All File Changes

v499_preview to v499_preview2 (2026-05-18 to 2026-05-25) v499

• confs/hgwbeta.hg.conf
  • lines changed 2, context: html, text, full: html, text
    1ae0734e9438c6c23224b8e4c6ecd5ac75c4523e Sun May 24 01:11:15 2026 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 4, context: html, text, full: html, text
    1ae0734e9438c6c23224b8e4c6ecd5ac75c4523e Sun May 24 01:11:15 2026 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html
  • lines changed 2, context: html, text, full: html, text
    e1ef784306e6c9739d0bd224b2dda1d17561364a Tue May 19 13:45:57 2026 -0700
    Adding clickable year4_yale timeline that connects to new milestone sheet
  • lines changed 2, context: html, text, full: html, text
    61a8427e29469d70dff48c661c9f9a97e46b12c3 Thu May 21 14:21:17 2026 -0700
    unifying end Q2 date to 9/30 vs 10/01
  • lines changed 6, context: html, text, full: html, text
    b8eab6d5d1b4da39007b0590d5813f205f0dff74 Fri May 22 09:05:07 2026 -0700
    Staging 2026Q3 (09-30) ADGC1 new milestone updates (ADGC1_Y4_)
• src/hg/hgBlat/hgBlat.c
  • lines changed 101, context: html, text, full: html, text
    2197f6d5208aff4c48ccbe42e61a116d988ac392 Tue May 19 08:23:54 2026 -0700
    hubApi: add /blat endpoint with apiKey gating, format=hgblat, and known-agent bypass New src/hg/hubApi/blat.c implements /blat/<type> (dna, protein, transRna, transDna, guess) backed by the same gfServer logic as hgBlat. Key details: - Requires an apiKey for rate-limiting; botException() and botExceptionUserAgent() exempt IPs/user-agents in hg.conf (same policy as captcha bypass elsewhere in the browser stack). - Invalid apiKey returns a clean JSON 403 rather than an HTML 500 (pre-validated in hubApi.c main() before hgBotDelayTimeFrac runs). - Extra bot-delay fraction (default 0.3, 10x hubApi default) is configurable via hubApi.blatDelayFraction in hg.conf. - format=text/psl -> PSL text; format=hgblat -> byte-for-byte hgBlat?output=json shape; jsonOutputArrays=1 -> hubApi envelope with arrays (parallel to getData behaviour); default -> objects. - botExceptionUserAgent() carved out of cart.c's static isUserAgentException() into botDelay.c so non-cart callers can use it. - Cross-reference comments added in hgBlat.c and blat.c noting the shared logic so fixes get applied to both. refs #36315 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/hgCustom/hgCustom.c
  • lines changed 1, context: html, text, full: html, text
    ba33f2c600399d5b4b97dd5fd987ed2db3c891ba Tue May 19 13:40:42 2026 -0700
    myVariants related fixes from code review. Standardize how the code determines we are about to do something myVariants related by #defining some strings and using sameOk to check for them, remove a dead code block, and have hgc use autoSql to load the myVariants item rather than check the raw sql result, refs #37528
• src/hg/hgPhyloPlace/hgPhyloPlace.c
  • lines changed 4, context: html, text, full: html, text
    08e93449229f8ef895072c40bc818fb9826c2572 Mon May 18 14:51:03 2026 -0700
    Add a link out to Taxonium as an alternative way to place sequences for pathogens not supported by hgPhyloPlace.
• src/hg/hgTables/bedList.c
  • lines changed 3, context: html, text, full: html, text
    ba33f2c600399d5b4b97dd5fd987ed2db3c891ba Tue May 19 13:40:42 2026 -0700
    myVariants related fixes from code review. Standardize how the code determines we are about to do something myVariants related by #defining some strings and using sameOk to check for them, remove a dead code block, and have hgc use autoSql to load the myVariants item rather than check the raw sql result, refs #37528
• src/hg/hgTables/custom.c
  • lines changed 4, context: html, text, full: html, text
    ba33f2c600399d5b4b97dd5fd987ed2db3c891ba Tue May 19 13:40:42 2026 -0700
    myVariants related fixes from code review. Standardize how the code determines we are about to do something myVariants related by #defining some strings and using sameOk to check for them, remove a dead code block, and have hgc use autoSql to load the myVariants item rather than check the raw sql result, refs #37528
• src/hg/hgTables/filterFields.c
  • lines changed 5, context: html, text, full: html, text
    ba33f2c600399d5b4b97dd5fd987ed2db3c891ba Tue May 19 13:40:42 2026 -0700
    myVariants related fixes from code review. Standardize how the code determines we are about to do something myVariants related by #defining some strings and using sameOk to check for them, remove a dead code block, and have hgc use autoSql to load the myVariants item rather than check the raw sql result, refs #37528
• src/hg/hgTables/hgTables.c
  • lines changed 8, context: html, text, full: html, text
    ba33f2c600399d5b4b97dd5fd987ed2db3c891ba Tue May 19 13:40:42 2026 -0700
    myVariants related fixes from code review. Standardize how the code determines we are about to do something myVariants related by #defining some strings and using sameOk to check for them, remove a dead code block, and have hgc use autoSql to load the myVariants item rather than check the raw sql result, refs #37528
• src/hg/hgTables/joining.c
  • lines changed 4, context: html, text, full: html, text
    ba33f2c600399d5b4b97dd5fd987ed2db3c891ba Tue May 19 13:40:42 2026 -0700
    myVariants related fixes from code review. Standardize how the code determines we are about to do something myVariants related by #defining some strings and using sameOk to check for them, remove a dead code block, and have hgc use autoSql to load the myVariants item rather than check the raw sql result, refs #37528
• src/hg/hgTables/schema.c
  • lines changed 1, context: html, text, full: html, text
    ba33f2c600399d5b4b97dd5fd987ed2db3c891ba Tue May 19 13:40:42 2026 -0700
    myVariants related fixes from code review. Standardize how the code determines we are about to do something myVariants related by #defining some strings and using sameOk to check for them, remove a dead code block, and have hgc use autoSql to load the myVariants item rather than check the raw sql result, refs #37528
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 7, context: html, text, full: html, text
    ba33f2c600399d5b4b97dd5fd987ed2db3c891ba Tue May 19 13:40:42 2026 -0700
    myVariants related fixes from code review. Standardize how the code determines we are about to do something myVariants related by #defining some strings and using sameOk to check for them, remove a dead code block, and have hgc use autoSql to load the myVariants item rather than check the raw sql result, refs #37528
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 15, context: html, text, full: html, text
    05c41aa8b79ce2d8d4b6982350264b8691487a07 Fri May 22 10:03:04 2026 -0700
    hgTracks: flag quickLift mouseOvers that substitute source coords, refs #37615 When a bigBed is rendered via quickLift, $chrom/${chromStart}/${chromEnd} in the mouseOver pattern still resolve against the source-assembly row, so the tooltip reports the pre-lift position while the position bar shows the lifted target position. When we detect a $chrom-bearing pattern under quickLift, append "(coordinates from source assembly <db>)" to the tooltip so the discrepancy is explicit rather than confusing.
