All File Changes

v495_base to v496_preview (2026-03-09 to 2026-03-16) v496

• confs/hgwbeta.hg.conf
  • lines changed 2, context: html, text, full: html, text
    55400bc5f4d70747093b4941327d8f90e5a5261d Sun Mar 15 01:11:16 2026 -0700
    Installing updated hg.conf files from UCSC servers
• docs/genomeBrowserGlossary.md
  • lines changed 41, context: html, text, full: html, text
    c1623f23f647a7a879d73454e4d9898bc03dc185 Mon Mar 9 11:18:28 2026 -0700
    Tweaks to descriptions for some glossary items, refs #35259
  • lines changed 3, context: html, text, full: html, text
    795e0dfc543020d5a353f1c27291d31de17992ec Sat Mar 14 12:57:37 2026 -0700
    minor tweak to genark entry, no refs
• python/lib/ucscGb/encode/cv.py
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• python/lib/ucscGb/gbData/ra/raStanza.py
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• python/lib/ucscGb/qa/tables/trackUtils.py
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• python/ucsc_virtualenv.py
  • lines changed 2, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/affyTransciptome/maxTranscriptomeExps.c
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • lines changed 2, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/encode3/importEncode2/encode2Meta/encode2Meta.c
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/hgBlat/hgBlat.c
  • lines changed 2, context: html, text, full: html, text
    7155e7f79fb01ff6db8b275ca46eb09f52afe3e2 Tue Mar 10 09:39:41 2026 -0700
    Fixing some typos, no RM.
  • lines changed 3, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/hgCoordConv/hgCoordConv.c
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/hgFetch/hgFetch.c
  • lines changed 94, context: html, text, full: html, text
    f73fe5e18b354f9595d22a4c2961b7b98b250b6a Mon Mar 16 01:31:11 2026 -0700
    First pass at a tool for users to fetch content from CORS-enabled track files, refs #36320
• src/hg/hgFetch/makefile
  • lines changed 18, context: html, text, full: html, text
    f73fe5e18b354f9595d22a4c2961b7b98b250b6a Mon Mar 16 01:31:11 2026 -0700
    First pass at a tool for users to fetch content from CORS-enabled track files, refs #36320
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 5, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/hgLiftOver/hgLiftOver.c
  • lines changed 2, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/hgSession/hgSession.c
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/hgTables/hgTables.c
  • lines changed 0, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 3, context: html, text, full: html, text
    97581eb831d5c2b70494276cd4df9e6d97d598b2 Mon Mar 16 09:34:02 2026 -0700
    We should HTML encode strings from trackDb when displaying them, refs #37090
• src/hg/hgTracks/searchTracks.c
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/hgUserSuggestion/hgUserSuggestion.c
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/hgc/mafClick.c
  • lines changed 185, context: html, text, full: html, text
    0529f8de2a72011dfcea8f9a1221b6d227341743 Tue Mar 10 17:34:58 2026 -0700
    hgc MAF click: use mafFrag to show only selected species with inserts removed Change the hgc MAF detail page to use hgMafFrag/hgBigMafFrag instead of displaying raw MAF blocks. This stitches alignments into a single continuous display in reference coordinates, filtering to only selected species and removing insertion columns where the reference has gaps. Key changes: - mafClick.c: rewrite mafOrAxtClick2 to build species orderList from trackDb settings (speciesOrder, speciesGroup, speciesUseFile) respecting speciesDefaultOff and cart on/off state via cartUsualBooleanClosestToHome, matching the hgTracks species selection logic in newSpeciesItems(). Add mafStripRefGaps() to remove insertion columns from mafFrag output. Show spaces instead of dots for matching bases in diff mode. - hgMaf.h/hgMaf.c: add hgMafFragFromMafList() public wrapper for pre-loaded mafLists (AXT/custom mafFile support). Change hgMafFragHelper to skip species not in orderList instead of errAbort. Track per-species source coordinates (src, start, end, srcSize, strand) in struct oneOrg so browser/DNA links work correctly in mafFrag output. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 145, context: html, text, full: html, text
    4d91bce1e029162895c6acde3100bd375ceee24e Tue Mar 10 18:14:44 2026 -0700
    Gate new mafFrag MAF click display behind hg.conf mafClickMafFrag setting The new stitched mafFrag display (species filtering, insertion removal, space-for-match in diff mode) is now controlled by the hg.conf boolean mafClickMafFrag. When off (default), the original block-by-block display is used. Set mafClickMafFrag=on to enable the new behavior. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 41, context: html, text, full: html, text
    715e2acf2dd9ef6106cc42ce79c724e1e52ad62e Thu Mar 12 09:14:28 2026 -0700
    NoDots MAF alignment display for hgc mafClick, with i-row preservation and mafFrag -noDots flag hgMaf.c: add hgMafFragHelperNoDots and public wrappers (hgMafFragNoDots, hgBigMafFragNoDots, hgMafFragFromMafListNoDots) that return a list of maf blocks containing only species with actual sequence — no dot-filled rows. Blocks are broken when the species set changes; gaps between same-species blocks are filled with native sequence for the reference and dashes for others. Preserve i-row data (leftStatus/rightStatus/leftLen/rightLen) through the NoDots path so insert annotations appear in emitted blocks. hgMaf.h: declare the new NoDots public functions. mafClick.c: use NoDots path when mafClickMafFrag is enabled. Fix block numbering (aliIx was never incremented in useMafFrag path). Use full textSize for NoDots line width. Use dots instead of spaces in diff mode for both paths. Fix species label width computation to check labelHash consistently so long assembly names don't misalign sequences. Strip ref gap columns where no other species has sequence. mafFrag: add -noDots option to invoke hgMafFragNoDots from the command line, with 4 new tests (noDots, noDotsRev, noDotsOutName, noDotsLarger). refs #21477 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 205, context: html, text, full: html, text
    147740e133aa59c5aa7938ef68f1b66f3696c701 Fri Mar 13 15:29:49 2026 -0700
    Revert noDots mafClick/mafFrag work from master, refs #21477 Remove the mafClickMafFrag/noDots code path from mafClick.c, hgMaf.c, hgMaf.h, and mafFrag.c. Also remove mafFrag unit tests added as part of this work. The code is preserved on the mafFragNoDots and mafClickMafFrag branches. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/hgsqlSwapTables/hgsqlSwapTables.c
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/FAQ/FAQblat.html
  • lines changed 3, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 6, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 8, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/FAQ/FAQgenes.html
  • lines changed 8, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/FAQ/FAQlicense.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/FAQ/FAQlink.html
  • lines changed 2, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/FAQ/FAQtracks.html
  • lines changed 4, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/admin/jk-install.html
  • lines changed 7, context: html, text, full: html, text
    373fd81f121df78b9e87e151161b2645412fdec1 Wed Mar 11 09:33:52 2026 -0700
    change cse -> soe in genome-mirror address, no refs
• src/hg/htdocs/assemblySearch.html
  • lines changed 0, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/cite.html
  • lines changed 2, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/covid19.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 2, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/goldenPath/help/api.html
  • lines changed 2, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/goldenPath/help/barChart.html
  • lines changed 3, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/goldenPath/help/bedMethyl.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/goldenPath/help/bigBed.html
  • lines changed 5, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/goldenPath/help/bigChain.html
  • lines changed 3, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/goldenPath/help/bigGenePred.html
  • lines changed 4, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/goldenPath/help/bigLolly.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/goldenPath/help/bigMaf.html
  • lines changed 2, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/goldenPath/help/bigPsl.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 4, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/goldenPath/help/heatmap.html
  • lines changed 14, context: html, text, full: html, text
    08afd09bf225ea50691998f829926e9d71d55b49 Wed Mar 11 19:21:42 2026 -0700
    Fixing small grammatical and consistency errors with the heatmap page and trackDb entry. Also some bigger fixes like a broken anchor. Refs #36176
  • lines changed 115, context: html, text, full: html, text
    349e3c4468ffd999aee6b856edc1f9ab697505a1 Fri Mar 13 13:42:46 2026 -0700
    Various improvements to the heatmap.html documentation as described in the ticket, refs #36176
• src/hg/htdocs/goldenPath/help/hgCodonColoringMrna.html
  • lines changed 0, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/goldenPath/help/hgConvert.html
  • lines changed 147, context: html, text, full: html, text
    64f5e1fb8b93253cf89a6f36fb00d67d2ededf1d Sun Mar 15 20:52:02 2026 -0700
    Updating the QuickLift documentation page and the Alignment Differences page, refs #35536
• src/hg/htdocs/goldenPath/help/hgGeneGraph.html
  • lines changed 3, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/goldenPath/help/hgSessionHelp.html
  • lines changed 8, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/goldenPath/help/hgTablesHelp.html
  • lines changed 3, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 3, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html
  • lines changed 5, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/goldenPath/help/hic.html
  • lines changed 2, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/goldenPath/help/hubQuickStart.html
  • lines changed 2, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/goldenPath/help/hubQuickStartGroups.html
  • lines changed 3, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/goldenPath/help/interact.html
  • lines changed 0, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/goldenPath/help/mirror.html
  • lines changed 4, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/goldenPath/help/quickLiftChain.html
  • lines changed 57, context: html, text, full: html, text
    64f5e1fb8b93253cf89a6f36fb00d67d2ededf1d Sun Mar 15 20:52:02 2026 -0700
    Updating the QuickLift documentation page and the Alignment Differences page, refs #35536
• src/hg/htdocs/goldenPath/help/sessions.html
  • lines changed 4, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/goldenPath/help/trackDb/changes.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 1, context: html, text, full: html, text
    08afd09bf225ea50691998f829926e9d71d55b49 Wed Mar 11 19:21:42 2026 -0700
    Fixing small grammatical and consistency errors with the heatmap page and trackDb entry. Also some bigger fixes like a broken anchor. Refs #36176
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 66, context: html, text, full: html, text
    12d5cbaaa39bb6a0f59f5ee9c25d9cfeacf0ccc0 Mon Mar 9 10:44:36 2026 -0700
    Redoing initial section of page based on feedback, refs #37080
  • lines changed 2, context: html, text, full: html, text
    311f384feb48161e2b131a6a8904d861312754c4 Mon Mar 9 11:09:42 2026 -0700
    adding link to hub docs, refs #37080
  • lines changed 4, context: html, text, full: html, text
    fb4ffcb9317cff2f672d44d692e1433288728c25 Wed Mar 11 08:59:36 2026 -0700
    Tweaks based on automated CR, refs #37221
  • lines changed 1, context: html, text, full: html, text
    08afd09bf225ea50691998f829926e9d71d55b49 Wed Mar 11 19:21:42 2026 -0700
    Fixing small grammatical and consistency errors with the heatmap page and trackDb entry. Also some bigger fixes like a broken anchor. Refs #36176
  • lines changed 2, context: html, text, full: html, text
    d2bf838b45fbf990acd77d9a1015b6176c92d36a Sat Mar 14 13:00:31 2026 -0700
    genark archive -> repository, refs #37221
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 5, context: html, text, full: html, text
    5b71760c9bfaa3aa819aa1d128eb822c95e9463e Mon Mar 9 10:46:45 2026 -0700
    tweaks to genome setting description to describe GenArk, no refs
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
  • lines changed 1, context: html, text, full: html, text
    08afd09bf225ea50691998f829926e9d71d55b49 Wed Mar 11 19:21:42 2026 -0700
    Fixing small grammatical and consistency errors with the heatmap page and trackDb entry. Also some bigger fixes like a broken anchor. Refs #36176
• src/hg/htdocs/goldenPath/help/vcf.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 15, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
  • lines changed 79, context: html, text, full: html, text
    9f25bb947c005d453ff47f8beac29dc18afde9c3 Fri Mar 13 15:32:43 2026 -0700
    Staging the announcement for the gnomAD coverage tracks, refs #37036
  • lines changed 45, context: html, text, full: html, text
    f279f92f74cafe040582a1bc8fe935e947f636a9 Fri Mar 13 18:23:40 2026 -0700
    Announcing the Human Methylation Atlas Summary and Signals tracks for hg38 and hg19, refs #36826
• src/hg/htdocs/images/QuickLift/quickLiftAlignmentDifferences.png
  • lines changed 0, context: html, text, full: html, text
    64f5e1fb8b93253cf89a6f36fb00d67d2ededf1d Sun Mar 15 20:52:02 2026 -0700
    Updating the QuickLift documentation page and the Alignment Differences page, refs #35536
• src/hg/htdocs/images/QuickLift/quickLiftGreenbuttons.png
  • lines changed 0, context: html, text, full: html, text
    c15405c93929fa4aa7929d3dcf4aa555ae6652c7 Sun Mar 15 20:58:02 2026 -0700
    Adding images for the QuickLift documentation page, #35536
• src/hg/htdocs/images/QuickLift/quickLiftTracks.png
  • lines changed 0, context: html, text, full: html, text
    c15405c93929fa4aa7929d3dcf4aa555ae6652c7 Sun Mar 15 20:58:02 2026 -0700
    Adding images for the QuickLift documentation page, #35536
• src/hg/htdocs/images/newsArchImages/humanMethylationAtlas.png
  • lines changed 0, context: html, text, full: html, text
    f279f92f74cafe040582a1bc8fe935e947f636a9 Fri Mar 13 18:23:40 2026 -0700
    Announcing the Human Methylation Atlas Summary and Signals tracks for hg38 and hg19, refs #36826
• src/hg/htdocs/inc/gbFooter.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/inc/gbPageStartHardcoded.html
  • lines changed 9, context: html, text, full: html, text
    30d7f0358fc7d3cec663333e0e9f2a1e0defe909 Mon Mar 9 16:48:55 2026 -0700
    Rolled back the local CDNs for hgdownload since it has some styling issues - some of the downloaded CNDs were missing from that computer. The goal of this was to increase speed on the GB, so for the download server this isn't a big deal. This came up now because I was updating the GenArk name, and this change went out along with it and broke the menus. All good now, refs #37027
• src/hg/htdocs/inc/gbsFooter.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/inc/jWestFooter.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/indexMeetings.html
  • lines changed 24, context: html, text, full: html, text
    d30fb57a294222a2458866d60eae82cc50cf6dde Tue Mar 10 15:15:21 2026 -0700
    Removing meetings that have passed and rearranging them in chronological order, no RM.
