Remove 'update custom track' button from hgTrackUi for myVariants tracks. Fix item clicks not working after item name update in last commit, refs #33808
  • lines changed 209, context: html, text, full: html, text
    630eb30bc3695afcf73a19be6e3bc9a2829b365f Wed May 13 13:04:37 2026 -0700
    Make myVariants items bed12+ rather than bed9+, refs #33808
  • lines changed 6, context: html, text, full: html, text
    80ab15c036bf35894b59df383c03c51cbeff30be Thu May 14 10:29:53 2026 -0700
    Stop myVariants from clobbering regular custom tracks by giving it its own cart variable (mvCtfile_<db>) instead of overloading ctfile_<db>, refs #37553
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    e7264355c83a0d0875b372b7ad26162adb363f6c Tue May 12 13:20:28 2026 -0700
    myVariants v1 follow-ups: CT edit gate, anon-user button gate, hgc duplicate link, item-name synthesis from ref/alt or HGVS, refs #33808
• src/hg/hgc/myVariantsClick.c
  • lines changed 70, context: html, text, full: html, text
    630eb30bc3695afcf73a19be6e3bc9a2829b365f Wed May 13 13:04:37 2026 -0700
    Make myVariants items bed12+ rather than bed9+, refs #33808
• src/hg/htdocs/inc/hgMyData.html
  • lines changed 10, context: html, text, full: html, text
    2c8a873e7286d797e88549d5a2825f0ea6fe3f04 Fri May 15 15:07:52 2026 -0700
    HubSpace now allows tracks hubs to be defined via hub.txt+genomes.txt+trackDb.txt files, refs Baihe email and #37566
• src/hg/inc/hgFind.h
  • lines changed 5, context: html, text, full: html, text
    17fe5238421ff301f2b7360c96db92104e405094 Tue May 12 12:09:08 2026 -0700
    myVariants fixes: widen drag-select dialog a bit to fit the new button, save only the actual variant position, not the variant plus padding position when making a variant out of an hgvs term, refs #33808
• src/hg/inc/myVariants.h
  • lines changed 6, context: html, text, full: html, text
    e7264355c83a0d0875b372b7ad26162adb363f6c Tue May 12 13:20:28 2026 -0700
    myVariants v1 follow-ups: CT edit gate, anon-user button gate, hgc duplicate link, item-name synthesis from ref/alt or HGVS, refs #33808
  • lines changed 16, context: html, text, full: html, text
    d7dd4f55e28699bb783563b8bece5bf23f392995 Wed May 13 11:07:57 2026 -0700
    Adds hg.conf myVariantsDataDir for writing ctfiles outside trash/, per-db short/long label rename on hgTrackUi, and a shared removal helper so the hgTrackUi remove button, hgTracks trash icon, and hgCustom checkbox all function the same, refs #33808
  • lines changed 4, context: html, text, full: html, text
    630eb30bc3695afcf73a19be6e3bc9a2829b365f Wed May 13 13:04:37 2026 -0700
    Make myVariants items bed12+ rather than bed9+, refs #33808
  • lines changed 5, context: html, text, full: html, text
    80ab15c036bf35894b59df383c03c51cbeff30be Thu May 14 10:29:53 2026 -0700
    Stop myVariants from clobbering regular custom tracks by giving it its own cart variable (mvCtfile_<db>) instead of overloading ctfile_<db>, refs #37553
• src/hg/js/hgMyData.js
  • lines changed 524, context: html, text, full: html, text
    2c8a873e7286d797e88549d5a2825f0ea6fe3f04 Fri May 15 15:07:52 2026 -0700
    HubSpace now allows tracks hubs to be defined via hub.txt+genomes.txt+trackDb.txt files, refs Baihe email and #37566
• src/hg/js/hgTracks.js
  • lines changed 1, context: html, text, full: html, text
    17fe5238421ff301f2b7360c96db92104e405094 Tue May 12 12:09:08 2026 -0700
    myVariants fixes: widen drag-select dialog a bit to fit the new button, save only the actual variant position, not the variant plus padding position when making a variant out of an hgvs term, refs #33808
  • lines changed 1, context: html, text, full: html, text
    e7264355c83a0d0875b372b7ad26162adb363f6c Tue May 12 13:20:28 2026 -0700
    myVariants v1 follow-ups: CT edit gate, anon-user button gate, hgc duplicate link, item-name synthesis from ref/alt or HGVS, refs #33808
  • lines changed 1, context: html, text, full: html, text
    3d006a7244d91a9d72260986a5741a5aa65787dc Tue May 12 15:01:28 2026 -0700
    Widen 'jump to position' dialog after creating a myVariants item via hgvs. Remove 'update custom track' button from hgTrackUi for myVariants tracks. Fix item clicks not working after item name update in last commit, refs #33808
  • lines changed 88, context: html, text, full: html, text
    630eb30bc3695afcf73a19be6e3bc9a2829b365f Wed May 13 13:04:37 2026 -0700