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    ba33f2c600399d5b4b97dd5fd987ed2db3c891ba Tue May 19 13:40:42 2026 -0700
    myVariants related fixes from code review. Standardize how the code determines we are about to do something myVariants related by #defining some strings and using sameOk to check for them, remove a dead code block, and have hgc use autoSql to load the myVariants item rather than check the raw sql result, refs #37528
• src/hg/hgTracks/myVariantsTrack.c
  • lines changed 2, context: html, text, full: html, text
    ba33f2c600399d5b4b97dd5fd987ed2db3c891ba Tue May 19 13:40:42 2026 -0700
    myVariants related fixes from code review. Standardize how the code determines we are about to do something myVariants related by #defining some strings and using sameOk to check for them, remove a dead code block, and have hgc use autoSql to load the myVariants item rather than check the raw sql result, refs #37528
  • lines changed 54, context: html, text, full: html, text
    ef4a5ad1ea45eda4fde693f56f2106c553e87d93 Wed May 20 15:24:30 2026 -0700
    Add cnv type to myVariants, refs #33808
• src/hg/hgTracks/simpleTracks.c
  • lines changed 8, context: html, text, full: html, text
    4c756ae28c7c8a654ba4a8877224f03513999b64 Tue May 19 14:16:27 2026 -0700
    More fixes from code review. Hopefully have cleared the last remaining vestiges of the first version of the tooltip implementation, refs #37528
• src/hg/hgc/hgc.c
  • lines changed 7, context: html, text, full: html, text
    ba33f2c600399d5b4b97dd5fd987ed2db3c891ba Tue May 19 13:40:42 2026 -0700
    myVariants related fixes from code review. Standardize how the code determines we are about to do something myVariants related by #defining some strings and using sameOk to check for them, remove a dead code block, and have hgc use autoSql to load the myVariants item rather than check the raw sql result, refs #37528
• src/hg/hgc/myVariantsClick.c
  • lines changed 8, context: html, text, full: html, text
    ba33f2c600399d5b4b97dd5fd987ed2db3c891ba Tue May 19 13:40:42 2026 -0700
    myVariants related fixes from code review. Standardize how the code determines we are about to do something myVariants related by #defining some strings and using sameOk to check for them, remove a dead code block, and have hgc use autoSql to load the myVariants item rather than check the raw sql result, refs #37528
  • lines changed 47, context: html, text, full: html, text
    ef4a5ad1ea45eda4fde693f56f2106c553e87d93 Wed May 20 15:24:30 2026 -0700
    Add cnv type to myVariants, refs #33808
• src/hg/hubApi/blat.c
  • lines changed 427, context: html, text, full: html, text
    2197f6d5208aff4c48ccbe42e61a116d988ac392 Tue May 19 08:23:54 2026 -0700
    hubApi: add /blat endpoint with apiKey gating, format=hgblat, and known-agent bypass New src/hg/hubApi/blat.c implements /blat/<type> (dna, protein, transRna, transDna, guess) backed by the same gfServer logic as hgBlat. Key details: - Requires an apiKey for rate-limiting; botException() and botExceptionUserAgent() exempt IPs/user-agents in hg.conf (same policy as captcha bypass elsewhere in the browser stack). - Invalid apiKey returns a clean JSON 403 rather than an HTML 500 (pre-validated in hubApi.c main() before hgBotDelayTimeFrac runs). - Extra bot-delay fraction (default 0.3, 10x hubApi default) is configurable via hubApi.blatDelayFraction in hg.conf. - format=text/psl -> PSL text; format=hgblat -> byte-for-byte hgBlat?output=json shape; jsonOutputArrays=1 -> hubApi envelope with arrays (parallel to getData behaviour); default -> objects. - botExceptionUserAgent() carved out of cart.c's static isUserAgentException() into botDelay.c so non-cart callers can use it. - Cross-reference comments added in hgBlat.c and blat.c noting the shared logic so fixes get applied to both. refs #36315 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
  • lines changed 25, context: html, text, full: html, text
    79e7ed894b39f65202ef820ae81af514f62e43dd Wed May 20 13:38:35 2026 -0700
    hubApi/blat: errCatch gfServer calls, fix comment, maxSeqCount from hg.conf, Content-Type spacing - Wrap gfServer block (mustOpen→gfDisconnect) in errCatch so a down or unreachable BLAT server returns a JSON 500 instead of a bare Apache error. - Fix comment: hgBlat's CGI interface and behavior remain unchanged (it was refactored internally in the previous commit). - Replace hardcoded maxSeqCount=25 with cfgOptionDefault("hgBlat.maxSequenceCount") to share the same hg.conf knob as hgBlat itself. - Remove spurious space in "Content-Type:text/plain" to match rest of hubApi. refs #36315 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/hubApi/dataApi.h
  • lines changed 11, context: html, text, full: html, text
    2197f6d5208aff4c48ccbe42e61a116d988ac392 Tue May 19 08:23:54 2026 -0700
    hubApi: add /blat endpoint with apiKey gating, format=hgblat, and known-agent bypass New src/hg/hubApi/blat.c implements /blat/<type> (dna, protein, transRna, transDna, guess) backed by the same gfServer logic as hgBlat. Key details: - Requires an apiKey for rate-limiting; botException() and botExceptionUserAgent() exempt IPs/user-agents in hg.conf (same policy as captcha bypass elsewhere in the browser stack). - Invalid apiKey returns a clean JSON 403 rather than an HTML 500 (pre-validated in hubApi.c main() before hgBotDelayTimeFrac runs). - Extra bot-delay fraction (default 0.3, 10x hubApi default) is configurable via hubApi.blatDelayFraction in hg.conf. - format=text/psl -> PSL text; format=hgblat -> byte-for-byte hgBlat?output=json shape; jsonOutputArrays=1 -> hubApi envelope with arrays (parallel to getData behaviour); default -> objects. - botExceptionUserAgent() carved out of cart.c's static isUserAgentException() into botDelay.c so non-cart callers can use it. - Cross-reference comments added in hgBlat.c and blat.c noting the shared logic so fixes get applied to both. refs #36315 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
  • lines changed 1, context: html, text, full: html, text
    0201e8ea6a448b2124e117c5909ced7ff4a253c8 Tue May 19 13:43:53 2026 -0700
    adding login verification to the liftRequest functions refs #31811
• src/hg/hubApi/hubApi.c
  • lines changed 18, context: html, text, full: html, text
    2197f6d5208aff4c48ccbe42e61a116d988ac392 Tue May 19 08:23:54 2026 -0700
    hubApi: add /blat endpoint with apiKey gating, format=hgblat, and known-agent bypass New src/hg/hubApi/blat.c implements /blat/<type> (dna, protein, transRna, transDna, guess) backed by the same gfServer logic as hgBlat. Key details: - Requires an apiKey for rate-limiting; botException() and botExceptionUserAgent() exempt IPs/user-agents in hg.conf (same policy as captcha bypass elsewhere in the browser stack). - Invalid apiKey returns a clean JSON 403 rather than an HTML 500 (pre-validated in hubApi.c main() before hgBotDelayTimeFrac runs). - Extra bot-delay fraction (default 0.3, 10x hubApi default) is configurable via hubApi.blatDelayFraction in hg.conf. - format=text/psl -> PSL text; format=hgblat -> byte-for-byte hgBlat?output=json shape; jsonOutputArrays=1 -> hubApi envelope with arrays (parallel to getData behaviour); default -> objects. - botExceptionUserAgent() carved out of cart.c's static isUserAgentException() into botDelay.c so non-cart callers can use it. - Cross-reference comments added in hgBlat.c and blat.c noting the shared logic so fixes get applied to both. refs #36315 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
  • lines changed 1, context: html, text, full: html, text
    0201e8ea6a448b2124e117c5909ced7ff4a253c8 Tue May 19 13:43:53 2026 -0700
    adding login verification to the liftRequest functions refs #31811
• src/hg/hubApi/liftOver.c
  • lines changed 79, context: html, text, full: html, text
    0201e8ea6a448b2124e117c5909ced7ff4a253c8 Tue May 19 13:43:53 2026 -0700
    adding login verification to the liftRequest functions refs #31811
• src/hg/hubApi/makefile
  • lines changed 2, context: html, text, full: html, text
    2197f6d5208aff4c48ccbe42e61a116d988ac392 Tue May 19 08:23:54 2026 -0700