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    9f25bb947c005d453ff47f8beac29dc18afde9c3 Fri Mar 13 15:32:43 2026 -0700
    Staging the announcement for the gnomAD coverage tracks, refs #37036
  • lines changed 12, context: html, text, full: html, text
    f279f92f74cafe040582a1bc8fe935e947f636a9 Fri Mar 13 18:23:40 2026 -0700
    Announcing the Human Methylation Atlas Summary and Signals tracks for hg38 and hg19, refs #36826
• src/hg/htdocs/staff.html
  • lines changed 0, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/htdocs/training/index.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/hubApi/apiUtils.c
  • lines changed 3, context: html, text, full: html, text
    a65ee2b4427852eca3993f8203b0b3ea8ce1cedc Mon Mar 9 14:27:14 2026 -0700
    Claude code fixing Claude code
• src/hg/hubApi/hubApi.c
  • lines changed 23, context: html, text, full: html, text
    4409063550e6c4cc87cfd37f92f7b8db2699f885 Fri Mar 13 17:13:14 2026 -0700
    with the aid of claude add a genome argument to the ucscGenomes endpoint and manage assembly alias a bit more than previously for ucscGenomes and genarkGenomes refs #35972
• src/hg/hubApi/list.c
  • lines changed 18, context: html, text, full: html, text
    4409063550e6c4cc87cfd37f92f7b8db2699f885 Fri Mar 13 17:13:14 2026 -0700
    with the aid of claude add a genome argument to the ucscGenomes endpoint and manage assembly alias a bit more than previously for ucscGenomes and genarkGenomes refs #35972
• src/hg/hubApi/tests/expected/err31.gz
  • lines changed 0, context: html, text, full: html, text
    4409063550e6c4cc87cfd37f92f7b8db2699f885 Fri Mar 13 17:13:14 2026 -0700
    with the aid of claude add a genome argument to the ucscGenomes endpoint and manage assembly alias a bit more than previously for ucscGenomes and genarkGenomes refs #35972
• src/hg/hubApi/tests/expected/list27b.gz
  • lines changed 0, context: html, text, full: html, text
    4409063550e6c4cc87cfd37f92f7b8db2699f885 Fri Mar 13 17:13:14 2026 -0700
    with the aid of claude add a genome argument to the ucscGenomes endpoint and manage assembly alias a bit more than previously for ucscGenomes and genarkGenomes refs #35972
• src/hg/hubApi/tests/expected/list27c.gz
  • lines changed 0, context: html, text, full: html, text
    4409063550e6c4cc87cfd37f92f7b8db2699f885 Fri Mar 13 17:13:14 2026 -0700
    with the aid of claude add a genome argument to the ucscGenomes endpoint and manage assembly alias a bit more than previously for ucscGenomes and genarkGenomes refs #35972
• src/hg/hubApi/tests/expected/notSup01.gz
  • lines changed 0, context: html, text, full: html, text
    4409063550e6c4cc87cfd37f92f7b8db2699f885 Fri Mar 13 17:13:14 2026 -0700
    with the aid of claude add a genome argument to the ucscGenomes endpoint and manage assembly alias a bit more than previously for ucscGenomes and genarkGenomes refs #35972
• src/hg/hubApi/tests/makefile
  • lines changed 13, context: html, text, full: html, text
    4409063550e6c4cc87cfd37f92f7b8db2699f885 Fri Mar 13 17:13:14 2026 -0700
    with the aid of claude add a genome argument to the ucscGenomes endpoint and manage assembly alias a bit more than previously for ucscGenomes and genarkGenomes refs #35972
• src/hg/inc/hgMaf.h
  • lines changed 14, context: html, text, full: html, text
    0529f8de2a72011dfcea8f9a1221b6d227341743 Tue Mar 10 17:34:58 2026 -0700
    hgc MAF click: use mafFrag to show only selected species with inserts removed Change the hgc MAF detail page to use hgMafFrag/hgBigMafFrag instead of displaying raw MAF blocks. This stitches alignments into a single continuous display in reference coordinates, filtering to only selected species and removing insertion columns where the reference has gaps. Key changes: - mafClick.c: rewrite mafOrAxtClick2 to build species orderList from trackDb settings (speciesOrder, speciesGroup, speciesUseFile) respecting speciesDefaultOff and cart on/off state via cartUsualBooleanClosestToHome, matching the hgTracks species selection logic in newSpeciesItems(). Add mafStripRefGaps() to remove insertion columns from mafFrag output. Show spaces instead of dots for matching bases in diff mode. - hgMaf.h/hgMaf.c: add hgMafFragFromMafList() public wrapper for pre-loaded mafLists (AXT/custom mafFile support). Change hgMafFragHelper to skip species not in orderList instead of errAbort. Track per-species source coordinates (src, start, end, srcSize, strand) in struct oneOrg so browser/DNA links work correctly in mafFrag output. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 40, context: html, text, full: html, text
    715e2acf2dd9ef6106cc42ce79c724e1e52ad62e Thu Mar 12 09:14:28 2026 -0700
    NoDots MAF alignment display for hgc mafClick, with i-row preservation and mafFrag -noDots flag hgMaf.c: add hgMafFragHelperNoDots and public wrappers (hgMafFragNoDots, hgBigMafFragNoDots, hgMafFragFromMafListNoDots) that return a list of maf blocks containing only species with actual sequence — no dot-filled rows. Blocks are broken when the species set changes; gaps between same-species blocks are filled with native sequence for the reference and dashes for others. Preserve i-row data (leftStatus/rightStatus/leftLen/rightLen) through the NoDots path so insert annotations appear in emitted blocks. hgMaf.h: declare the new NoDots public functions. mafClick.c: use NoDots path when mafClickMafFrag is enabled. Fix block numbering (aliIx was never incremented in useMafFrag path). Use full textSize for NoDots line width. Use dots instead of spaces in diff mode for both paths. Fix species label width computation to check labelHash consistently so long assembly names don't misalign sequences. Strip ref gap columns where no other species has sequence. mafFrag: add -noDots option to invoke hgMafFragNoDots from the command line, with 4 new tests (noDots, noDotsRev, noDotsOutName, noDotsLarger). refs #21477 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 54, context: html, text, full: html, text
    147740e133aa59c5aa7938ef68f1b66f3696c701 Fri Mar 13 15:29:49 2026 -0700
    Revert noDots mafClick/mafFrag work from master, refs #21477 Remove the mafClickMafFrag/noDots code path from mafClick.c, hgMaf.c, hgMaf.h, and mafFrag.c. Also remove mafFrag unit tests added as part of this work. The code is preserved on the mafFragNoDots and mafClickMafFrag branches. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/js/facetedComposite.js
  • lines changed 30, context: html, text, full: html, text
    f0e12555bca2d035cbd2d80414e2d4e154543f9b Fri Mar 13 18:12:59 2026 -0700
    Removing local storage cache in facetedComposite.js - it's too easy to reach the storage limit, and the browser's own file cache should mostly satisfy this need. We'll work next on adding a forced refresh when udcTimeout is set in the cart, to facilitate development, refs #36320
• src/hg/js/hgTracks.js
  • lines changed 3, context: html, text, full: html, text
    4c4592f3425753099d19b07c7a623e091b4f5197 Mon Mar 9 16:18:07 2026 -0700
    Fix for mouseover wiggles not showing up on page load, refs #37205
• src/hg/js/react/hgIntegrator/hgIntegrator.jsx
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/js/subCfg.js
  • lines changed 46, context: html, text, full: html, text
    31a8f798f6eb4466ccb1a7b76e5644b55c369980 Fri Mar 13 06:16:40 2026 -0700
    subCfg: auto-show/hide composite vis on subtrack checkbox changes, refs #37182 Move the logic that auto-sets composite visibility to pack/hide when subtracks are checked/unchecked into a separate onUserCbChange handler bound via native addEventListener. jQuery .trigger('change') only fires jQuery handlers, not native ones, so this correctly distinguishes real user clicks from programmatic triggers during page init. Also bind it on matCB (matrix) checkboxes and check only visible subCBs to avoid counting hidden-but-checked subtracks. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/js/utils.js
  • lines changed 50, context: html, text, full: html, text
    be67cde22f4d9af8323ef62560754b5ef925d020 Mon Mar 9 16:19:25 2026 -0700
    Fix two regression in tooltip code from commit ddfed922f22d47: not clearing tooltips on mouse scroll and not clearing tooltips when showing a wiggle mouseover, refs #37205
• src/hg/lib/baseMaskCommon.c
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/lib/genomeRangeTreeFile.c
  • lines changed 2, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/lib/hdb.c
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/lib/hgMaf.c
  • lines changed 45, context: html, text, full: html, text
    0529f8de2a72011dfcea8f9a1221b6d227341743 Tue Mar 10 17:34:58 2026 -0700
    hgc MAF click: use mafFrag to show only selected species with inserts removed Change the hgc MAF detail page to use hgMafFrag/hgBigMafFrag instead of displaying raw MAF blocks. This stitches alignments into a single continuous display in reference coordinates, filtering to only selected species and removing insertion columns where the reference has gaps. Key changes: - mafClick.c: rewrite mafOrAxtClick2 to build species orderList from trackDb settings (speciesOrder, speciesGroup, speciesUseFile) respecting speciesDefaultOff and cart on/off state via cartUsualBooleanClosestToHome, matching the hgTracks species selection logic in newSpeciesItems(). Add mafStripRefGaps() to remove insertion columns from mafFrag output. Show spaces instead of dots for matching bases in diff mode. - hgMaf.h/hgMaf.c: add hgMafFragFromMafList() public wrapper for pre-loaded mafLists (AXT/custom mafFile support). Change hgMafFragHelper to skip species not in orderList instead of errAbort. Track per-species source coordinates (src, start, end, srcSize, strand) in struct oneOrg so browser/DNA links work correctly in mafFrag output. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 589, context: html, text, full: html, text
    715e2acf2dd9ef6106cc42ce79c724e1e52ad62e Thu Mar 12 09:14:28 2026 -0700
    NoDots MAF alignment display for hgc mafClick, with i-row preservation and mafFrag -noDots flag hgMaf.c: add hgMafFragHelperNoDots and public wrappers (hgMafFragNoDots, hgBigMafFragNoDots, hgMafFragFromMafListNoDots) that return a list of maf blocks containing only species with actual sequence — no dot-filled rows. Blocks are broken when the species set changes; gaps between same-species blocks are filled with native sequence for the reference and dashes for others. Preserve i-row data (leftStatus/rightStatus/leftLen/rightLen) through the NoDots path so insert annotations appear in emitted blocks. hgMaf.h: declare the new NoDots public functions. mafClick.c: use NoDots path when mafClickMafFrag is enabled. Fix block numbering (aliIx was never incremented in useMafFrag path). Use full textSize for NoDots line width. Use dots instead of spaces in diff mode for both paths. Fix species label width computation to check labelHash consistently so long assembly names don't misalign sequences. Strip ref gap columns where no other species has sequence. mafFrag: add -noDots option to invoke hgMafFragNoDots from the command line, with 4 new tests (noDots, noDotsRev, noDotsOutName, noDotsLarger). refs #21477 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 634, context: html, text, full: html, text
