Commits for hiram

v496_base to v497_preview (2026-03-30 to 2026-04-06) v497

713cc06056876ff148c7555a4eb520e8987fb793 Mon Mar 30 12:53:19 2026 -0700

• switch gcOnFly to bigWig file at a specified density refs #35958
  • src/hg/hgTracks/bigWigTrack.c - lines changed 13, context: html, text, full: html, text

f3a4a303938f64a47233dc52a6bb766442466b4c Mon Mar 30 13:15:16 2026 -0700

• correctly calculate to end of sequence and sequences smaller than the window size refs #35958
  • src/hg/makeDb/hgGcPercent/hgGcPercent.c - lines changed 9, context: html, text, full: html, text

b29509b0535fc8c0151dc3dc47d7be9ec2833294 Mon Mar 30 14:28:59 2026 -0700

• gcOnFly now with a density switch to go to backup bigWig file to avoid big computation refs #35958
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 2, context: html, text, full: html, text

7d3f3b3e910daec7cc31cbbdafc45e5e71cdacf4 Mon Mar 30 14:51:27 2026 -0700

• no longer need the debug TDB label on gcOnFly track - it can be determined by item or UI clicks refs #35958
  • src/hg/makeDb/trackDb/trackDb.ra - lines changed 2, context: html, text, full: html, text

4e24d58253928c3ed5ac02745b9dd6c4573217d1 Tue Mar 31 13:05:33 2026 -0700

• BRC update refs #34337
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 6, context: html, text, full: html, text

7410356b01b1eb4f83338e08c69c4ca347111f00 Tue Mar 31 19:57:24 2026 -0700

• catching up some orphaned assemblies probably VGP update
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 50, context: html, text, full: html, text

5c4623f2e8dd4a64a99c228c201a260076e71ff5 Tue Mar 31 20:09:41 2026 -0700

• one mor stray assembly added
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 2, context: html, text, full: html, text

0c04445d60f81af3c436f224efeacac0fd32d47b Tue Mar 31 20:12:20 2026 -0700

• catchin g up stray assemblies
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv - lines changed 1, context: html, text, full: html, text

2544f90d5a0bac3b30417ffa57e11b8bd6e4aa15 Tue Mar 31 20:14:50 2026 -0700

• an obsolete version of GCA_016700215.2
  • src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt - lines changed 1, context: html, text, full: html, text

fa475271932759b28815cf54128e58e28a983ed2 Fri Apr 3 12:42:21 2026 -0700

• adding evaSnp8 contrib track refs #36957
  • src/hg/makeDb/trackDb/betaGenArk.txt - lines changed 1, context: html, text, full: html, text

9749d0a9af52aead1611244dbfddcbcbccc96c22 Fri Apr 3 13:00:00 2026 -0700

• adding these contrib tracks to the GenArk browsers refs #36957
  • src/hg/makeDb/doc/evaSnp8.txt - lines changed 103, context: html, text, full: html, text

790660dbd19f460e345fad829ce38ea978e29c7b Sun Apr 5 19:01:24 2026 -0700

• claude author rewrite of mafAddIRows for 5X to 10X improvement in peak memory usage, and 100s of time faster for VGP 577 way alignments
  • src/hg/ratStuff/mafAddIRowsStream/mafAddIRowsStream.c - lines changed 924, context: html, text, full: html, text
  • src/hg/ratStuff/mafAddIRowsStream/makefile - lines changed 3, context: html, text, full: html, text