    hubApi: add /blat endpoint with apiKey gating, format=hgblat, and known-agent bypass New src/hg/hubApi/blat.c implements /blat/<type> (dna, protein, transRna, transDna, guess) backed by the same gfServer logic as hgBlat. Key details: - Requires an apiKey for rate-limiting; botException() and botExceptionUserAgent() exempt IPs/user-agents in hg.conf (same policy as captcha bypass elsewhere in the browser stack). - Invalid apiKey returns a clean JSON 403 rather than an HTML 500 (pre-validated in hubApi.c main() before hgBotDelayTimeFrac runs). - Extra bot-delay fraction (default 0.3, 10x hubApi default) is configurable via hubApi.blatDelayFraction in hg.conf. - format=text/psl -> PSL text; format=hgblat -> byte-for-byte hgBlat?output=json shape; jsonOutputArrays=1 -> hubApi envelope with arrays (parallel to getData behaviour); default -> objects. - botExceptionUserAgent() carved out of cart.c's static isUserAgentException() into botDelay.c so non-cart callers can use it. - Cross-reference comments added in hgBlat.c and blat.c noting the shared logic so fixes get applied to both. refs #36315 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/hubApi/tests/makefile
  • lines changed 29, context: html, text, full: html, text
    2197f6d5208aff4c48ccbe42e61a116d988ac392 Tue May 19 08:23:54 2026 -0700
    hubApi: add /blat endpoint with apiKey gating, format=hgblat, and known-agent bypass New src/hg/hubApi/blat.c implements /blat/<type> (dna, protein, transRna, transDna, guess) backed by the same gfServer logic as hgBlat. Key details: - Requires an apiKey for rate-limiting; botException() and botExceptionUserAgent() exempt IPs/user-agents in hg.conf (same policy as captcha bypass elsewhere in the browser stack). - Invalid apiKey returns a clean JSON 403 rather than an HTML 500 (pre-validated in hubApi.c main() before hgBotDelayTimeFrac runs). - Extra bot-delay fraction (default 0.3, 10x hubApi default) is configurable via hubApi.blatDelayFraction in hg.conf. - format=text/psl -> PSL text; format=hgblat -> byte-for-byte hgBlat?output=json shape; jsonOutputArrays=1 -> hubApi envelope with arrays (parallel to getData behaviour); default -> objects. - botExceptionUserAgent() carved out of cart.c's static isUserAgentException() into botDelay.c so non-cart callers can use it. - Cross-reference comments added in hgBlat.c and blat.c noting the shared logic so fixes get applied to both. refs #36315 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/inc/blatServers.h
  • lines changed 21, context: html, text, full: html, text
    2197f6d5208aff4c48ccbe42e61a116d988ac392 Tue May 19 08:23:54 2026 -0700
    hubApi: add /blat endpoint with apiKey gating, format=hgblat, and known-agent bypass New src/hg/hubApi/blat.c implements /blat/<type> (dna, protein, transRna, transDna, guess) backed by the same gfServer logic as hgBlat. Key details: - Requires an apiKey for rate-limiting; botException() and botExceptionUserAgent() exempt IPs/user-agents in hg.conf (same policy as captcha bypass elsewhere in the browser stack). - Invalid apiKey returns a clean JSON 403 rather than an HTML 500 (pre-validated in hubApi.c main() before hgBotDelayTimeFrac runs). - Extra bot-delay fraction (default 0.3, 10x hubApi default) is configurable via hubApi.blatDelayFraction in hg.conf. - format=text/psl -> PSL text; format=hgblat -> byte-for-byte hgBlat?output=json shape; jsonOutputArrays=1 -> hubApi envelope with arrays (parallel to getData behaviour); default -> objects. - botExceptionUserAgent() carved out of cart.c's static isUserAgentException() into botDelay.c so non-cart callers can use it. - Cross-reference comments added in hgBlat.c and blat.c noting the shared logic so fixes get applied to both. refs #36315 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/inc/botDelay.h
  • lines changed 3, context: html, text, full: html, text
    2197f6d5208aff4c48ccbe42e61a116d988ac392 Tue May 19 08:23:54 2026 -0700
    hubApi: add /blat endpoint with apiKey gating, format=hgblat, and known-agent bypass New src/hg/hubApi/blat.c implements /blat/<type> (dna, protein, transRna, transDna, guess) backed by the same gfServer logic as hgBlat. Key details: - Requires an apiKey for rate-limiting; botException() and botExceptionUserAgent() exempt IPs/user-agents in hg.conf (same policy as captcha bypass elsewhere in the browser stack). - Invalid apiKey returns a clean JSON 403 rather than an HTML 500 (pre-validated in hubApi.c main() before hgBotDelayTimeFrac runs). - Extra bot-delay fraction (default 0.3, 10x hubApi default) is configurable via hubApi.blatDelayFraction in hg.conf. - format=text/psl -> PSL text; format=hgblat -> byte-for-byte hgBlat?output=json shape; jsonOutputArrays=1 -> hubApi envelope with arrays (parallel to getData behaviour); default -> objects. - botExceptionUserAgent() carved out of cart.c's static isUserAgentException() into botDelay.c so non-cart callers can use it. - Cross-reference comments added in hgBlat.c and blat.c noting the shared logic so fixes get applied to both. refs #36315 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/inc/myVariants.h
  • lines changed 14, context: html, text, full: html, text
    ba33f2c600399d5b4b97dd5fd987ed2db3c891ba Tue May 19 13:40:42 2026 -0700
    myVariants related fixes from code review. Standardize how the code determines we are about to do something myVariants related by #defining some strings and using sameOk to check for them, remove a dead code block, and have hgc use autoSql to load the myVariants item rather than check the raw sql result, refs #37528
  • lines changed 16, context: html, text, full: html, text
    ef4a5ad1ea45eda4fde693f56f2106c553e87d93 Wed May 20 15:24:30 2026 -0700
    Add cnv type to myVariants, refs #33808
• src/hg/inc/myVariantsShare.h
  • lines changed 6, context: html, text, full: html, text
    ba33f2c600399d5b4b97dd5fd987ed2db3c891ba Tue May 19 13:40:42 2026 -0700
    myVariants related fixes from code review. Standardize how the code determines we are about to do something myVariants related by #defining some strings and using sameOk to check for them, remove a dead code block, and have hgc use autoSql to load the myVariants item rather than check the raw sql result, refs #37528
• src/hg/js/hgMyData.js
  • lines changed 48, context: html, text, full: html, text
    e5d2a3ffc3900795526144f1834612cd8c9ddf24 Wed May 20 12:25:29 2026 -0700
    Fix last two remaining bugs from #37411: genome name and hub name should be defaults if you click upload from the hubSpace top level, and should update appropriatly if you select a previously uploaded assembly hub genome from the genome dropdown list, refs #37411
• src/hg/js/hgTracks.js
  • lines changed 1, context: html, text, full: html, text
    4c756ae28c7c8a654ba4a8877224f03513999b64 Tue May 19 14:16:27 2026 -0700
    More fixes from code review. Hopefully have cleared the last remaining vestiges of the first version of the tooltip implementation, refs #37528
  • lines changed 342, context: html, text, full: html, text
    ef4a5ad1ea45eda4fde693f56f2106c553e87d93 Wed May 20 15:24:30 2026 -0700
    Add cnv type to myVariants, refs #33808
• src/hg/js/liftRequest.js
  • lines changed 95, context: html, text, full: html, text
    0201e8ea6a448b2124e117c5909ced7ff4a253c8 Tue May 19 13:43:53 2026 -0700
    adding login verification to the liftRequest functions refs #31811
• src/hg/js/utils.js
  • lines changed 1, context: html, text, full: html, text
    4c756ae28c7c8a654ba4a8877224f03513999b64 Tue May 19 14:16:27 2026 -0700
    More fixes from code review. Hopefully have cleared the last remaining vestiges of the first version of the tooltip implementation, refs #37528
• src/hg/lib/blatServers.c
  • lines changed 85, context: html, text, full: html, text
    2197f6d5208aff4c48ccbe42e61a116d988ac392 Tue May 19 08:23:54 2026 -0700
    hubApi: add /blat endpoint with apiKey gating, format=hgblat, and known-agent bypass New src/hg/hubApi/blat.c implements /blat/<type> (dna, protein, transRna, transDna, guess) backed by the same gfServer logic as hgBlat. Key details: - Requires an apiKey for rate-limiting; botException() and botExceptionUserAgent() exempt IPs/user-agents in hg.conf (same policy as captcha bypass elsewhere in the browser stack). - Invalid apiKey returns a clean JSON 403 rather than an HTML 500 (pre-validated in hubApi.c main() before hgBotDelayTimeFrac runs). - Extra bot-delay fraction (default 0.3, 10x hubApi default) is configurable via hubApi.blatDelayFraction in hg.conf. - format=text/psl -> PSL text; format=hgblat -> byte-for-byte hgBlat?output=json shape; jsonOutputArrays=1 -> hubApi envelope with arrays (parallel to getData behaviour); default -> objects. - botExceptionUserAgent() carved out of cart.c's static isUserAgentException() into botDelay.c so non-cart callers can use it. - Cross-reference comments added in hgBlat.c and blat.c noting the shared logic so fixes get applied to both. refs #36315 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/lib/botDelay.c
  • lines changed 23, context: html, text, full: html, text
    2197f6d5208aff4c48ccbe42e61a116d988ac392 Tue May 19 08:23:54 2026 -0700