    147740e133aa59c5aa7938ef68f1b66f3696c701 Fri Mar 13 15:29:49 2026 -0700
    Revert noDots mafClick/mafFrag work from master, refs #21477 Remove the mafClickMafFrag/noDots code path from mafClick.c, hgMaf.c, hgMaf.h, and mafFrag.c. Also remove mafFrag unit tests added as part of this work. The code is preserved on the mafFragNoDots and mafClickMafFrag branches. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/lib/hubConnect.c
  • lines changed 74, context: html, text, full: html, text
    3024edbfb4af164c8ef34eded35ec41015437c5c Wed Mar 11 14:56:35 2026 -0700
    allow GenArk hubs to exist as "curated" hubs with a dbDb entry such as rn8 and a nibPath to the GenArk /gbdb/ directory refs #32985
• src/hg/lib/hui.c
  • lines changed 5, context: html, text, full: html, text
    1bbbf05971f950d48fcd67ac9e8e6d395bae9761 Tue Mar 10 09:29:23 2026 -0700
    fix problem with composites with only one child and noParentConfig on (refs #37130)
  • lines changed 1, context: html, text, full: html, text
    48e28c6ab25cc0c901be5531c594868fe28920fb Tue Mar 10 11:14:46 2026 -0700
    Expanding the error message to print out all the possible values, refs #37219
  • lines changed 1, context: html, text, full: html, text
    903fa16639cacdeb96b1cb4eb8ba706d70c93236 Tue Mar 10 14:46:10 2026 -0700
    better err msg, refs #37219
• src/hg/lib/trackDbCustom.c
  • lines changed 1, context: html, text, full: html, text
    48e28c6ab25cc0c901be5531c594868fe28920fb Tue Mar 10 11:14:46 2026 -0700
    Expanding the error message to print out all the possible values, refs #37219
  • lines changed 7, context: html, text, full: html, text
    a71215bcc4a26e1641770d82127dc57ced1842c8 Tue Mar 10 12:37:04 2026 -0700
    Detect tracks that list themselves as their own parent, preventing infinite loop refs #35986 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/lib/trackHub.c
  • lines changed 3, context: html, text, full: html, text
    a71215bcc4a26e1641770d82127dc57ced1842c8 Tue Mar 10 12:37:04 2026 -0700
    Detect tracks that list themselves as their own parent, preventing infinite loop refs #35986 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 86, context: html, text, full: html, text
    cab953dd5332d8e2a52af9d6b01c9245fd13d29a Tue Mar 10 21:16:23 2026 -0700
    VGP update in progress
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 24, context: html, text, full: html, text
    cab953dd5332d8e2a52af9d6b01c9245fd13d29a Tue Mar 10 21:16:23 2026 -0700
    VGP update in progress
• src/hg/makeDb/doc/galGal6/lastzRuns.txt
  • lines changed 28, context: html, text, full: html, text
    7931c9562bb9808463e9b3ede322b0d415986de3 Wed Mar 11 10:37:13 2026 -0700
    Made galGal6ToGCF_016699485.2.chainBridge.over.chain.gz for MLQ #37185
• src/hg/makeDb/doc/hg19.txt
  • lines changed 28, context: html, text, full: html, text
    cbffb0dd48c0c9621532fd6d129845128c743655 Fri Mar 13 11:04:18 2026 -0700
    Made hg19ToHg38.chainBridge.over.chain.gz for MLQ #37156
• src/hg/makeDb/doc/hg38/gnomadStr.txt
  • lines changed 33, context: html, text, full: html, text
    f43f1239645183b88a00b3de83f74fd5553e6ce1 Thu Mar 12 07:52:35 2026 -0700
    Add gnomAD STR genotype track under gnomadVariants supertrack 87 disease-associated STR loci from gnomAD v3.1.3, aggregated from ~1.4M individual genotypes (18,511 WGS samples, ExpansionHunter v5). Includes allele frequency distributions and population breakdowns. Added relatedTracks links to strVar supertrack, refs #35420, refs #36652 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/doc/hg38/mpravardb.txt
  • lines changed 22, context: html, text, full: html, text
    ce180274fa3ba3db5c10ecbd9ae2479d4816e972 Tue Mar 10 04:00:45 2026 -0700
    Add MPRAVarDB track: 239k MPRA-tested regulatory variants from 18 studies Convert MPRAVarDB CSV (Wang et al. 2024) to bigBed9+ with liftOver of hg19 variants to hg38. Color by significance (red=FDR<0.05, orange=p<0.05, grey=not significant). MouseOver shows ref/alt/cell line/log2FC/p/FDR. Track added to existing MPRAs superTrack, refs #34284 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 3, context: html, text, full: html, text
    56c1481dcd7988e497207c1a69bda2da42e986d0 Tue Mar 10 04:03:37 2026 -0700
    docs change after claude
• src/hg/makeDb/doc/hg38/strchive.txt
  • lines changed 32, context: html, text, full: html, text
    e82a8101c1aa495e0e6c841f83f4d6c980fddf49 Thu Mar 12 07:28:49 2026 -0700
    Add STRchive disease-associated STR loci track to strVar supertrack 75 curated disease-associated tandem repeat expansion loci from STRchive (Hiatt et al. 2025), with pathogenic thresholds, inheritance modes, and disease annotations. Colored by inheritance mode, refs #36652 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/doc/hg38/webstr.txt
  • lines changed 40, context: html, text, full: html, text
    6bb46ba4e8d91ab3670d354ef18d8bf5321ec9ee Thu Mar 12 07:15:29 2026 -0700
    Add WebSTR short tandem repeat track under new strVar supertrack New track with 1.7M STR loci from WebSTR EnsembleTR panel (hg38), with allele frequency data for 5 populations from 1000 Genomes (3,550 samples). Includes conversion script, .as schema, trackDb, and full HTML documentation, refs #36652 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/genbank/src/align/gbAlignInstall.c
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/mdbUpdate/mdbPrint.c
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/scripts/gnomadStr/gnomadStr.as
  • lines changed 21, context: html, text, full: html, text
    f43f1239645183b88a00b3de83f74fd5553e6ce1 Thu Mar 12 07:52:35 2026 -0700
    Add gnomAD STR genotype track under gnomadVariants supertrack 87 disease-associated STR loci from gnomAD v3.1.3, aggregated from ~1.4M individual genotypes (18,511 WGS samples, ExpansionHunter v5). Includes allele frequency distributions and population breakdowns. Added relatedTracks links to strVar supertrack, refs #35420, refs #36652 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/scripts/gnomadStr/gnomadStrToBed.py
  • lines changed 126, context: html, text, full: html, text
    f43f1239645183b88a00b3de83f74fd5553e6ce1 Thu Mar 12 07:52:35 2026 -0700
    Add gnomAD STR genotype track under gnomadVariants supertrack 87 disease-associated STR loci from gnomAD v3.1.3, aggregated from ~1.4M individual genotypes (18,511 WGS samples, ExpansionHunter v5). Includes allele frequency distributions and population breakdowns. Added relatedTracks links to strVar supertrack, refs #35420, refs #36652 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/scripts/mpravardb/mpravardb.as
  • lines changed 26, context: html, text, full: html, text
    ce180274fa3ba3db5c10ecbd9ae2479d4816e972 Tue Mar 10 04:00:45 2026 -0700
    Add MPRAVarDB track: 239k MPRA-tested regulatory variants from 18 studies Convert MPRAVarDB CSV (Wang et al. 2024) to bigBed9+ with liftOver of hg19 variants to hg38. Color by significance (red=FDR<0.05, orange=p<0.05, grey=not significant). MouseOver shows ref/alt/cell line/log2FC/p/FDR. Track added to existing MPRAs superTrack, refs #34284 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/scripts/mpravardb/mpravardbToBed.py
  • lines changed 173, context: html, text, full: html, text
    ce180274fa3ba3db5c10ecbd9ae2479d4816e972 Tue Mar 10 04:00:45 2026 -0700
    Add MPRAVarDB track: 239k MPRA-tested regulatory variants from 18 studies Convert MPRAVarDB CSV (Wang et al. 2024) to bigBed9+ with liftOver of hg19 variants to hg38. Color by significance (red=FDR<0.05, orange=p<0.05, grey=not significant). MouseOver shows ref/alt/cell line/log2FC/p/FDR. Track added to existing MPRAs superTrack, refs #34284 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/scripts/strchive/strchive.as
  • lines changed 19, context: html, text, full: html, text
    e82a8101c1aa495e0e6c841f83f4d6c980fddf49 Thu Mar 12 07:28:49 2026 -0700
    Add STRchive disease-associated STR loci track to strVar supertrack 75 curated disease-associated tandem repeat expansion loci from STRchive (Hiatt et al. 2025), with pathogenic thresholds, inheritance modes, and disease annotations. Colored by inheritance mode, refs #36652 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/scripts/strchive/strchiveToBed.py
  • lines changed 61, context: html, text, full: html, text
    e82a8101c1aa495e0e6c841f83f4d6c980fddf49 Thu Mar 12 07:28:49 2026 -0700
    Add STRchive disease-associated STR loci track to strVar supertrack 75 curated disease-associated tandem repeat expansion loci from STRchive (Hiatt et al. 2025), with pathogenic thresholds, inheritance modes, and disease annotations. Colored by inheritance mode, refs #36652 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/scripts/webstr/webstr.as
  • lines changed 31, context: html, text, full: html, text
    6bb46ba4e8d91ab3670d354ef18d8bf5321ec9ee Thu Mar 12 07:15:29 2026 -0700
    Add WebSTR short tandem repeat track under new strVar supertrack New track with 1.7M STR loci from WebSTR EnsembleTR panel (hg38), with allele frequency data for 5 populations from 1000 Genomes (3,550 samples). Includes conversion script, .as schema, trackDb, and full HTML documentation, refs #36652 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/scripts/webstr/webstrToBed.py
  • lines changed 115, context: html, text, full: html, text
    6bb46ba4e8d91ab3670d354ef18d8bf5321ec9ee Thu Mar 12 07:15:29 2026 -0700
    Add WebSTR short tandem repeat track under new strVar supertrack New track with 1.7M STR loci from WebSTR EnsembleTR panel (hg38), with allele frequency data for 5 populations from 1000 Genomes (3,550 samples). Includes conversion script, .as schema, trackDb, and full HTML documentation, refs #36652 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/affy.html
  • lines changed 2, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/cow/bosTau6/numtSeq2012.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 2, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 2, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 2, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/ebola/gireIntraHost.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/geneid.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/chm13/html/GCA_009914755.4_T2T-CHM13v2.0.t2tRepeatMasker.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/clinvar.html
