Commits for hiram

v496_preview to v496_preview2 (2026-03-16 to 2026-03-23) v496

a4d9c97c1a9bff4e6c0a7d54b02b89f11a4ee0fd Mon Mar 16 14:12:28 2026 -0700

• add mixed operation fasta and 2bit in one argument set no redmine
  • src/utils/faSize/tests/expected/mixed.txt - lines changed 6, context: html, text, full: html, text
  • src/utils/faSize/tests/expected/mixedDetailed.txt - lines changed 8, context: html, text, full: html, text
  • src/utils/faSize/tests/expected/mixedVeryDetailed.txt - lines changed 8, context: html, text, full: html, text
  • src/utils/faSize/tests/makefile - lines changed 15, context: html, text, full: html, text

b1bf46da53916a9741f163ea439ac459b3957b0a Mon Mar 16 14:39:59 2026 -0700

• enhanced command to allow 2bit inputs - code by claude assistance - no redmine
  • src/utils/faCount/faCount.c - lines changed 14, context: html, text, full: html, text
  • src/utils/faCount/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/faCount/tests/expected/allThree.txt - lines changed 6, context: html, text, full: html, text
  • src/utils/faCount/tests/expected/allThree_2bit.txt - lines changed 6, context: html, text, full: html, text
  • src/utils/faCount/tests/expected/mixed.txt - lines changed 10, context: html, text, full: html, text
  • src/utils/faCount/tests/expected/mixedDinuc.txt - lines changed 10, context: html, text, full: html, text
  • src/utils/faCount/tests/expected/mixedStrands.txt - lines changed 10, context: html, text, full: html, text
  • src/utils/faCount/tests/expected/mixedSummary.txt - lines changed 3, context: html, text, full: html, text
  • src/utils/faCount/tests/expected/s1.s2.dinuc.txt - lines changed 4, context: html, text, full: html, text
  • src/utils/faCount/tests/expected/s1.s2.strands.txt - lines changed 4, context: html, text, full: html, text
  • src/utils/faCount/tests/expected/s1.s2.summary.txt - lines changed 3, context: html, text, full: html, text
  • src/utils/faCount/tests/expected/s1.s2.txt - lines changed 4, context: html, text, full: html, text
  • src/utils/faCount/tests/expected/s1.s2_2bit.dinuc.txt - lines changed 4, context: html, text, full: html, text
  • src/utils/faCount/tests/expected/s1.s2_2bit.strands.txt - lines changed 4, context: html, text, full: html, text
  • src/utils/faCount/tests/expected/s1.s2_2bit.summary.txt - lines changed 3, context: html, text, full: html, text
  • src/utils/faCount/tests/expected/s1.s2_2bit.txt - lines changed 4, context: html, text, full: html, text
  • src/utils/faCount/tests/expected/s1.txt - lines changed 3, context: html, text, full: html, text
  • src/utils/faCount/tests/expected/s1Ands2.txt - lines changed 4, context: html, text, full: html, text
  • src/utils/faCount/tests/expected/s1Ands2_2bit.txt - lines changed 4, context: html, text, full: html, text
  • src/utils/faCount/tests/expected/s1_2bit.txt - lines changed 3, context: html, text, full: html, text
  • src/utils/faCount/tests/expected/s2.txt - lines changed 3, context: html, text, full: html, text
  • src/utils/faCount/tests/expected/s2_2bit.txt - lines changed 3, context: html, text, full: html, text
  • src/utils/faCount/tests/makefile - lines changed 100, context: html, text, full: html, text

10801162f7e4bbb3a4f704c7545043056ebaecb5 Mon Mar 16 14:43:44 2026 -0700

• enhanced command to allow 2bit inputs - code by claude assistance - no redmine
  • src/utils/faCount/tests/input/s1.2bit - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/utils/faCount/tests/input/s1.fa.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/utils/faCount/tests/input/s1.s2.2bit - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/utils/faCount/tests/input/s1.s2.fa.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/utils/faCount/tests/input/s2.2bit - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/utils/faCount/tests/input/s2.fa.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

da33d70c10ddaae6c3290cb900d7d0cc2b6ee01b Tue Mar 17 13:57:24 2026 -0700

• allow calculation of GC percent on the fly with code help from claude refs #35958
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 33, context: html, text, full: html, text
  • src/hg/hgTracks/bigWigTrack.c - lines changed 155, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c - lines changed 14, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.h - lines changed 5, context: html, text, full: html, text
  • src/hg/hgc/hgc.c - lines changed 37, context: html, text, full: html, text
  • src/hg/hgc/togaClick.c - lines changed 4, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/gcOnFly.html - lines changed 18, context: html, text, full: html, text
  • src/hg/inc/hui.h - lines changed 13, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 12, context: html, text, full: html, text

fa3c5feacf9d226310d8c7c775b8e8690aa4baf3 Tue Mar 17 14:39:15 2026 -0700

• add in the rest of the wiggle configurations for this onTheFly track refs #35958
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 2, context: html, text, full: html, text

a55016e7b323196b8a41e1f98fb511f70aaf4271 Fri Mar 20 11:15:58 2026 -0700

• VGP update in progress
  • src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 6, 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/legacyAsmHub/legacy.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv - lines changed 1, context: html, text, full: html, text

7eb59a7b92b6256391c21256af4033ae03fff257 Fri Mar 20 16:39:11 2026 -0700

• minor issues discovered by claude code review
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 2, context: html, text, full: html, text

3d4620f77d5ee2dca36cef39359e756c6a3624a0 Mon Mar 23 09:20:55 2026 -0700

• reset the GC on the fly to default off and same other defaults as the regular track refs #35958
  • src/hg/hgTracks/bigWigTrack.c - lines changed 8, context: html, text, full: html, text

68bc2fb0b79a074d3a0050db46bcb8b46a11600d Mon Mar 23 09:31:49 2026 -0700

• fix by claude, strip html highlighting markup when populating the input box with the text selections refs there is some RM but I can not find that
  • src/hg/js/autocompleteCat.js - lines changed 6, context: html, text, full: html, text