    hubApi: add /blat endpoint with apiKey gating, format=hgblat, and known-agent bypass New src/hg/hubApi/blat.c implements /blat/<type> (dna, protein, transRna, transDna, guess) backed by the same gfServer logic as hgBlat. Key details: - Requires an apiKey for rate-limiting; botException() and botExceptionUserAgent() exempt IPs/user-agents in hg.conf (same policy as captcha bypass elsewhere in the browser stack). - Invalid apiKey returns a clean JSON 403 rather than an HTML 500 (pre-validated in hubApi.c main() before hgBotDelayTimeFrac runs). - Extra bot-delay fraction (default 0.3, 10x hubApi default) is configurable via hubApi.blatDelayFraction in hg.conf. - format=text/psl -> PSL text; format=hgblat -> byte-for-byte hgBlat?output=json shape; jsonOutputArrays=1 -> hubApi envelope with arrays (parallel to getData behaviour); default -> objects. - botExceptionUserAgent() carved out of cart.c's static isUserAgentException() into botDelay.c so non-cart callers can use it. - Cross-reference comments added in hgBlat.c and blat.c noting the shared logic so fixes get applied to both. refs #36315 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
  • lines changed 14, context: html, text, full: html, text
    279166ca6fde058a85d9889501a1509499251d16 Wed May 20 11:40:23 2026 -0700
    Cleaning up an earlyBotCheck persistent SQL connection that snuck in, and ensuring that sqlCleanupAll doesn't crash. Some CGIs set up carefulMemHandler after earlyBotCheck, so the connection list is a mix of two memory allocation setups. Instead of trying to manually free that memory at exit, sqlCleanupAll can let the system handle it. refs #37494
  • lines changed 3, context: html, text, full: html, text
    e09c2a865147bf97bc9bc218d6baeb921cb2448b Thu May 21 07:17:31 2026 -0700
    Gotta remember to close early connections in botDelay stuff, refs #37494
• src/hg/lib/cart.c
  • lines changed 19, context: html, text, full: html, text
    2197f6d5208aff4c48ccbe42e61a116d988ac392 Tue May 19 08:23:54 2026 -0700
    hubApi: add /blat endpoint with apiKey gating, format=hgblat, and known-agent bypass New src/hg/hubApi/blat.c implements /blat/<type> (dna, protein, transRna, transDna, guess) backed by the same gfServer logic as hgBlat. Key details: - Requires an apiKey for rate-limiting; botException() and botExceptionUserAgent() exempt IPs/user-agents in hg.conf (same policy as captcha bypass elsewhere in the browser stack). - Invalid apiKey returns a clean JSON 403 rather than an HTML 500 (pre-validated in hubApi.c main() before hgBotDelayTimeFrac runs). - Extra bot-delay fraction (default 0.3, 10x hubApi default) is configurable via hubApi.blatDelayFraction in hg.conf. - format=text/psl -> PSL text; format=hgblat -> byte-for-byte hgBlat?output=json shape; jsonOutputArrays=1 -> hubApi envelope with arrays (parallel to getData behaviour); default -> objects. - botExceptionUserAgent() carved out of cart.c's static isUserAgentException() into botDelay.c so non-cart callers can use it. - Cross-reference comments added in hgBlat.c and blat.c noting the shared logic so fixes get applied to both. refs #36315 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/lib/customFactory.c
  • lines changed 4, context: html, text, full: html, text
    ba33f2c600399d5b4b97dd5fd987ed2db3c891ba Tue May 19 13:40:42 2026 -0700
    myVariants related fixes from code review. Standardize how the code determines we are about to do something myVariants related by #defining some strings and using sameOk to check for them, remove a dead code block, and have hgc use autoSql to load the myVariants item rather than check the raw sql result, refs #37528
• src/hg/lib/customTrack.c
  • lines changed 2, context: html, text, full: html, text
    ba33f2c600399d5b4b97dd5fd987ed2db3c891ba Tue May 19 13:40:42 2026 -0700
    myVariants related fixes from code review. Standardize how the code determines we are about to do something myVariants related by #defining some strings and using sameOk to check for them, remove a dead code block, and have hgc use autoSql to load the myVariants item rather than check the raw sql result, refs #37528
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    ba33f2c600399d5b4b97dd5fd987ed2db3c891ba Tue May 19 13:40:42 2026 -0700
    myVariants related fixes from code review. Standardize how the code determines we are about to do something myVariants related by #defining some strings and using sameOk to check for them, remove a dead code block, and have hgc use autoSql to load the myVariants item rather than check the raw sql result, refs #37528
• src/hg/lib/jksql.c
  • lines changed 1, context: html, text, full: html, text
    279166ca6fde058a85d9889501a1509499251d16 Wed May 20 11:40:23 2026 -0700
    Cleaning up an earlyBotCheck persistent SQL connection that snuck in, and ensuring that sqlCleanupAll doesn't crash. Some CGIs set up carefulMemHandler after earlyBotCheck, so the connection list is a mix of two memory allocation setups. Instead of trying to manually free that memory at exit, sqlCleanupAll can let the system handle it. refs #37494
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    2197f6d5208aff4c48ccbe42e61a116d988ac392 Tue May 19 08:23:54 2026 -0700
    hubApi: add /blat endpoint with apiKey gating, format=hgblat, and known-agent bypass New src/hg/hubApi/blat.c implements /blat/<type> (dna, protein, transRna, transDna, guess) backed by the same gfServer logic as hgBlat. Key details: - Requires an apiKey for rate-limiting; botException() and botExceptionUserAgent() exempt IPs/user-agents in hg.conf (same policy as captcha bypass elsewhere in the browser stack). - Invalid apiKey returns a clean JSON 403 rather than an HTML 500 (pre-validated in hubApi.c main() before hgBotDelayTimeFrac runs). - Extra bot-delay fraction (default 0.3, 10x hubApi default) is configurable via hubApi.blatDelayFraction in hg.conf. - format=text/psl -> PSL text; format=hgblat -> byte-for-byte hgBlat?output=json shape; jsonOutputArrays=1 -> hubApi envelope with arrays (parallel to getData behaviour); default -> objects. - botExceptionUserAgent() carved out of cart.c's static isUserAgentException() into botDelay.c so non-cart callers can use it. - Cross-reference comments added in hgBlat.c and blat.c noting the shared logic so fixes get applied to both. refs #36315 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/lib/myVariants.as
  • lines changed 2, context: html, text, full: html, text
    ef4a5ad1ea45eda4fde693f56f2106c553e87d93 Wed May 20 15:24:30 2026 -0700
    Add cnv type to myVariants, refs #33808
• src/hg/lib/myVariants.c
  • lines changed 32, context: html, text, full: html, text
    ba33f2c600399d5b4b97dd5fd987ed2db3c891ba Tue May 19 13:40:42 2026 -0700
    myVariants related fixes from code review. Standardize how the code determines we are about to do something myVariants related by #defining some strings and using sameOk to check for them, remove a dead code block, and have hgc use autoSql to load the myVariants item rather than check the raw sql result, refs #37528
  • lines changed 55, context: html, text, full: html, text
    ef4a5ad1ea45eda4fde693f56f2106c553e87d93 Wed May 20 15:24:30 2026 -0700
    Add cnv type to myVariants, refs #33808
• src/hg/lib/myVariants.sql
  • lines changed 2, context: html, text, full: html, text
    ef4a5ad1ea45eda4fde693f56f2106c553e87d93 Wed May 20 15:24:30 2026 -0700
    Add cnv type to myVariants, refs #33808
• src/hg/lib/myVariantsShare.c
  • lines changed 40, context: html, text, full: html, text
    ba33f2c600399d5b4b97dd5fd987ed2db3c891ba Tue May 19 13:40:42 2026 -0700
    myVariants related fixes from code review. Standardize how the code determines we are about to do something myVariants related by #defining some strings and using sameOk to check for them, remove a dead code block, and have hgc use autoSql to load the myVariants item rather than check the raw sql result, refs #37528
• src/hg/lib/ottoRequest.sql
  • lines changed 4, context: html, text, full: html, text
    366bbd6166c2d220b559ae13307d7a60e9cee3a9 Thu May 21 14:43:49 2026 -0700
    ottoRequest table should be InnoDB and allow international characters for email addresses refs #31811
• src/hg/lib/trackDbCache.c
  • lines changed 7, context: html, text, full: html, text
    aa1713ed7bcb1b52032542f990363316cd7b1364 Wed May 20 11:21:58 2026 -0700
    Mac OSX does not have posix_fallocate() function
• src/hg/lib/trackDbCustom.c
  • lines changed 2, context: html, text, full: html, text
    ba33f2c600399d5b4b97dd5fd987ed2db3c891ba Tue May 19 13:40:42 2026 -0700