  • lines changed 2, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/dbSnp153Composite.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/dbSnp155Composite.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/dnaMethylation.html
  • lines changed 7, context: html, text, full: html, text
    88094bfcf5dbf48fbc8147f8b457b334e3025d9b Tue Mar 10 16:43:41 2026 -0700
    Updating the DNA Methylation superTrack track description and adding the yLineOnOff setting for the Human Methylation Atlas Signals track, refs #36826
• src/hg/makeDb/trackDb/human/encodeEgaspUpdate.html
  • lines changed 13, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/encodeUncFaire.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/encodeYaleMASPlacRNATars.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/encodeYaleRnaSuper.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/haplotype.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/hg17/cnp.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/hg18/cnp.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/hg18/cnpRedon.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/hg18/pgPop.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/hg18/pgYri.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/hg19/ctgPos.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/hg19/ctgPos2.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/hg19/gnomad.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/hg19/gnomadMpc.html
  • lines changed 2, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/hg19/tfbsConsSites.html
  • lines changed 3, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSc.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTfbsClusteredV3.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/hg38/cactus447way.html
  • lines changed 5, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/hg38/cons100way.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/hg38/cons241way.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/hg38/description.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/hg38/encode.cCREs.override.ra
  • lines changed 1, context: html, text, full: html, text
    785f82c6a4c5443431c8029fee829999c6982864 Mon Mar 9 14:51:18 2026 -0700
    Making the new cCREs track squish as feedback from Zhiping. It looks better since the track just has single coverage and the mouseOvers work in squish mode. Refs #37131
• src/hg/makeDb/trackDb/human/hg38/encodeCcreCombined.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 14, context: html, text, full: html, text
    f43f1239645183b88a00b3de83f74fd5553e6ce1 Thu Mar 12 07:52:35 2026 -0700
    Add gnomAD STR genotype track under gnomadVariants supertrack 87 disease-associated STR loci from gnomAD v3.1.3, aggregated from ~1.4M individual genotypes (18,511 WGS samples, ExpansionHunter v5). Includes allele frequency distributions and population breakdowns. Added relatedTracks links to strVar supertrack, refs #35420, refs #36652 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    44a568b95d278dc404a42e24c5877b523aa42e50 Fri Mar 13 07:37:16 2026 -0700
    adding a note to gnomad to make it clear that 3.1 should not be used, email from Chris
  • lines changed 2, context: html, text, full: html, text
    b0c906a6201e5c88b7cb936f9f5e8f87da38b2fc Fri Mar 13 07:43:13 2026 -0700
    gnomad track is now much more than variants, so removing the variants name from the shortlabel, no redmine
  • lines changed 1, context: html, text, full: html, text
    4ae93ebba6aaec8d3b587130b05f43889171527f Fri Mar 13 12:18:16 2026 -0700
    Staging the gnomAD coverage tracks for hg38, refs #37036
• src/hg/makeDb/trackDb/human/hg38/gnomad4ExomeCoverage.html
  • lines changed 1, context: html, text, full: html, text
    d1c631fc9a4937edd0e01ac4d05089621db40efb Wed Mar 11 10:24:53 2026 -0700
    Fixing a typo, refs #37217
• src/hg/makeDb/trackDb/human/hg38/gnomadCoverage.ra
  • lines changed 2, context: html, text, full: html, text
    2e591d0d8b7c1f2bd105893e230fdf6a8033beb9 Wed Mar 11 10:26:19 2026 -0700
    Changing the order of the Coverage tracks for gnomAD so v4 appears first on the list, refs #37036
• src/hg/makeDb/trackDb/human/hg38/gnomadPLI.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/hg38/gnomadStr.html
  • lines changed 125, context: html, text, full: html, text
    f43f1239645183b88a00b3de83f74fd5553e6ce1 Thu Mar 12 07:52:35 2026 -0700
    Add gnomAD STR genotype track under gnomadVariants supertrack 87 disease-associated STR loci from gnomAD v3.1.3, aggregated from ~1.4M individual genotypes (18,511 WGS samples, ExpansionHunter v5). Includes allele frequency distributions and population breakdowns. Added relatedTracks links to strVar supertrack, refs #35420, refs #36652 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/gnomadV4.1.html
  • lines changed 14, context: html, text, full: html, text
    44a568b95d278dc404a42e24c5877b523aa42e50 Fri Mar 13 07:37:16 2026 -0700
    adding a note to gnomad to make it clear that 3.1 should not be used, email from Chris
  • lines changed 25, context: html, text, full: html, text
    7577ca944ad2c81bd75ad35993c8b86dc471fef1 Fri Mar 13 07:48:31 2026 -0700
    the gnomad track had no intro at all anymore, so I added one, no redmine
• src/hg/makeDb/trackDb/human/hg38/mpra.html
  • lines changed 209, context: html, text, full: html, text
    ce180274fa3ba3db5c10ecbd9ae2479d4816e972 Tue Mar 10 04:00:45 2026 -0700
    Add MPRAVarDB track: 239k MPRA-tested regulatory variants from 18 studies Convert MPRAVarDB CSV (Wang et al. 2024) to bigBed9+ with liftOver of hg19 variants to hg38. Color by significance (red=FDR<0.05, orange=p<0.05, grey=not significant). MouseOver shows ref/alt/cell line/log2FC/p/FDR. Track added to existing MPRAs superTrack, refs #34284 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/mpra.ra
  • lines changed 12, context: html, text, full: html, text
    ce180274fa3ba3db5c10ecbd9ae2479d4816e972 Tue Mar 10 04:00:45 2026 -0700
    Add MPRAVarDB track: 239k MPRA-tested regulatory variants from 18 studies Convert MPRAVarDB CSV (Wang et al. 2024) to bigBed9+ with liftOver of hg19 variants to hg38. Color by significance (red=FDR<0.05, orange=p<0.05, grey=not significant). MouseOver shows ref/alt/cell line/log2FC/p/FDR. Track added to existing MPRAs superTrack, refs #34284 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/ncOrfs.ra
  • lines changed 60, context: html, text, full: html, text
    8a818d25a85939496ec2c133bb37c3702921fe43 Fri Mar 13 15:02:19 2026 -0700
    commit missing files due to build problems, refs #37036
• src/hg/makeDb/trackDb/human/hg38/rmsk.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/hg38/strVar.html
  • lines changed 27, context: html, text, full: html, text
    6bb46ba4e8d91ab3670d354ef18d8bf5321ec9ee Thu Mar 12 07:15:29 2026 -0700
    Add WebSTR short tandem repeat track under new strVar supertrack New track with 1.7M STR loci from WebSTR EnsembleTR panel (hg38), with allele frequency data for 5 populations from 1000 Genomes (3,550 samples). Includes conversion script, .as schema, trackDb, and full HTML documentation, refs #36652 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 6, context: html, text, full: html, text
    e82a8101c1aa495e0e6c841f83f4d6c980fddf49 Thu Mar 12 07:28:49 2026 -0700
    Add STRchive disease-associated STR loci track to strVar supertrack 75 curated disease-associated tandem repeat expansion loci from STRchive (Hiatt et al. 2025), with pathogenic thresholds, inheritance modes, and disease annotations. Colored by inheritance mode, refs #36652 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 4, context: html, text, full: html, text
    8a818d25a85939496ec2c133bb37c3702921fe43 Fri Mar 13 15:02:19 2026 -0700
    commit missing files due to build problems, refs #37036
• src/hg/makeDb/trackDb/human/hg38/strVar.ra
  • lines changed 5, context: html, text, full: html, text
    31a8f798f6eb4466ccb1a7b76e5644b55c369980 Fri Mar 13 06:16:40 2026 -0700
    subCfg: auto-show/hide composite vis on subtrack checkbox changes, refs #37182 Move the logic that auto-sets composite visibility to pack/hide when subtracks are checked/unchecked into a separate onUserCbChange handler bound via native addEventListener. jQuery .trigger('change') only fires jQuery handlers, not native ones, so this correctly distinguishes real user clicks from programmatic triggers during page init. Also bind it on matCB (matrix) checkboxes and check only visible subCBs to avoid counting hidden-but-checked subtracks. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/strchive.html
  • lines changed 98, context: html, text, full: html, text
    e82a8101c1aa495e0e6c841f83f4d6c980fddf49 Thu Mar 12 07:28:49 2026 -0700
    Add STRchive disease-associated STR loci track to strVar supertrack 75 curated disease-associated tandem repeat expansion loci from STRchive (Hiatt et al. 2025), with pathogenic thresholds, inheritance modes, and disease annotations. Colored by inheritance mode, refs #36652 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/tgpArchive.ra
  • lines changed 1, context: html, text, full: html, text
    de6c27b63c74c93c069030f93a2817b93bf71b8e Tue Mar 10 15:49:39 2026 -0700
    Update lorax track iframeUrl to point to new lorax.ucsc.edu server
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 13, context: html, text, full: html, text
    6bb46ba4e8d91ab3670d354ef18d8bf5321ec9ee Thu Mar 12 07:15:29 2026 -0700
    Add WebSTR short tandem repeat track under new strVar supertrack New track with 1.7M STR loci from WebSTR EnsembleTR panel (hg38), with allele frequency data for 5 populations from 1000 Genomes (3,550 samples). Includes conversion script, .as schema, trackDb, and full HTML documentation, refs #36652 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 1, context: html, text, full: html, text
    31a8f798f6eb4466ccb1a7b76e5644b55c369980 Fri Mar 13 06:16:40 2026 -0700
    subCfg: auto-show/hide composite vis on subtrack checkbox changes, refs #37182 Move the logic that auto-sets composite visibility to pack/hide when subtracks are checked/unchecked into a separate onUserCbChange handler bound via native addEventListener. jQuery .trigger('change') only fires jQuery handlers, not native ones, so this correctly distinguishes real user clicks from programmatic triggers during page init. Also bind it on matCB (matrix) checkboxes and check only visible subCBs to avoid counting hidden-but-checked subtracks. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/webstr.html
