Commits for hiram

v496_preview2 to v496_base (2026-03-23 to 2026-03-30) v496

a513cccc30dd0697dc78935f51a636e52a0793f0 Mon Mar 23 16:36:04 2026 -0700

• manage gcOnFly track regarding sessions refs #35958
  • src/hg/hgTracks/bigWigTrack.c - lines changed 4, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c - lines changed 12, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.h - lines changed 3, context: html, text, full: html, text

6195179b836111bd4a82ae5f5c73b2f8d36e7abb Mon Mar 23 17:58:36 2026 -0700

• more simple vis restoration for gcOnFly no need for all the rigamerol refs #35958
  • src/hg/hgTracks/bigWigTrack.c - lines changed 4, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c - lines changed 12, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.h - lines changed 3, context: html, text, full: html, text

3701c3297c0f24c57b3e4ec266ff2f3551eb5365 Mon Mar 23 21:26:00 2026 -0700

• fixing up GCA_040938575.1_UKY_AmexF1_1
  • src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt - lines changed 1, context: html, text, full: html, text

19af47f0b0e49796e6f909b093b72eff2f480e4b Mon Mar 23 21:27:27 2026 -0700

• VGP update in progress
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 98, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 105, context: html, text, full: html, text
  • src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 2, context: html, text, full: html, text

1e04d78b65b35678e80d9f5929e6fec0f7b2fbbb Tue Mar 24 13:32:54 2026 -0700

• refactor the GC on fly calculation to move into a library function rfefs #35958
  • src/hg/hgTracks/bigWigTrack.c - lines changed 29, context: html, text, full: html, text
  • src/hg/inc/wiggle.h - lines changed 17, context: html, text, full: html, text
  • src/hg/lib/wigDataStream.c - lines changed 50, context: html, text, full: html, text

ab5f6fcc68340efac0c30cd90058d083594943ef Tue Mar 24 15:00:46 2026 -0700

• correctly manage gcOnFly visibility from click to click refs #35958
  • src/hg/hgTracks/bigWigTrack.c - lines changed 4, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c - lines changed 3, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.h - lines changed 3, context: html, text, full: html, text

2fc33abc4c89f2ca1881911666b7dbea8b6ae343 Tue Mar 24 15:05:26 2026 -0700

• refactor the GC on fly calculation to move into a library function rfefs #35958
  • src/hg/hgc/hgc.c - lines changed 16, context: html, text, full: html, text

c3bb4207fb2a58064b937ba9fef1cc11852f7576 Wed Mar 25 10:48:49 2026 -0700

• allow trackDb entry to override the in-code defaults of the gcOnFly track refs #35958
  • src/hg/hgTracks/bigWigTrack.c - lines changed 10, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c - lines changed 11, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.h - lines changed 6, context: html, text, full: html, text
  • src/hg/lib/hdb.c - lines changed 2, context: html, text, full: html, text

c7302b60850a3f7f99088a8a99b0a7d389f64605 Wed Mar 25 10:49:52 2026 -0700

• allow trackDb entry to override the in-code defaults of the gcOnFly track refs #35958
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 2, context: html, text, full: html, text

4fd52b1b34d170c15d3aacfeaf4fbb26fff224b1 Wed Mar 25 12:52:00 2026 -0700

• fix bugs for chrom size at 2^31 and manage partial computation windows at beginning or end of drawing window for gcOnFly refs #35958
  • src/hg/hgTracks/bigWigTrack.c - lines changed 7, context: html, text, full: html, text
  • src/hg/lib/wigDataStream.c - lines changed 27, context: html, text, full: html, text

c6e82cfec526eeec7abb93e0610e303406d03820 Wed Mar 25 14:53:49 2026 -0700

• allow hgGcPercent to read a 2bit file from a URL and add unit tests as suggested by claude refs #35958
  • src/hg/makeDb/hgGcPercent/hgGcPercent.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/hgGcPercent/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/hgGcPercent/tests/expected/test0.out - lines changed 107, context: html, text, full: html, text
  • src/hg/makeDb/hgGcPercent/tests/expected/test1.out - lines changed 107, context: html, text, full: html, text
  • src/hg/makeDb/hgGcPercent/tests/expected/url.md5sum - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/hgGcPercent/tests/inputs/test.2bit - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/makeDb/hgGcPercent/tests/inputs/test.fa - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/hgGcPercent/tests/makefile - lines changed 42, context: html, text, full: html, text

cc54e8ee46e408773d86ab0492d5aed3244baff6 Wed Mar 25 14:59:21 2026 -0700

• provide data access instruction for gcOnFly track data refs #35958
  • src/hg/hgc/hgc.c - lines changed 21, context: html, text, full: html, text

f12abfa6cad0164a03d39d3968986874a8c9a6b8 Wed Mar 25 16:58:16 2026 -0700

• same change to track Ui to indicate how to get the data for the gcOnFly synthetic track refs #35958
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 21, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/gcOnFly.html - lines changed 2, context: html, text, full: html, text

e09c0d375e198e5c74164dbbbb4010a57bf13607 Wed Mar 25 17:44:45 2026 -0700

• correct UI operation on the synthetic bigWig gcOnFly track refs #35958
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 12, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 3, context: html, text, full: html, text

69b00a9ddead8bdc0c3717a33a620f103f70bf94 Wed Mar 25 17:47:26 2026 -0700

• a default entry for gcOnFly synthetic track so it will correctly work with saves sessions refs #35958
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 21, context: html, text, full: html, text

956500207b58c263485009212f223836152176d3 Thu Mar 26 14:58:55 2026 -0700

• simplify the gcOnFly track - it does not need to by completely synthetic - it only comes in from trackDb stanzas refs #35958
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 25, context: html, text, full: html, text
  • src/hg/hgTracks/bigWigTrack.c - lines changed 58, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c - lines changed 35, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.h - lines changed 6, context: html, text, full: html, text
  • src/hg/hgc/hgc.c - lines changed 1, context: html, text, full: html, text

778a5fc121bbf71e8ed92064eee8d8869a94ad41 Thu Mar 26 15:42:38 2026 -0700

• set the gcOnFly track to release alpha refs #35958
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 1, context: html, text, full: html, text