    myVariants related fixes from code review. Standardize how the code determines we are about to do something myVariants related by #defining some strings and using sameOk to check for them, remove a dead code block, and have hgc use autoSql to load the myVariants item rather than check the raw sql result, refs #37528
• src/hg/lib/web.c
  • lines changed 5, context: html, text, full: html, text
    1085258edb736464f12732c1bdec74ae1182875b Sat May 23 18:04:37 2026 -0700
    Increase several fixed-size string buffers in web.c from 128 to 4096. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/doc/InSiGHT.txt
  • lines changed 20, context: html, text, full: html, text
    46f3b4d35904ddc3df91e916ad15c05ad878b3d1 Thu May 21 08:02:58 2026 -0700
    Adding PMS2 Pseudogene Caution track to InSiGHT hub. refs #36582
• src/hg/makeDb/doc/dm6/lastzRuns.txt
  • lines changed 84, context: html, text, full: html, text
    7d5971d28428ab92599a16d80fb8842bca65c7bd Sat May 23 14:47:38 2026 -0700
    dm6 to GCA_000181055.3 (Rhodnius prolixus) lastz/chain/net run for user, refs #37598
• src/hg/makeDb/doc/hg38/mpra.txt
  • lines changed 28, context: html, text, full: html, text
    1525618a814bcf6eb64c4147b99c520509a55d60 Tue May 19 07:37:29 2026 -0700
    Refresh mpraVarDB to 2026-05-19 snapshot; fix hg19 pos in name field. Upstream landed the Mouri/Tewhey pvalue correction (5,092 rows with pvalue > 1 -> 0) and replaced 47,156 placeholder fdr=1.0 values with NaN. Rebuild from the new CSV; remove the temporary "pending upstream fix" note in mpraVarDb.html. Also closes the pre-existing "hg19 pos in non-rs name field" issue: mpravardbToBed.py gained a post-liftOver step that rewrites the chr:pos prefix inside non-rs names with the hg38 coordinates. 47,160 names were rewritten in this build (e.g. chr1:1403972:C>CG at hg38 chr1:1468591 now reads chr1:1468592:C>CG). itemCount preserved at 239,028. refs #37359 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/doc/hg38/ncOrfs.txt
  • lines changed 44, context: html, text, full: html, text
    2c38ad38c6edbcc5c71099acf373fe99386b1ecd Tue May 19 06:24:48 2026 -0700
    ncOrfs: color by Kozak strength, MANE+GENCODE intron grafting, hidden _teRgb Color: itemRgb now reflects categorical Kozak strength (Strong=golden yellow, Moderate=steel blue, Weak=medium gray, non-ATG=black, no-context =light gray) instead of the Noderer TE gradient. The TE-bin color is preserved as a hidden _teRgb field (underscore prefix => skipped by hgc) for a future second-color rendering. Every subtrack html now has its own swatch legend; the parent page legend was converted to the same style. UTRannotator intron grafting: addIntrons.py now uses MANE Select / MANE Plus Clinical as the primary donor, with the full GENCODE comprehensive set (gencodeV49) as fallback when every MANE candidate is rejected. Containment was relaxed to overlap so uORFs that extend past either end of the host transcript still get the host introns inside the overlap plus a single bridging block for the orphan portion. uORFs whose endpoint falls in a host intron are left single-block to avoid inventing exon structure. The chosen donor transcript ID is stored in intronsSource. Replaced the previous multi-database matching against gencNcOrfs/nuorfdb/metamorf/openprot. Counts on 44,435 uORFs: 5,934 MANE-grafted + 2,795 GENCODE-grafted = 8,729 spliced (was 5,318 with the old multi-db matching), 4,843 rejected for endpoint-in-intron, 143 with no host in either pool. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/doc/hg38/varFreqs.txt
  • lines changed 66, context: html, text, full: html, text
    af9d8fe39e88f7b7cec3792ea797dab44f1416b0 Tue May 19 04:36:02 2026 -0700
    varFreqs: rebuild varFreqsAll with WBBC/TPMI/ChinaMAP/GenomeIndia, drop IndiGen, harden build pipeline Rebuilds /gbdb/hg38/varFreqs/_all/varFreqsAll.bb to fold in the four new subtracks registered earlier in May (WBBC 78.6M, TPMI 672k, ChinaMAP 147M, GenomeIndia 130M) and to drop IndiGen, which ships only a VRT bit and contributed an always-empty AC/AF column. New bb is 47 GB / 147 fields / 1.34 billion items (was 44 GB / 133 / 1.22B). Two pipeline fixes were necessary mid-rebuild: - bcftools 1.22 csq is stricter than earlier versions. Added --unify-chr-names chr,-,chr (Ensembl GFF3 uses bare "1" while merged VCF + FASTA use "chr1") and --force (5 SCHEMA alt contigs end up in the merge but aren't annotated in the GFF3) to the csq invocation in mergeAndAnnotate.sh. Four follow-up cleanups to the build scripts (no track change, just safer next rebuild): - mergeAndAnnotate.sh now reads VCF paths directly from databases.tsv in both the per-VCF strip+norm step and the merge step. The previous "files.txt + find normalized/" model could silently re-merge stale norm cache entries after a database was dropped from databases.tsv. - vcfToBigBed.py concat step streams sort stdout straight to disk instead of capture_output=True, which buffered the whole sorted chromosome (~24 GB for chr1) in Python RAM. - vcfToBigBed.py generate_trackdb_fragment() now emits the three customizations that used to have to be added on top of the auto-fragment by hand: filterType.consequence multipleListOr, the expanded consequence buckets (3_prime_utr, 5_prime_utr, non_coding, others), and skipEmptyFields on. - trackDb/human/varFreqs.ra updated to match the new bb columns (WBBC/TPMI/ChinaMAP/GenomeIndia AC+AF filters, WBBC 4-region population filters, IndiGen filter removed). refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • lines changed 36, context: html, text, full: html, text
    0ef7d0ffeea25371b4828fc23051cdd27598439f Wed May 20 14:57:51 2026 -0700
    varFreqs: add Genome of the Netherlands (GoNL) subtrack on hg38, GRCh38 re-analysis v1.0, 498 unrelated parents (250 fathers + 248 mothers), 36.4M biallelic records after dropping decoy/EBV contigs and bcftools norm split+left-align, refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
  • lines changed 3, context: html, text, full: html, text
    5c88f2b10f443d95e3f9c8e4bbc81534b78d9222 Thu May 21 00:40:38 2026 -0700
    varFreqs: rename supertrack to "SNV Frequencies"; add GoNL (Netherlands, ~13x SR) to databases.tsv and to the varFreqsAll filter UI so the next combined-track rebuild picks it up. refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/doc/hs1/varFreqs.txt
  • lines changed 22, context: html, text, full: html, text
    57c0c8dd69163aac91d9aa7ad7d301baf6feb584 Mon May 18 08:20:26 2026 -0700
    varFreqs: enable SweGen swefreq subtrack on hs1 with CHM13-specific supertrack description page, refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 5, context: html, text, full: html, text
    0f34cba6fd9a27695e4793b8352d4cfde21b12d3 Wed May 20 22:14:45 2026 -0700
    adding three rats per user request
• src/hg/makeDb/doc/mm10.txt
  • lines changed 93, context: html, text, full: html, text
    4eb8ce4c1204debcf7cf81f1de5af5a3dd9343d3 Fri May 22 17:27:25 2026 -0700
    The author requested updating the per-tissue colors to gradients. Updated the mouseDevTimecourse legend HTML to match the new colors and documented the data file update in the mm10 and mm39 makedocs. refs #37001
• src/hg/makeDb/doc/mm39/mouseDevTimecourse.txt
  • lines changed 91, context: html, text, full: html, text
    4eb8ce4c1204debcf7cf81f1de5af5a3dd9343d3 Fri May 22 17:27:25 2026 -0700
    The author requested updating the per-tissue colors to gradients. Updated the mouseDevTimecourse legend HTML to match the new colors and documented the data file update in the mm10 and mm39 makedocs. refs #37001
• src/hg/makeDb/scripts/insight/insightPMS2Caution.py
  • lines changed 221, context: html, text, full: html, text
    46f3b4d35904ddc3df91e916ad15c05ad878b3d1 Thu May 21 08:02:58 2026 -0700
    Adding PMS2 Pseudogene Caution track to InSiGHT hub. refs #36582
• src/hg/makeDb/scripts/mpravardb/mpravardbToBed.py
  • lines changed 27, context: html, text, full: html, text
    1525618a814bcf6eb64c4147b99c520509a55d60 Tue May 19 07:37:29 2026 -0700
    Refresh mpraVarDB to 2026-05-19 snapshot; fix hg19 pos in name field. Upstream landed the Mouri/Tewhey pvalue correction (5,092 rows with pvalue > 1 -> 0) and replaced 47,156 placeholder fdr=1.0 values with NaN. Rebuild from the new CSV; remove the temporary "pending upstream fix" note in mpraVarDb.html. Also closes the pre-existing "hg19 pos in non-rs name field" issue: mpravardbToBed.py gained a post-liftOver step that rewrites the chr:pos prefix inside non-rs names with the hg38 coordinates. 47,160 names were rewritten in this build (e.g. chr1:1403972:C>CG at hg38 chr1:1468591 now reads chr1:1468592:C>CG). itemCount preserved at 239,028. refs #37359 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/ncOrfs/addIntrons.py
  • lines changed 238, context: html, text, full: html, text