  • lines changed 115, context: html, text, full: html, text
    6bb46ba4e8d91ab3670d354ef18d8bf5321ec9ee Thu Mar 12 07:15:29 2026 -0700
    Add WebSTR short tandem repeat track under new strVar supertrack New track with 1.7M STR loci from WebSTR EnsembleTR panel (hg38), with allele frequency data for 5 populations from 1000 Genomes (3,550 samples). Includes conversion script, .as schema, trackDb, and full HTML documentation, refs #36652 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/webstr.ra
  • lines changed 21, context: html, text, full: html, text
    6bb46ba4e8d91ab3670d354ef18d8bf5321ec9ee Thu Mar 12 07:15:29 2026 -0700
    Add WebSTR short tandem repeat track under new strVar supertrack New track with 1.7M STR loci from WebSTR EnsembleTR panel (hg38), with allele frequency data for 5 populations from 1000 Genomes (3,550 samples). Includes conversion script, .as schema, trackDb, and full HTML documentation, refs #36652 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 14, context: html, text, full: html, text
    e82a8101c1aa495e0e6c841f83f4d6c980fddf49 Thu Mar 12 07:28:49 2026 -0700
    Add STRchive disease-associated STR loci track to strVar supertrack 75 curated disease-associated tandem repeat expansion loci from STRchive (Hiatt et al. 2025), with pathogenic thresholds, inheritance modes, and disease annotations. Colored by inheritance mode, refs #36652 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/hg38/wgEncodeRegDnase.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/hs1/html/t2tRepeatMasker.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/humanMethylationAtlas.ra
  • lines changed 49, context: html, text, full: html, text
    710dd5a15d434aa67588901bd85a5ec1dfb26357 Mon Mar 9 18:11:59 2026 -0700
    Forgot to commit the Human Methylation Atlas Signals track description page, and remove the humanMethylationAtlas.ra/humanMethylationAtlas.html files in my last commit for the DNA Methylation track, refs #36826
• src/hg/makeDb/trackDb/human/longReadVariants.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/methylationAtlasSignals.html
  • lines changed 32, context: html, text, full: html, text
    710dd5a15d434aa67588901bd85a5ec1dfb26357 Mon Mar 9 18:11:59 2026 -0700
    Forgot to commit the Human Methylation Atlas Signals track description page, and remove the humanMethylationAtlas.ra/humanMethylationAtlas.html files in my last commit for the DNA Methylation track, refs #36826
• src/hg/makeDb/trackDb/human/methylationAtlasSignals.ra
  • lines changed 1, context: html, text, full: html, text
    88094bfcf5dbf48fbc8147f8b457b334e3025d9b Tue Mar 10 16:43:41 2026 -0700
    Updating the DNA Methylation superTrack track description and adding the yLineOnOff setting for the Human Methylation Atlas Signals track, refs #36826
• src/hg/makeDb/trackDb/human/numtSeq.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/refSeqComposite.html
  • lines changed 0, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    c2cf7d570d6980c8cf4a44be1bdf7a68fb06d9c6 Thu Mar 12 22:12:52 2026 -0700
    Updating the longLabel and pennantIcon for the DNA Methylation superTrack, refs #36826
  • lines changed 1, context: html, text, full: html, text
    f279f92f74cafe040582a1bc8fe935e947f636a9 Fri Mar 13 18:23:40 2026 -0700
    Announcing the Human Methylation Atlas Summary and Signals tracks for hg38 and hg19, refs #36826
• src/hg/makeDb/trackDb/human/ucsfBrainMethyl.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/mouse/mm10/encode.cCREs.override.ra
  • lines changed 1, context: html, text, full: html, text
    785f82c6a4c5443431c8029fee829999c6982864 Mon Mar 9 14:51:18 2026 -0700
    Making the new cCREs track squish as feedback from Zhiping. It looks better since the track just has single coverage and the mouseOvers work in squish mode. Refs #37131
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.release3.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.release4.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/other/centromeres1/description.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/pig/susScr2/numtSeq2012.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/relatedTracks.ra
  • lines changed 3, context: html, text, full: html, text
    f43f1239645183b88a00b3de83f74fd5553e6ce1 Thu Mar 12 07:52:35 2026 -0700
    Add gnomAD STR genotype track under gnomadVariants supertrack 87 disease-associated STR loci from gnomAD v3.1.3, aggregated from ~1.4M individual genotypes (18,511 WGS samples, ExpansionHunter v5). Includes allele frequency distributions and population breakdowns. Added relatedTracks links to strVar supertrack, refs #35420, refs #36652 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/virus/mpxvRivers/html/repeatMasker.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/virus/wuhCor1/cas13Crispr.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/virus/wuhCor1/pbm.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/virus/wuhCor1/recomb.html
  • lines changed 3, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/virus/wuhCor1/strains.ra
  • lines changed 9, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/virus/wuhCor1/transcriptome.html
  • lines changed 2, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/virus/wuhCor1/variantMuts.html
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/makeDb/trackDb/virus/wuhCor1/variantMuts.ra
  • lines changed 18, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/mouseStuff/chainInfo/chainInfo.c
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/protein/lib/pbUtil.c
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/pslPairs/pslPairs.c
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/randomPlacement/randomPlacement.c
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/ratStuff/mafFrag/mafFrag.c
  • lines changed 27, context: html, text, full: html, text
    715e2acf2dd9ef6106cc42ce79c724e1e52ad62e Thu Mar 12 09:14:28 2026 -0700
    NoDots MAF alignment display for hgc mafClick, with i-row preservation and mafFrag -noDots flag hgMaf.c: add hgMafFragHelperNoDots and public wrappers (hgMafFragNoDots, hgBigMafFragNoDots, hgMafFragFromMafListNoDots) that return a list of maf blocks containing only species with actual sequence — no dot-filled rows. Blocks are broken when the species set changes; gaps between same-species blocks are filled with native sequence for the reference and dashes for others. Preserve i-row data (leftStatus/rightStatus/leftLen/rightLen) through the NoDots path so insert annotations appear in emitted blocks. hgMaf.h: declare the new NoDots public functions. mafClick.c: use NoDots path when mafClickMafFrag is enabled. Fix block numbering (aliIx was never incremented in useMafFrag path). Use full textSize for NoDots line width. Use dots instead of spaces in diff mode for both paths. Fix species label width computation to check labelHash consistently so long assembly names don't misalign sequences. Strip ref gap columns where no other species has sequence. mafFrag: add -noDots option to invoke hgMafFragNoDots from the command line, with 4 new tests (noDots, noDotsRev, noDotsOutName, noDotsLarger). refs #21477 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 27, context: html, text, full: html, text
    147740e133aa59c5aa7938ef68f1b66f3696c701 Fri Mar 13 15:29:49 2026 -0700
    Revert noDots mafClick/mafFrag work from master, refs #21477 Remove the mafClickMafFrag/noDots code path from mafClick.c, hgMaf.c, hgMaf.h, and mafFrag.c. Also remove mafFrag unit tests added as part of this work. The code is preserved on the mafFragNoDots and mafClickMafFrag branches. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/ratStuff/mafFrag/makefile
  • lines changed 5, context: html, text, full: html, text
    2f032b790bd3d0354f1d61de5dcadb2e469c1817 Tue Mar 10 17:42:42 2026 -0700
    Add unit tests for mafFrag tool Add test suite with 5 tests covering basic extraction, reverse strand, custom outName, small region, and larger multi-block region using hg38 multiz100way. Replace broken old test target that referenced a missing expected.maf file. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 5, context: html, text, full: html, text
    147740e133aa59c5aa7938ef68f1b66f3696c701 Fri Mar 13 15:29:49 2026 -0700
    Revert noDots mafClick/mafFrag work from master, refs #21477 Remove the mafClickMafFrag/noDots code path from mafClick.c, hgMaf.c, hgMaf.h, and mafFrag.c. Also remove mafFrag unit tests added as part of this work. The code is preserved on the mafFragNoDots and mafClickMafFrag branches. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/ratStuff/mafFrag/tests/expected/basic.maf
  • lines changed 5, context: html, text, full: html, text
    2f032b790bd3d0354f1d61de5dcadb2e469c1817 Tue Mar 10 17:42:42 2026 -0700
    Add unit tests for mafFrag tool Add test suite with 5 tests covering basic extraction, reverse strand, custom outName, small region, and larger multi-block region using hg38 multiz100way. Replace broken old test target that referenced a missing expected.maf file. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 1, context: html, text, full: html, text
    2da16dce988cd42c7d97019eebd9660bfe20b68b Tue Mar 10 17:55:26 2026 -0700
    Update mafFrag test expected outputs for source coordinate tracking Regenerate expected files to reflect hgMafFragHelper now preserving full source (db.chrom), start, size, srcSize, and strand for non-reference species instead of placeholder values. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 5, context: html, text, full: html, text
    147740e133aa59c5aa7938ef68f1b66f3696c701 Fri Mar 13 15:29:49 2026 -0700
    Revert noDots mafClick/mafFrag work from master, refs #21477 Remove the mafClickMafFrag/noDots code path from mafClick.c, hgMaf.c, hgMaf.h, and mafFrag.c. Also remove mafFrag unit tests added as part of this work. The code is preserved on the mafFragNoDots and mafClickMafFrag branches. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/ratStuff/mafFrag/tests/expected/larger.maf
  • lines changed 29, context: html, text, full: html, text
    2f032b790bd3d0354f1d61de5dcadb2e469c1817 Tue Mar 10 17:42:42 2026 -0700
    Add unit tests for mafFrag tool Add test suite with 5 tests covering basic extraction, reverse strand, custom outName, small region, and larger multi-block region using hg38 multiz100way. Replace broken old test target that referenced a missing expected.maf file. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 25, context: html, text, full: html, text