    Make myVariants items bed12+ rather than bed9+, refs #33808
• src/hg/js/makefile
  • lines changed 2, context: html, text, full: html, text
    630eb30bc3695afcf73a19be6e3bc9a2829b365f Wed May 13 13:04:37 2026 -0700
    Make myVariants items bed12+ rather than bed9+, refs #33808
• src/hg/js/myVariantsBlocks.js
  • lines changed 263, context: html, text, full: html, text
    630eb30bc3695afcf73a19be6e3bc9a2829b365f Wed May 13 13:04:37 2026 -0700
    Make myVariants items bed12+ rather than bed9+, refs #33808
• src/hg/js/utils.js
  • lines changed 17, context: html, text, full: html, text
    59982d783b66d2be7d73ef89ab1b6d741a257f7e Mon May 11 10:12:37 2026 -0700
    Remove dead code block pointed out in nightly code review
• src/hg/lib/customTrack.c
  • lines changed 11, context: html, text, full: html, text
    d7dd4f55e28699bb783563b8bece5bf23f392995 Wed May 13 11:07:57 2026 -0700
    Adds hg.conf myVariantsDataDir for writing ctfiles outside trash/, per-db short/long label rename on hgTrackUi, and a shared removal helper so the hgTrackUi remove button, hgTracks trash icon, and hgCustom checkbox all function the same, refs #33808
  • lines changed 48, context: html, text, full: html, text
    80ab15c036bf35894b59df383c03c51cbeff30be Thu May 14 10:29:53 2026 -0700
    Stop myVariants from clobbering regular custom tracks by giving it its own cart variable (mvCtfile_<db>) instead of overloading ctfile_<db>, refs #37553
• src/hg/lib/hgFind.c
  • lines changed 1, context: html, text, full: html, text
    17fe5238421ff301f2b7360c96db92104e405094 Tue May 12 12:09:08 2026 -0700
    myVariants fixes: widen drag-select dialog a bit to fit the new button, save only the actual variant position, not the variant plus padding position when making a variant out of an hgvs term, refs #33808
• src/hg/lib/myVariants.as
  • lines changed 3, context: html, text, full: html, text
    630eb30bc3695afcf73a19be6e3bc9a2829b365f Wed May 13 13:04:37 2026 -0700
    Make myVariants items bed12+ rather than bed9+, refs #33808
• src/hg/lib/myVariants.c
  • lines changed 1, context: html, text, full: html, text
    00590f0f1b1b91a318f0d76308bc513a83dc2ad7 Tue May 12 11:26:52 2026 -0700
    Move myVariants tables from myisam to innodb, refs #33808
  • lines changed 21, context: html, text, full: html, text
    e7264355c83a0d0875b372b7ad26162adb363f6c Tue May 12 13:20:28 2026 -0700
    myVariants v1 follow-ups: CT edit gate, anon-user button gate, hgc duplicate link, item-name synthesis from ref/alt or HGVS, refs #33808
  • lines changed 206, context: html, text, full: html, text
    d7dd4f55e28699bb783563b8bece5bf23f392995 Wed May 13 11:07:57 2026 -0700
    Adds hg.conf myVariantsDataDir for writing ctfiles outside trash/, per-db short/long label rename on hgTrackUi, and a shared removal helper so the hgTrackUi remove button, hgTracks trash icon, and hgCustom checkbox all function the same, refs #33808
  • lines changed 102, context: html, text, full: html, text
    630eb30bc3695afcf73a19be6e3bc9a2829b365f Wed May 13 13:04:37 2026 -0700
    Make myVariants items bed12+ rather than bed9+, refs #33808
  • lines changed 23, context: html, text, full: html, text
    80ab15c036bf35894b59df383c03c51cbeff30be Thu May 14 10:29:53 2026 -0700
    Stop myVariants from clobbering regular custom tracks by giving it its own cart variable (mvCtfile_<db>) instead of overloading ctfile_<db>, refs #37553
• src/hg/lib/myVariants.sql
  • lines changed 1, context: html, text, full: html, text
    00590f0f1b1b91a318f0d76308bc513a83dc2ad7 Tue May 12 11:26:52 2026 -0700
    Move myVariants tables from myisam to innodb, refs #33808
  • lines changed 3, context: html, text, full: html, text
    630eb30bc3695afcf73a19be6e3bc9a2829b365f Wed May 13 13:04:37 2026 -0700
    Make myVariants items bed12+ rather than bed9+, refs #33808
• src/hg/lib/myVariantsShare.sql
  • lines changed 1, context: html, text, full: html, text
    00590f0f1b1b91a318f0d76308bc513a83dc2ad7 Tue May 12 11:26:52 2026 -0700
    Move myVariants tables from myisam to innodb, refs #33808
• src/hg/lib/userdata.c
  • lines changed 23, context: html, text, full: html, text
    2c8a873e7286d797e88549d5a2825f0ea6fe3f04 Fri May 15 15:07:52 2026 -0700
    HubSpace now allows tracks hubs to be defined via hub.txt+genomes.txt+trackDb.txt files, refs Baihe email and #37566