    2c38ad38c6edbcc5c71099acf373fe99386b1ecd Tue May 19 06:24:48 2026 -0700
    ncOrfs: color by Kozak strength, MANE+GENCODE intron grafting, hidden _teRgb Color: itemRgb now reflects categorical Kozak strength (Strong=golden yellow, Moderate=steel blue, Weak=medium gray, non-ATG=black, no-context =light gray) instead of the Noderer TE gradient. The TE-bin color is preserved as a hidden _teRgb field (underscore prefix => skipped by hgc) for a future second-color rendering. Every subtrack html now has its own swatch legend; the parent page legend was converted to the same style. UTRannotator intron grafting: addIntrons.py now uses MANE Select / MANE Plus Clinical as the primary donor, with the full GENCODE comprehensive set (gencodeV49) as fallback when every MANE candidate is rejected. Containment was relaxed to overlap so uORFs that extend past either end of the host transcript still get the host introns inside the overlap plus a single bridging block for the orphan portion. uORFs whose endpoint falls in a host intron are left single-block to avoid inventing exon structure. The chosen donor transcript ID is stored in intronsSource. Replaced the previous multi-database matching against gencNcOrfs/nuorfdb/metamorf/openprot. Counts on 44,435 uORFs: 5,934 MANE-grafted + 2,795 GENCODE-grafted = 8,729 spliced (was 5,318 with the old multi-db matching), 4,843 rejected for endpoint-in-intron, 143 with no host in either pool. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/ncOrfs/colorByKozak.py
  • lines changed 75, context: html, text, full: html, text
    2c38ad38c6edbcc5c71099acf373fe99386b1ecd Tue May 19 06:24:48 2026 -0700
    ncOrfs: color by Kozak strength, MANE+GENCODE intron grafting, hidden _teRgb Color: itemRgb now reflects categorical Kozak strength (Strong=golden yellow, Moderate=steel blue, Weak=medium gray, non-ATG=black, no-context =light gray) instead of the Noderer TE gradient. The TE-bin color is preserved as a hidden _teRgb field (underscore prefix => skipped by hgc) for a future second-color rendering. Every subtrack html now has its own swatch legend; the parent page legend was converted to the same style. UTRannotator intron grafting: addIntrons.py now uses MANE Select / MANE Plus Clinical as the primary donor, with the full GENCODE comprehensive set (gencodeV49) as fallback when every MANE candidate is rejected. Containment was relaxed to overlap so uORFs that extend past either end of the host transcript still get the host introns inside the overlap plus a single bridging block for the orphan portion. uORFs whose endpoint falls in a host intron are left single-block to avoid inventing exon structure. The chosen donor transcript ID is stored in intronsSource. Replaced the previous multi-database matching against gencNcOrfs/nuorfdb/metamorf/openprot. Counts on 44,435 uORFs: 5,934 MANE-grafted + 2,795 GENCODE-grafted = 8,729 spliced (was 5,318 with the old multi-db matching), 4,843 rejected for endpoint-in-intron, 143 with no host in either pool. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/ncOrfs/gencNcOrf.as
  • lines changed 2, context: html, text, full: html, text
    2c38ad38c6edbcc5c71099acf373fe99386b1ecd Tue May 19 06:24:48 2026 -0700
    ncOrfs: color by Kozak strength, MANE+GENCODE intron grafting, hidden _teRgb Color: itemRgb now reflects categorical Kozak strength (Strong=golden yellow, Moderate=steel blue, Weak=medium gray, non-ATG=black, no-context =light gray) instead of the Noderer TE gradient. The TE-bin color is preserved as a hidden _teRgb field (underscore prefix => skipped by hgc) for a future second-color rendering. Every subtrack html now has its own swatch legend; the parent page legend was converted to the same style. UTRannotator intron grafting: addIntrons.py now uses MANE Select / MANE Plus Clinical as the primary donor, with the full GENCODE comprehensive set (gencodeV49) as fallback when every MANE candidate is rejected. Containment was relaxed to overlap so uORFs that extend past either end of the host transcript still get the host introns inside the overlap plus a single bridging block for the orphan portion. uORFs whose endpoint falls in a host intron are left single-block to avoid inventing exon structure. The chosen donor transcript ID is stored in intronsSource. Replaced the previous multi-database matching against gencNcOrfs/nuorfdb/metamorf/openprot. Counts on 44,435 uORFs: 5,934 MANE-grafted + 2,795 GENCODE-grafted = 8,729 spliced (was 5,318 with the old multi-db matching), 4,843 rejected for endpoint-in-intron, 143 with no host in either pool. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/ncOrfs/gencNcOrfPhase2.as
  • lines changed 2, context: html, text, full: html, text
    2c38ad38c6edbcc5c71099acf373fe99386b1ecd Tue May 19 06:24:48 2026 -0700
    ncOrfs: color by Kozak strength, MANE+GENCODE intron grafting, hidden _teRgb Color: itemRgb now reflects categorical Kozak strength (Strong=golden yellow, Moderate=steel blue, Weak=medium gray, non-ATG=black, no-context =light gray) instead of the Noderer TE gradient. The TE-bin color is preserved as a hidden _teRgb field (underscore prefix => skipped by hgc) for a future second-color rendering. Every subtrack html now has its own swatch legend; the parent page legend was converted to the same style. UTRannotator intron grafting: addIntrons.py now uses MANE Select / MANE Plus Clinical as the primary donor, with the full GENCODE comprehensive set (gencodeV49) as fallback when every MANE candidate is rejected. Containment was relaxed to overlap so uORFs that extend past either end of the host transcript still get the host introns inside the overlap plus a single bridging block for the orphan portion. uORFs whose endpoint falls in a host intron are left single-block to avoid inventing exon structure. The chosen donor transcript ID is stored in intronsSource. Replaced the previous multi-database matching against gencNcOrfs/nuorfdb/metamorf/openprot. Counts on 44,435 uORFs: 5,934 MANE-grafted + 2,795 GENCODE-grafted = 8,729 spliced (was 5,318 with the old multi-db matching), 4,843 rejected for endpoint-in-intron, 143 with no host in either pool. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/ncOrfs/metamorf.as
  • lines changed 2, context: html, text, full: html, text
    2c38ad38c6edbcc5c71099acf373fe99386b1ecd Tue May 19 06:24:48 2026 -0700
    ncOrfs: color by Kozak strength, MANE+GENCODE intron grafting, hidden _teRgb Color: itemRgb now reflects categorical Kozak strength (Strong=golden yellow, Moderate=steel blue, Weak=medium gray, non-ATG=black, no-context =light gray) instead of the Noderer TE gradient. The TE-bin color is preserved as a hidden _teRgb field (underscore prefix => skipped by hgc) for a future second-color rendering. Every subtrack html now has its own swatch legend; the parent page legend was converted to the same style. UTRannotator intron grafting: addIntrons.py now uses MANE Select / MANE Plus Clinical as the primary donor, with the full GENCODE comprehensive set (gencodeV49) as fallback when every MANE candidate is rejected. Containment was relaxed to overlap so uORFs that extend past either end of the host transcript still get the host introns inside the overlap plus a single bridging block for the orphan portion. uORFs whose endpoint falls in a host intron are left single-block to avoid inventing exon structure. The chosen donor transcript ID is stored in intronsSource. Replaced the previous multi-database matching against gencNcOrfs/nuorfdb/metamorf/openprot. Counts on 44,435 uORFs: 5,934 MANE-grafted + 2,795 GENCODE-grafted = 8,729 spliced (was 5,318 with the old multi-db matching), 4,843 rejected for endpoint-in-intron, 143 with no host in either pool. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/ncOrfs/nuorfdb.as
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    2c38ad38c6edbcc5c71099acf373fe99386b1ecd Tue May 19 06:24:48 2026 -0700