    2da16dce988cd42c7d97019eebd9660bfe20b68b Tue Mar 10 17:55:26 2026 -0700
    Update mafFrag test expected outputs for source coordinate tracking Regenerate expected files to reflect hgMafFragHelper now preserving full source (db.chrom), start, size, srcSize, and strand for non-reference species instead of placeholder values. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 29, context: html, text, full: html, text
    147740e133aa59c5aa7938ef68f1b66f3696c701 Fri Mar 13 15:29:49 2026 -0700
    Revert noDots mafClick/mafFrag work from master, refs #21477 Remove the mafClickMafFrag/noDots code path from mafClick.c, hgMaf.c, hgMaf.h, and mafFrag.c. Also remove mafFrag unit tests added as part of this work. The code is preserved on the mafFragNoDots and mafClickMafFrag branches. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/ratStuff/mafFrag/tests/expected/noDots.maf
  • lines changed 6, context: html, text, full: html, text
    715e2acf2dd9ef6106cc42ce79c724e1e52ad62e Thu Mar 12 09:14:28 2026 -0700
    NoDots MAF alignment display for hgc mafClick, with i-row preservation and mafFrag -noDots flag hgMaf.c: add hgMafFragHelperNoDots and public wrappers (hgMafFragNoDots, hgBigMafFragNoDots, hgMafFragFromMafListNoDots) that return a list of maf blocks containing only species with actual sequence — no dot-filled rows. Blocks are broken when the species set changes; gaps between same-species blocks are filled with native sequence for the reference and dashes for others. Preserve i-row data (leftStatus/rightStatus/leftLen/rightLen) through the NoDots path so insert annotations appear in emitted blocks. hgMaf.h: declare the new NoDots public functions. mafClick.c: use NoDots path when mafClickMafFrag is enabled. Fix block numbering (aliIx was never incremented in useMafFrag path). Use full textSize for NoDots line width. Use dots instead of spaces in diff mode for both paths. Fix species label width computation to check labelHash consistently so long assembly names don't misalign sequences. Strip ref gap columns where no other species has sequence. mafFrag: add -noDots option to invoke hgMafFragNoDots from the command line, with 4 new tests (noDots, noDotsRev, noDotsOutName, noDotsLarger). refs #21477 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 6, context: html, text, full: html, text
    147740e133aa59c5aa7938ef68f1b66f3696c701 Fri Mar 13 15:29:49 2026 -0700
    Revert noDots mafClick/mafFrag work from master, refs #21477 Remove the mafClickMafFrag/noDots code path from mafClick.c, hgMaf.c, hgMaf.h, and mafFrag.c. Also remove mafFrag unit tests added as part of this work. The code is preserved on the mafFragNoDots and mafClickMafFrag branches. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/ratStuff/mafFrag/tests/expected/noDotsLarger.maf
  • lines changed 254, context: html, text, full: html, text
    715e2acf2dd9ef6106cc42ce79c724e1e52ad62e Thu Mar 12 09:14:28 2026 -0700
    NoDots MAF alignment display for hgc mafClick, with i-row preservation and mafFrag -noDots flag hgMaf.c: add hgMafFragHelperNoDots and public wrappers (hgMafFragNoDots, hgBigMafFragNoDots, hgMafFragFromMafListNoDots) that return a list of maf blocks containing only species with actual sequence — no dot-filled rows. Blocks are broken when the species set changes; gaps between same-species blocks are filled with native sequence for the reference and dashes for others. Preserve i-row data (leftStatus/rightStatus/leftLen/rightLen) through the NoDots path so insert annotations appear in emitted blocks. hgMaf.h: declare the new NoDots public functions. mafClick.c: use NoDots path when mafClickMafFrag is enabled. Fix block numbering (aliIx was never incremented in useMafFrag path). Use full textSize for NoDots line width. Use dots instead of spaces in diff mode for both paths. Fix species label width computation to check labelHash consistently so long assembly names don't misalign sequences. Strip ref gap columns where no other species has sequence. mafFrag: add -noDots option to invoke hgMafFragNoDots from the command line, with 4 new tests (noDots, noDotsRev, noDotsOutName, noDotsLarger). refs #21477 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 254, context: html, text, full: html, text
    147740e133aa59c5aa7938ef68f1b66f3696c701 Fri Mar 13 15:29:49 2026 -0700
    Revert noDots mafClick/mafFrag work from master, refs #21477 Remove the mafClickMafFrag/noDots code path from mafClick.c, hgMaf.c, hgMaf.h, and mafFrag.c. Also remove mafFrag unit tests added as part of this work. The code is preserved on the mafFragNoDots and mafClickMafFrag branches. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/ratStuff/mafFrag/tests/expected/noDotsOutName.maf
  • lines changed 6, context: html, text, full: html, text
    715e2acf2dd9ef6106cc42ce79c724e1e52ad62e Thu Mar 12 09:14:28 2026 -0700
    NoDots MAF alignment display for hgc mafClick, with i-row preservation and mafFrag -noDots flag hgMaf.c: add hgMafFragHelperNoDots and public wrappers (hgMafFragNoDots, hgBigMafFragNoDots, hgMafFragFromMafListNoDots) that return a list of maf blocks containing only species with actual sequence — no dot-filled rows. Blocks are broken when the species set changes; gaps between same-species blocks are filled with native sequence for the reference and dashes for others. Preserve i-row data (leftStatus/rightStatus/leftLen/rightLen) through the NoDots path so insert annotations appear in emitted blocks. hgMaf.h: declare the new NoDots public functions. mafClick.c: use NoDots path when mafClickMafFrag is enabled. Fix block numbering (aliIx was never incremented in useMafFrag path). Use full textSize for NoDots line width. Use dots instead of spaces in diff mode for both paths. Fix species label width computation to check labelHash consistently so long assembly names don't misalign sequences. Strip ref gap columns where no other species has sequence. mafFrag: add -noDots option to invoke hgMafFragNoDots from the command line, with 4 new tests (noDots, noDotsRev, noDotsOutName, noDotsLarger). refs #21477 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 6, context: html, text, full: html, text
    147740e133aa59c5aa7938ef68f1b66f3696c701 Fri Mar 13 15:29:49 2026 -0700
    Revert noDots mafClick/mafFrag work from master, refs #21477 Remove the mafClickMafFrag/noDots code path from mafClick.c, hgMaf.c, hgMaf.h, and mafFrag.c. Also remove mafFrag unit tests added as part of this work. The code is preserved on the mafFragNoDots and mafClickMafFrag branches. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/ratStuff/mafFrag/tests/expected/noDotsRev.maf
  • lines changed 6, context: html, text, full: html, text
    715e2acf2dd9ef6106cc42ce79c724e1e52ad62e Thu Mar 12 09:14:28 2026 -0700
    NoDots MAF alignment display for hgc mafClick, with i-row preservation and mafFrag -noDots flag hgMaf.c: add hgMafFragHelperNoDots and public wrappers (hgMafFragNoDots, hgBigMafFragNoDots, hgMafFragFromMafListNoDots) that return a list of maf blocks containing only species with actual sequence — no dot-filled rows. Blocks are broken when the species set changes; gaps between same-species blocks are filled with native sequence for the reference and dashes for others. Preserve i-row data (leftStatus/rightStatus/leftLen/rightLen) through the NoDots path so insert annotations appear in emitted blocks. hgMaf.h: declare the new NoDots public functions. mafClick.c: use NoDots path when mafClickMafFrag is enabled. Fix block numbering (aliIx was never incremented in useMafFrag path). Use full textSize for NoDots line width. Use dots instead of spaces in diff mode for both paths. Fix species label width computation to check labelHash consistently so long assembly names don't misalign sequences. Strip ref gap columns where no other species has sequence. mafFrag: add -noDots option to invoke hgMafFragNoDots from the command line, with 4 new tests (noDots, noDotsRev, noDotsOutName, noDotsLarger). refs #21477 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 6, context: html, text, full: html, text
    147740e133aa59c5aa7938ef68f1b66f3696c701 Fri Mar 13 15:29:49 2026 -0700
    Revert noDots mafClick/mafFrag work from master, refs #21477 Remove the mafClickMafFrag/noDots code path from mafClick.c, hgMaf.c, hgMaf.h, and mafFrag.c. Also remove mafFrag unit tests added as part of this work. The code is preserved on the mafFragNoDots and mafClickMafFrag branches. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/ratStuff/mafFrag/tests/expected/outName.maf
  • lines changed 5, context: html, text, full: html, text
    2f032b790bd3d0354f1d61de5dcadb2e469c1817 Tue Mar 10 17:42:42 2026 -0700
    Add unit tests for mafFrag tool Add test suite with 5 tests covering basic extraction, reverse strand, custom outName, small region, and larger multi-block region using hg38 multiz100way. Replace broken old test target that referenced a missing expected.maf file. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 1, context: html, text, full: html, text
    2da16dce988cd42c7d97019eebd9660bfe20b68b Tue Mar 10 17:55:26 2026 -0700
    Update mafFrag test expected outputs for source coordinate tracking Regenerate expected files to reflect hgMafFragHelper now preserving full source (db.chrom), start, size, srcSize, and strand for non-reference species instead of placeholder values. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 5, context: html, text, full: html, text
    147740e133aa59c5aa7938ef68f1b66f3696c701 Fri Mar 13 15:29:49 2026 -0700
    Revert noDots mafClick/mafFrag work from master, refs #21477 Remove the mafClickMafFrag/noDots code path from mafClick.c, hgMaf.c, hgMaf.h, and mafFrag.c. Also remove mafFrag unit tests added as part of this work. The code is preserved on the mafFragNoDots and mafClickMafFrag branches. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/ratStuff/mafFrag/tests/expected/revStrand.maf
  • lines changed 5, context: html, text, full: html, text
    2f032b790bd3d0354f1d61de5dcadb2e469c1817 Tue Mar 10 17:42:42 2026 -0700
    Add unit tests for mafFrag tool Add test suite with 5 tests covering basic extraction, reverse strand, custom outName, small region, and larger multi-block region using hg38 multiz100way. Replace broken old test target that referenced a missing expected.maf file. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 1, context: html, text, full: html, text
    2da16dce988cd42c7d97019eebd9660bfe20b68b Tue Mar 10 17:55:26 2026 -0700
    Update mafFrag test expected outputs for source coordinate tracking Regenerate expected files to reflect hgMafFragHelper now preserving full source (db.chrom), start, size, srcSize, and strand for non-reference species instead of placeholder values. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 5, context: html, text, full: html, text
    147740e133aa59c5aa7938ef68f1b66f3696c701 Fri Mar 13 15:29:49 2026 -0700
    Revert noDots mafClick/mafFrag work from master, refs #21477 Remove the mafClickMafFrag/noDots code path from mafClick.c, hgMaf.c, hgMaf.h, and mafFrag.c. Also remove mafFrag unit tests added as part of this work. The code is preserved on the mafFragNoDots and mafClickMafFrag branches. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/ratStuff/mafFrag/tests/expected/small.maf
  • lines changed 5, context: html, text, full: html, text
    2f032b790bd3d0354f1d61de5dcadb2e469c1817 Tue Mar 10 17:42:42 2026 -0700
    Add unit tests for mafFrag tool Add test suite with 5 tests covering basic extraction, reverse strand, custom outName, small region, and larger multi-block region using hg38 multiz100way. Replace broken old test target that referenced a missing expected.maf file. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 1, context: html, text, full: html, text
    2da16dce988cd42c7d97019eebd9660bfe20b68b Tue Mar 10 17:55:26 2026 -0700
    Update mafFrag test expected outputs for source coordinate tracking Regenerate expected files to reflect hgMafFragHelper now preserving full source (db.chrom), start, size, srcSize, and strand for non-reference species instead of placeholder values. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 5, context: html, text, full: html, text
    147740e133aa59c5aa7938ef68f1b66f3696c701 Fri Mar 13 15:29:49 2026 -0700
    Revert noDots mafClick/mafFrag work from master, refs #21477 Remove the mafClickMafFrag/noDots code path from mafClick.c, hgMaf.c, hgMaf.h, and mafFrag.c. Also remove mafFrag unit tests added as part of this work. The code is preserved on the mafFragNoDots and mafClickMafFrag branches. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/ratStuff/mafFrag/tests/makefile
  • lines changed 35, context: html, text, full: html, text
    2f032b790bd3d0354f1d61de5dcadb2e469c1817 Tue Mar 10 17:42:42 2026 -0700
    Add unit tests for mafFrag tool Add test suite with 5 tests covering basic extraction, reverse strand, custom outName, small region, and larger multi-block region using hg38 multiz100way. Replace broken old test target that referenced a missing expected.maf file. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 17, context: html, text, full: html, text
    715e2acf2dd9ef6106cc42ce79c724e1e52ad62e Thu Mar 12 09:14:28 2026 -0700
    NoDots MAF alignment display for hgc mafClick, with i-row preservation and mafFrag -noDots flag hgMaf.c: add hgMafFragHelperNoDots and public wrappers (hgMafFragNoDots, hgBigMafFragNoDots, hgMafFragFromMafListNoDots) that return a list of maf blocks containing only species with actual sequence — no dot-filled rows. Blocks are broken when the species set changes; gaps between same-species blocks are filled with native sequence for the reference and dashes for others. Preserve i-row data (leftStatus/rightStatus/leftLen/rightLen) through the NoDots path so insert annotations appear in emitted blocks. hgMaf.h: declare the new NoDots public functions. mafClick.c: use NoDots path when mafClickMafFrag is enabled. Fix block numbering (aliIx was never incremented in useMafFrag path). Use full textSize for NoDots line width. Use dots instead of spaces in diff mode for both paths. Fix species label width computation to check labelHash consistently so long assembly names don't misalign sequences. Strip ref gap columns where no other species has sequence. mafFrag: add -noDots option to invoke hgMafFragNoDots from the command line, with 4 new tests (noDots, noDotsRev, noDotsOutName, noDotsLarger). refs #21477 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 51, context: html, text, full: html, text
    147740e133aa59c5aa7938ef68f1b66f3696c701 Fri Mar 13 15:29:49 2026 -0700
    Revert noDots mafClick/mafFrag work from master, refs #21477 Remove the mafClickMafFrag/noDots code path from mafClick.c, hgMaf.c, hgMaf.h, and mafFrag.c. Also remove mafFrag unit tests added as part of this work. The code is preserved on the mafFragNoDots and mafClickMafFrag branches. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
• src/hg/utils/fixTrackDb/fixTrackDb.c
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/utils/gtfToGenePred/gtfToGenePred.c
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/utils/hubCheck/hubCheck.c
  • lines changed 45, context: html, text, full: html, text
    36e79dca2dc1ba9ef65c7ea13424ff8475e2bc72 Tue Mar 10 10:43:50 2026 -0700
    hubCheck: validate sequence names in 2bit files for illegal characters (refs #37174) Add check that sequence names contain only [A-Za-z0-9._-], start with a letter or digit, and are at most 254 characters. Warns per sequence with the offending character and suggests chromAlias. New -noSeqNameCheck flag disables the check. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 14, context: html, text, full: html, text
    8bf67a4375f3d5f15a109bea5a33a782c602fe67 Tue Mar 10 13:07:00 2026 -0700
    hubCheck: warn about periods in track names refs #37223 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/utils/hubCheck/tests/expected/dotInName.output.txt
  • lines changed 8, context: html, text, full: html, text
    8bf67a4375f3d5f15a109bea5a33a782c602fe67 Tue Mar 10 13:07:00 2026 -0700
    hubCheck: warn about periods in track names refs #37223 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/utils/hubCheck/tests/expected/manyErrors.output.txt
  • lines changed 3, context: html, text, full: html, text
    8bf67a4375f3d5f15a109bea5a33a782c602fe67 Tue Mar 10 13:07:00 2026 -0700
    hubCheck: warn about periods in track names refs #37223 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/utils/hubCheck/tests/expected/noSeqNameCheck.output.txt
  • lines changed 3, context: html, text, full: html, text
    71b7edde11d143446fcc9e72c14c8f213e74c900 Tue Mar 10 10:49:54 2026 -0700
    hubCheck: add unit tests for sequence name validation (refs #37174) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/utils/hubCheck/tests/expected/selfParent.output.txt
  • lines changed 3, context: html, text, full: html, text
    a71215bcc4a26e1641770d82127dc57ced1842c8 Tue Mar 10 12:37:04 2026 -0700
    Detect tracks that list themselves as their own parent, preventing infinite loop refs #35986 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/utils/hubCheck/tests/expected/seqNameCheck.output.txt
  • lines changed 7, context: html, text, full: html, text
    71b7edde11d143446fcc9e72c14c8f213e74c900 Tue Mar 10 10:49:54 2026 -0700
    hubCheck: add unit tests for sequence name validation (refs #37174) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/utils/hubCheck/tests/input/dotInName.txt
  • lines changed 27, context: html, text, full: html, text
    8bf67a4375f3d5f15a109bea5a33a782c602fe67 Tue Mar 10 13:07:00 2026 -0700
    hubCheck: warn about periods in track names refs #37223 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/utils/hubCheck/tests/input/selfParent.txt
  • lines changed 14, context: html, text, full: html, text
    a71215bcc4a26e1641770d82127dc57ced1842c8 Tue Mar 10 12:37:04 2026 -0700
    Detect tracks that list themselves as their own parent, preventing infinite loop refs #35986 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/utils/hubCheck/tests/input/seqNameGenomes.txt
  • lines changed 7, context: html, text, full: html, text
    71b7edde11d143446fcc9e72c14c8f213e74c900 Tue Mar 10 10:49:54 2026 -0700
    hubCheck: add unit tests for sequence name validation (refs #37174) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/utils/hubCheck/tests/input/seqNameHub.txt
  • lines changed 5, context: html, text, full: html, text
    71b7edde11d143446fcc9e72c14c8f213e74c900 Tue Mar 10 10:49:54 2026 -0700
    hubCheck: add unit tests for sequence name validation (refs #37174) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/utils/hubCheck/tests/input/seqNameTest.2bit
  • lines changed 0, context: html, text, full: html, text
    71b7edde11d143446fcc9e72c14c8f213e74c900 Tue Mar 10 10:49:54 2026 -0700
    hubCheck: add unit tests for sequence name validation (refs #37174) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/utils/hubCheck/tests/input/seqNameTrackDb.txt
  • lines changed 0, context: html, text, full: html, text
    71b7edde11d143446fcc9e72c14c8f213e74c900 Tue Mar 10 10:49:54 2026 -0700
    hubCheck: add unit tests for sequence name validation (refs #37174) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/utils/hubCheck/tests/makefile
  • lines changed 9, context: html, text, full: html, text
    71b7edde11d143446fcc9e72c14c8f213e74c900 Tue Mar 10 10:49:54 2026 -0700
    hubCheck: add unit tests for sequence name validation (refs #37174) Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 5, context: html, text, full: html, text
    a71215bcc4a26e1641770d82127dc57ced1842c8 Tue Mar 10 12:37:04 2026 -0700
    Detect tracks that list themselves as their own parent, preventing infinite loop refs #35986 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 5, context: html, text, full: html, text
    8bf67a4375f3d5f15a109bea5a33a782c602fe67 Tue Mar 10 13:07:00 2026 -0700
    hubCheck: warn about periods in track names refs #37223 Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
• src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
  • lines changed 8, context: html, text, full: html, text
    2c7413be1d0412785eb7238454dacefc57de05bc Tue Mar 10 15:53:08 2026 -0700
    Mask reversions caused by dropout in BA.3.2
• src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv
  • lines changed 12, context: html, text, full: html, text
    3397b75245fd2bfc21439e1568b1eac855739cd3 Tue Mar 10 15:54:38 2026 -0700
    Adding several more sequences by request
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
  • lines changed 76, context: html, text, full: html, text
    89d5c7e854fc4f5360852a5cb0657e20f962ae6a Thu Jan 22 15:22:07 2026 -0800
    Some shortening of paths where auto-collapsing didn't work, some new lineages, and tweaks to QC.6 and XFG.4.1.5 because they were assigned to single sequences instead of the appropriate branches.
  • lines changed 12, context: html, text, full: html, text
    9ed022cb1f0b16bc57c95a629a0abd4243e750cc Tue Mar 10 15:51:25 2026 -0700
    New lineages, small corrections to RD.1.1.1 and PQ.25.2, new label for split lineage.