    ncOrfs: color by Kozak strength, MANE+GENCODE intron grafting, hidden _teRgb Color: itemRgb now reflects categorical Kozak strength (Strong=golden yellow, Moderate=steel blue, Weak=medium gray, non-ATG=black, no-context =light gray) instead of the Noderer TE gradient. The TE-bin color is preserved as a hidden _teRgb field (underscore prefix => skipped by hgc) for a future second-color rendering. Every subtrack html now has its own swatch legend; the parent page legend was converted to the same style. UTRannotator intron grafting: addIntrons.py now uses MANE Select / MANE Plus Clinical as the primary donor, with the full GENCODE comprehensive set (gencodeV49) as fallback when every MANE candidate is rejected. Containment was relaxed to overlap so uORFs that extend past either end of the host transcript still get the host introns inside the overlap plus a single bridging block for the orphan portion. uORFs whose endpoint falls in a host intron are left single-block to avoid inventing exon structure. The chosen donor transcript ID is stored in intronsSource. Replaced the previous multi-database matching against gencNcOrfs/nuorfdb/metamorf/openprot. Counts on 44,435 uORFs: 5,934 MANE-grafted + 2,795 GENCODE-grafted = 8,729 spliced (was 5,318 with the old multi-db matching), 4,843 rejected for endpoint-in-intron, 143 with no host in either pool. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/ncOrfs/openprot.as
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    2c38ad38c6edbcc5c71099acf373fe99386b1ecd Tue May 19 06:24:48 2026 -0700
    ncOrfs: color by Kozak strength, MANE+GENCODE intron grafting, hidden _teRgb Color: itemRgb now reflects categorical Kozak strength (Strong=golden yellow, Moderate=steel blue, Weak=medium gray, non-ATG=black, no-context =light gray) instead of the Noderer TE gradient. The TE-bin color is preserved as a hidden _teRgb field (underscore prefix => skipped by hgc) for a future second-color rendering. Every subtrack html now has its own swatch legend; the parent page legend was converted to the same style. UTRannotator intron grafting: addIntrons.py now uses MANE Select / MANE Plus Clinical as the primary donor, with the full GENCODE comprehensive set (gencodeV49) as fallback when every MANE candidate is rejected. Containment was relaxed to overlap so uORFs that extend past either end of the host transcript still get the host introns inside the overlap plus a single bridging block for the orphan portion. uORFs whose endpoint falls in a host intron are left single-block to avoid inventing exon structure. The chosen donor transcript ID is stored in intronsSource. Replaced the previous multi-database matching against gencNcOrfs/nuorfdb/metamorf/openprot. Counts on 44,435 uORFs: 5,934 MANE-grafted + 2,795 GENCODE-grafted = 8,729 spliced (was 5,318 with the old multi-db matching), 4,843 rejected for endpoint-in-intron, 143 with no host in either pool. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/ncOrfs/run_kozak.sh
  • lines changed 3, context: html, text, full: html, text
    2c38ad38c6edbcc5c71099acf373fe99386b1ecd Tue May 19 06:24:48 2026 -0700
    ncOrfs: color by Kozak strength, MANE+GENCODE intron grafting, hidden _teRgb Color: itemRgb now reflects categorical Kozak strength (Strong=golden yellow, Moderate=steel blue, Weak=medium gray, non-ATG=black, no-context =light gray) instead of the Noderer TE gradient. The TE-bin color is preserved as a hidden _teRgb field (underscore prefix => skipped by hgc) for a future second-color rendering. Every subtrack html now has its own swatch legend; the parent page legend was converted to the same style. UTRannotator intron grafting: addIntrons.py now uses MANE Select / MANE Plus Clinical as the primary donor, with the full GENCODE comprehensive set (gencodeV49) as fallback when every MANE candidate is rejected. Containment was relaxed to overlap so uORFs that extend past either end of the host transcript still get the host introns inside the overlap plus a single bridging block for the orphan portion. uORFs whose endpoint falls in a host intron are left single-block to avoid inventing exon structure. The chosen donor transcript ID is stored in intronsSource. Replaced the previous multi-database matching against gencNcOrfs/nuorfdb/metamorf/openprot. Counts on 44,435 uORFs: 5,934 MANE-grafted + 2,795 GENCODE-grafted = 8,729 spliced (was 5,318 with the old multi-db matching), 4,843 rejected for endpoint-in-intron, 143 with no host in either pool. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/ncOrfs/utrAnnotUorfs.as
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    2c38ad38c6edbcc5c71099acf373fe99386b1ecd Tue May 19 06:24:48 2026 -0700
    ncOrfs: color by Kozak strength, MANE+GENCODE intron grafting, hidden _teRgb Color: itemRgb now reflects categorical Kozak strength (Strong=golden yellow, Moderate=steel blue, Weak=medium gray, non-ATG=black, no-context =light gray) instead of the Noderer TE gradient. The TE-bin color is preserved as a hidden _teRgb field (underscore prefix => skipped by hgc) for a future second-color rendering. Every subtrack html now has its own swatch legend; the parent page legend was converted to the same style. UTRannotator intron grafting: addIntrons.py now uses MANE Select / MANE Plus Clinical as the primary donor, with the full GENCODE comprehensive set (gencodeV49) as fallback when every MANE candidate is rejected. Containment was relaxed to overlap so uORFs that extend past either end of the host transcript still get the host introns inside the overlap plus a single bridging block for the orphan portion. uORFs whose endpoint falls in a host intron are left single-block to avoid inventing exon structure. The chosen donor transcript ID is stored in intronsSource. Replaced the previous multi-database matching against gencNcOrfs/nuorfdb/metamorf/openprot. Counts on 44,435 uORFs: 5,934 MANE-grafted + 2,795 GENCODE-grafted = 8,729 spliced (was 5,318 with the old multi-db matching), 4,843 rejected for endpoint-in-intron, 143 with no host in either pool. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/nmd/nmdDetectAi/makeBigBed.py
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    a95508a8614511de9cb72966524ef62d8f85517c Mon May 18 07:38:56 2026 -0700
    NMDetective-AI track polish: shorter longLabels, taller bigWig, item label without gene prefix. Drop the "Veiner et al., " parenthetical from both AI subtrack longLabels, bump the AI bigWig default height to 120 px, add the AI tracks to the NMD supertrack description page (under NMDetective scores), and strip the "<gene>:" prefix from the per-variant bigBed item labels (gene symbol is still in the geneName column and the mouseover). refs #33737 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/varFreqs/databases.tsv
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    5c88f2b10f443d95e3f9c8e4bbc81534b78d9222 Thu May 21 00:40:38 2026 -0700
    varFreqs: rename supertrack to "SNV Frequencies"; add GoNL (Netherlands, ~13x SR) to databases.tsv and to the varFreqsAll filter UI so the next combined-track rebuild picks it up. refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/scripts/varFreqs/mergeAndAnnotate.sh
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    af9d8fe39e88f7b7cec3792ea797dab44f1416b0 Tue May 19 04:36:02 2026 -0700
    varFreqs: rebuild varFreqsAll with WBBC/TPMI/ChinaMAP/GenomeIndia, drop IndiGen, harden build pipeline Rebuilds /gbdb/hg38/varFreqs/_all/varFreqsAll.bb to fold in the four new subtracks registered earlier in May (WBBC 78.6M, TPMI 672k, ChinaMAP 147M, GenomeIndia 130M) and to drop IndiGen, which ships only a VRT bit and contributed an always-empty AC/AF column. New bb is 47 GB / 147 fields / 1.34 billion items (was 44 GB / 133 / 1.22B). Two pipeline fixes were necessary mid-rebuild: - bcftools 1.22 csq is stricter than earlier versions. Added --unify-chr-names chr,-,chr (Ensembl GFF3 uses bare "1" while merged VCF + FASTA use "chr1") and --force (5 SCHEMA alt contigs end up in the merge but aren't annotated in the GFF3) to the csq invocation in mergeAndAnnotate.sh. Four follow-up cleanups to the build scripts (no track change, just safer next rebuild): - mergeAndAnnotate.sh now reads VCF paths directly from databases.tsv in both the per-VCF strip+norm step and the merge step. The previous "files.txt + find normalized/" model could silently re-merge stale norm cache entries after a database was dropped from databases.tsv. - vcfToBigBed.py concat step streams sort stdout straight to disk instead of capture_output=True, which buffered the whole sorted chromosome (~24 GB for chr1) in Python RAM. - vcfToBigBed.py generate_trackdb_fragment() now emits the three customizations that used to have to be added on top of the auto-fragment by hand: filterType.consequence multipleListOr, the expanded consequence buckets (3_prime_utr, 5_prime_utr, non_coding, others), and skipEmptyFields on. - trackDb/human/varFreqs.ra updated to match the new bb columns (WBBC/TPMI/ChinaMAP/GenomeIndia AC+AF filters, WBBC 4-region population filters, IndiGen filter removed). refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/varFreqs/vcfToBigBed.py
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    af9d8fe39e88f7b7cec3792ea797dab44f1416b0 Tue May 19 04:36:02 2026 -0700