• src/hg/utils/positionalTblCheck/positionalTblCheck.c
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/utils/pslMismatchGapToBed/pslMismatchGapToBed.c
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/utils/tdbQuery/tdbQuery.c
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/utils/transMapPslToGenePred/transMapPslToGenePred.c
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/hg/zoo/analyze4d/analyze.c
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/inc/meta.h
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/inc/obscure.h
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/inc/twoBit.h
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/lib/cheapcgi.c
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/lib/common.c
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/lib/gemfont.h
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/lib/meta.c
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/lib/obscure.c
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/lib/options.c
  • lines changed 2, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/lib/trix.c
  • lines changed 2, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/lib/vcf.c
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/oneShot/randDNA/makefile
  • lines changed 3, context: html, text, full: html, text
    1ef3fd9ec2124b1e8a88370d6ac9629aebed02a8 Fri Mar 13 12:30:21 2026 -0700
    should have a compile target no redmine
• src/utils/bedGraphToBigWig/bedGraphToBigWig.c
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/utils/bedToBigBed/bedToBigBed.c
  • lines changed 1, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/utils/codeReviewAi.py
  • lines changed 1637, context: html, text, full: html, text
    c17beac2e24b5e0cd8b6e4e828265d5a5df2bbd5 Mon Mar 16 08:54:14 2026 -0700
    Adding new script to perform CRs. It is used in -daily mode to run overnight CRs, or can also be pointed towards specific commits, or towrads all build tickets. Refs #36890
• src/utils/countChars/countChars.c
  • lines changed 2, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/utils/faSize/faSize.c
  • lines changed 21, context: html, text, full: html, text
    e89a47bff299bdd888d5b7f0a470b20aed221e01 Fri Mar 13 12:57:40 2026 -0700
    improved faSize inputs to allow 2bit files and added tests - code by claude
• src/utils/faSize/makefile
  • lines changed 3, context: html, text, full: html, text
    e89a47bff299bdd888d5b7f0a470b20aed221e01 Fri Mar 13 12:57:40 2026 -0700
    improved faSize inputs to allow 2bit files and added tests - code by claude
• src/utils/faSize/tests/expected/allThree.txt
  • lines changed 6, context: html, text, full: html, text
    1883f988de556896f2f60633ca0e3e87bbc8ae18 Fri Mar 13 12:54:20 2026 -0700
    adding tests for the newly improved faSize command
• src/utils/faSize/tests/expected/s1.s2.detailed.txt
  • lines changed 2, context: html, text, full: html, text
    976f6c37c274d5ec80b98883b5f2018496763174 Fri Mar 13 13:13:33 2026 -0700
    add the detailed tab and veryDetailed test options no redmine
• src/utils/faSize/tests/expected/s1.s2.tab.txt
  • lines changed 22, context: html, text, full: html, text
    976f6c37c274d5ec80b98883b5f2018496763174 Fri Mar 13 13:13:33 2026 -0700
    add the detailed tab and veryDetailed test options no redmine
• src/utils/faSize/tests/expected/s1.s2.txt
  • lines changed 6, context: html, text, full: html, text
    1883f988de556896f2f60633ca0e3e87bbc8ae18 Fri Mar 13 12:54:20 2026 -0700
    adding tests for the newly improved faSize command
• src/utils/faSize/tests/expected/s1.s2.veryDetailed.txt
  • lines changed 2, context: html, text, full: html, text
    976f6c37c274d5ec80b98883b5f2018496763174 Fri Mar 13 13:13:33 2026 -0700
    add the detailed tab and veryDetailed test options no redmine
• src/utils/faSize/tests/expected/s1.txt
  • lines changed 2, context: html, text, full: html, text
    1883f988de556896f2f60633ca0e3e87bbc8ae18 Fri Mar 13 12:54:20 2026 -0700
    adding tests for the newly improved faSize command
• src/utils/faSize/tests/expected/s1Ands2.txt
  • lines changed 6, context: html, text, full: html, text
    1883f988de556896f2f60633ca0e3e87bbc8ae18 Fri Mar 13 12:54:20 2026 -0700
    adding tests for the newly improved faSize command
• src/utils/faSize/tests/expected/s2.txt
  • lines changed 2, context: html, text, full: html, text
    1883f988de556896f2f60633ca0e3e87bbc8ae18 Fri Mar 13 12:54:20 2026 -0700
    adding tests for the newly improved faSize command
• src/utils/faSize/tests/input/s1.2bit
  • lines changed 0, context: html, text, full: html, text
    1883f988de556896f2f60633ca0e3e87bbc8ae18 Fri Mar 13 12:54:20 2026 -0700
    adding tests for the newly improved faSize command
• src/utils/faSize/tests/input/s1.fa.gz
  • lines changed 0, context: html, text, full: html, text
    1883f988de556896f2f60633ca0e3e87bbc8ae18 Fri Mar 13 12:54:20 2026 -0700
    adding tests for the newly improved faSize command
• src/utils/faSize/tests/input/s1.s2.2bit
  • lines changed 0, context: html, text, full: html, text
    1883f988de556896f2f60633ca0e3e87bbc8ae18 Fri Mar 13 12:54:20 2026 -0700
    adding tests for the newly improved faSize command
• src/utils/faSize/tests/input/s1.s2.fa.gz
  • lines changed 0, context: html, text, full: html, text
    1883f988de556896f2f60633ca0e3e87bbc8ae18 Fri Mar 13 12:54:20 2026 -0700
    adding tests for the newly improved faSize command
• src/utils/faSize/tests/input/s2.2bit
  • lines changed 0, context: html, text, full: html, text
    1883f988de556896f2f60633ca0e3e87bbc8ae18 Fri Mar 13 12:54:20 2026 -0700
    adding tests for the newly improved faSize command
• src/utils/faSize/tests/input/s2.fa.gz
  • lines changed 0, context: html, text, full: html, text
    1883f988de556896f2f60633ca0e3e87bbc8ae18 Fri Mar 13 12:54:20 2026 -0700
    adding tests for the newly improved faSize command
• src/utils/faSize/tests/makefile
  • lines changed 52, context: html, text, full: html, text
    1883f988de556896f2f60633ca0e3e87bbc8ae18 Fri Mar 13 12:54:20 2026 -0700
    adding tests for the newly improved faSize command
  • lines changed 26, context: html, text, full: html, text
    976f6c37c274d5ec80b98883b5f2018496763174 Fri Mar 13 13:13:33 2026 -0700
    add the detailed tab and veryDetailed test options no redmine
• src/utils/jimgrep/jimgrep.c
  • lines changed 2, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    eef33606ff233b6ce9afd612e89fe80b99744312 Tue Mar 10 05:49:20 2026 -0700
    Add redmineDump script to dump Redmine tickets as Markdown, refs #36890 Python script that reads redmine.apiKey from ~/.hg.conf, fetches a ticket with all journals/attachments via the Redmine API, and outputs the full discussion in Markdown. Supports --images to download attachments to a temp directory. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 2, context: html, text, full: html, text
    c1f42e37c13dab40740b9994daa2040422dd3b30 Tue Mar 10 06:02:12 2026 -0700
    cleanup after claude
  • lines changed 2, context: html, text, full: html, text
    72bb682e10783656300effd6c4d00141907da610 Thu Mar 12 05:35:40 2026 -0700
    fixing build error
  • lines changed 1, context: html, text, full: html, text
    f6989c2ec9dc36e82a71e735d181d4ebecbace42 Fri Mar 13 13:38:58 2026 -0700
    Adding a script for claude redmine communication, it extends on max's redmineDump and allows all RM functionality (make ticket, post, etc.) while also signing posts with a claude signature. No RM.
  • lines changed 1, context: html, text, full: html, text
    c17beac2e24b5e0cd8b6e4e828265d5a5df2bbd5 Mon Mar 16 08:54:14 2026 -0700
    Adding new script to perform CRs. It is used in -daily mode to run overnight CRs, or can also be pointed towards specific commits, or towrads all build tickets. Refs #36890
  • lines changed 2, context: html, text, full: html, text
    a8a9567f7b38e02f36edfc58ab733c2cbeefe134 Mon Mar 16 08:55:55 2026 -0700
    Oops, placed the CR script in the wrong section of the makefile with the C utils instead of the standalone scripts. Refs #36890
  • lines changed 1, context: html, text, full: html, text
    6570715c5cd53f3c7a71460a6806e13ade21909d Mon Mar 16 09:07:31 2026 -0700
    Removing redmineDump script as it was replaced by redmineCli, refs conversation with Max.
• src/utils/methylateGenome/methylateGenome.c
  • lines changed 2, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.
• src/utils/qa/hubPublicAutoUpdate
  • lines changed 10, context: html, text, full: html, text
    b68199a7676fbce5ede8ff948128981183dd1cd4 Mon Mar 9 17:37:03 2026 -0700
    Expanding the script to now also update the new hubPublic field for the hub's email (if possible). Now, when a hub fails, the contact email is printed on hgTracks. Also fixed a small logic bug in the 'if not' loop. Refs #33571
• src/utils/qa/makefile
  • lines changed 1, context: html, text, full: html, text
    98004ba10f89d74192132ac37d9be95ebfdb3d0e Mon Mar 9 16:13:35 2026 -0700
    Adding MLQ automate script to the tree, this runs on a qateam crontab and checks for any updated or new MLQs, accepts pending questions that pass a spam check, and creates/updates redmine tickets. It has been running for months on my personal crontab and is now being migrated to qateam. Refs #36801
• src/utils/qa/mlqAutomate.py
  • lines changed 1901, context: html, text, full: html, text
    98004ba10f89d74192132ac37d9be95ebfdb3d0e Mon Mar 9 16:13:35 2026 -0700
    Adding MLQ automate script to the tree, this runs on a qateam crontab and checks for any updated or new MLQs, accepts pending questions that pass a spam check, and creates/updates redmine tickets. It has been running for months on my personal crontab and is now being migrated to qateam. Refs #36801
  • lines changed 2, context: html, text, full: html, text
    47d5af90d317bffde6f0843beabd2d72c88fbfce Tue Mar 10 08:18:06 2026 -0700
    Adding retry logic around the gmail API call, because it fails periodically (but then works next time it runs). Refs #36801
• src/utils/qa/qaTestScript.py
  • lines changed 2, context: html, text, full: html, text
    aafd1b5058f9f8a5c044d58d6ca90cb2ffa1304f Thu Mar 12 08:32:42 2026 -0700
    Updating the area index and the text for the position link for the multiRegion test case, No RM
• src/utils/redmineCli
  • lines changed 650, context: html, text, full: html, text
    f6989c2ec9dc36e82a71e735d181d4ebecbace42 Fri Mar 13 13:38:58 2026 -0700
    Adding a script for claude redmine communication, it extends on max's redmineDump and allows all RM functionality (make ticket, post, etc.) while also signing posts with a claude signature. No RM.
  • lines changed 6, context: html, text, full: html, text
    ff25bb5db197e1b8a048154cc9d34dc098ebd434 Mon Mar 16 09:19:20 2026 -0700
    Feedback from AI CR.
  • lines changed 13, context: html, text, full: html, text
    ec013b7cd85204640ee339dd860b6c819c912bf0 Mon Mar 16 09:31:08 2026 -0700
    More feedback from CR.
• src/utils/redmineDump
  • lines changed 247, context: html, text, full: html, text
    eef33606ff233b6ce9afd612e89fe80b99744312 Tue Mar 10 05:49:20 2026 -0700
    Add redmineDump script to dump Redmine tickets as Markdown, refs #36890 Python script that reads redmine.apiKey from ~/.hg.conf, fetches a ticket with all journals/attachments via the Redmine API, and outputs the full discussion in Markdown. Supports --images to download attachments to a temp directory. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
  • lines changed 247, context: html, text, full: html, text
    6570715c5cd53f3c7a71460a6806e13ade21909d Mon Mar 16 09:07:31 2026 -0700
    Removing redmineDump script as it was replaced by redmineCli, refs conversation with Max.
• src/utils/tabFmt/tabFmt.c
  • lines changed 2, context: html, text, full: html, text
    198c9b8daecc44fbda6a6494c566c723920f030a Wed Mar 11 18:25:21 2026 -0700
    Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.

• lines changed: 11014
• files changed: 350