    varFreqs: rebuild varFreqsAll with WBBC/TPMI/ChinaMAP/GenomeIndia, drop IndiGen, harden build pipeline Rebuilds /gbdb/hg38/varFreqs/_all/varFreqsAll.bb to fold in the four new subtracks registered earlier in May (WBBC 78.6M, TPMI 672k, ChinaMAP 147M, GenomeIndia 130M) and to drop IndiGen, which ships only a VRT bit and contributed an always-empty AC/AF column. New bb is 47 GB / 147 fields / 1.34 billion items (was 44 GB / 133 / 1.22B). Two pipeline fixes were necessary mid-rebuild: - bcftools 1.22 csq is stricter than earlier versions. Added --unify-chr-names chr,-,chr (Ensembl GFF3 uses bare "1" while merged VCF + FASTA use "chr1") and --force (5 SCHEMA alt contigs end up in the merge but aren't annotated in the GFF3) to the csq invocation in mergeAndAnnotate.sh. Four follow-up cleanups to the build scripts (no track change, just safer next rebuild): - mergeAndAnnotate.sh now reads VCF paths directly from databases.tsv in both the per-VCF strip+norm step and the merge step. The previous "files.txt + find normalized/" model could silently re-merge stale norm cache entries after a database was dropped from databases.tsv. - vcfToBigBed.py concat step streams sort stdout straight to disk instead of capture_output=True, which buffered the whole sorted chromosome (~24 GB for chr1) in Python RAM. - vcfToBigBed.py generate_trackdb_fragment() now emits the three customizations that used to have to be added on top of the auto-fragment by hand: filterType.consequence multipleListOr, the expanded consequence buckets (3_prime_utr, 5_prime_utr, non_coding, others), and skipEmptyFields on. - trackDb/human/varFreqs.ra updated to match the new bb columns (WBBC/TPMI/ChinaMAP/GenomeIndia AC+AF filters, WBBC 4-region population filters, IndiGen filter removed). refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/betaGenArk.txt
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    4f3c5867733dd64868cff1ce30538e86146009c8 Sat May 23 08:54:43 2026 -0700
    allow HPRCv2 and lowelab to become official beta tracks
• src/hg/makeDb/trackDb/human/abraom.html
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    9bfd58221b1539193cb7f0a317b4e959c1c7e49a Thu May 21 01:00:45 2026 -0700
    varFreqs: AI generated text sounds bad, hard to read, so remove typical AI language. "humanizer" pass on all 31 varFreqs description pages — cut em dashes, copula avoidance ("serves as", "stands as"), "-ing" puffery, and boilerplate filler ("We provide documentation that indicates how..."). Title-case headings and meaningful <b> emphasis preserved. No facts/URLs/counts/versions changed. tpmi.html added as a new file (was previously uncommitted). refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/alfaVcf.html
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    9bfd58221b1539193cb7f0a317b4e959c1c7e49a Thu May 21 01:00:45 2026 -0700
    varFreqs: AI generated text sounds bad, hard to read, so remove typical AI language. "humanizer" pass on all 31 varFreqs description pages — cut em dashes, copula avoidance ("serves as", "stands as"), "-ing" puffery, and boilerplate filler ("We provide documentation that indicates how..."). Title-case headings and meaningful <b> emphasis preserved. No facts/URLs/counts/versions changed. tpmi.html added as a new file (was previously uncommitted). refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/allofus.html
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    9bfd58221b1539193cb7f0a317b4e959c1c7e49a Thu May 21 01:00:45 2026 -0700
    varFreqs: AI generated text sounds bad, hard to read, so remove typical AI language. "humanizer" pass on all 31 varFreqs description pages — cut em dashes, copula avoidance ("serves as", "stands as"), "-ing" puffery, and boilerplate filler ("We provide documentation that indicates how..."). Title-case headings and meaningful <b> emphasis preserved. No facts/URLs/counts/versions changed. tpmi.html added as a new file (was previously uncommitted). refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/chinamap.html
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    9bfd58221b1539193cb7f0a317b4e959c1c7e49a Thu May 21 01:00:45 2026 -0700
    varFreqs: AI generated text sounds bad, hard to read, so remove typical AI language. "humanizer" pass on all 31 varFreqs description pages — cut em dashes, copula avoidance ("serves as", "stands as"), "-ing" puffery, and boilerplate filler ("We provide documentation that indicates how..."). Title-case headings and meaningful <b> emphasis preserved. No facts/URLs/counts/versions changed. tpmi.html added as a new file (was previously uncommitted). refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/colorsDbSnv.html
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    9bfd58221b1539193cb7f0a317b4e959c1c7e49a Thu May 21 01:00:45 2026 -0700
    varFreqs: AI generated text sounds bad, hard to read, so remove typical AI language. "humanizer" pass on all 31 varFreqs description pages — cut em dashes, copula avoidance ("serves as", "stands as"), "-ing" puffery, and boilerplate filler ("We provide documentation that indicates how..."). Title-case headings and meaningful <b> emphasis preserved. No facts/URLs/counts/versions changed. tpmi.html added as a new file (was previously uncommitted). refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/finngen.html
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    9bfd58221b1539193cb7f0a317b4e959c1c7e49a Thu May 21 01:00:45 2026 -0700
    varFreqs: AI generated text sounds bad, hard to read, so remove typical AI language. "humanizer" pass on all 31 varFreqs description pages — cut em dashes, copula avoidance ("serves as", "stands as"), "-ing" puffery, and boilerplate filler ("We provide documentation that indicates how..."). Title-case headings and meaningful <b> emphasis preserved. No facts/URLs/counts/versions changed. tpmi.html added as a new file (was previously uncommitted). refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/ga4kSnv.html
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    9bfd58221b1539193cb7f0a317b4e959c1c7e49a Thu May 21 01:00:45 2026 -0700
    varFreqs: AI generated text sounds bad, hard to read, so remove typical AI language. "humanizer" pass on all 31 varFreqs description pages — cut em dashes, copula avoidance ("serves as", "stands as"), "-ing" puffery, and boilerplate filler ("We provide documentation that indicates how..."). Title-case headings and meaningful <b> emphasis preserved. No facts/URLs/counts/versions changed. tpmi.html added as a new file (was previously uncommitted). refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/gasp.html
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    9bfd58221b1539193cb7f0a317b4e959c1c7e49a Thu May 21 01:00:45 2026 -0700
    varFreqs: AI generated text sounds bad, hard to read, so remove typical AI language. "humanizer" pass on all 31 varFreqs description pages — cut em dashes, copula avoidance ("serves as", "stands as"), "-ing" puffery, and boilerplate filler ("We provide documentation that indicates how..."). Title-case headings and meaningful <b> emphasis preserved. No facts/URLs/counts/versions changed. tpmi.html added as a new file (was previously uncommitted). refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/genomeindia.html
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    9bfd58221b1539193cb7f0a317b4e959c1c7e49a Thu May 21 01:00:45 2026 -0700
    varFreqs: AI generated text sounds bad, hard to read, so remove typical AI language. "humanizer" pass on all 31 varFreqs description pages — cut em dashes, copula avoidance ("serves as", "stands as"), "-ing" puffery, and boilerplate filler ("We provide documentation that indicates how..."). Title-case headings and meaningful <b> emphasis preserved. No facts/URLs/counts/versions changed. tpmi.html added as a new file (was previously uncommitted). refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/gonl.html
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    0ef7d0ffeea25371b4828fc23051cdd27598439f Wed May 20 14:57:51 2026 -0700
    varFreqs: add Genome of the Netherlands (GoNL) subtrack on hg38, GRCh38 re-analysis v1.0, 498 unrelated parents (250 fathers + 248 mothers), 36.4M biallelic records after dropping decoy/EBV contigs and bcftools norm split+left-align, refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/gregor.html
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    9bfd58221b1539193cb7f0a317b4e959c1c7e49a Thu May 21 01:00:45 2026 -0700
    varFreqs: AI generated text sounds bad, hard to read, so remove typical AI language. "humanizer" pass on all 31 varFreqs description pages — cut em dashes, copula avoidance ("serves as", "stands as"), "-ing" puffery, and boilerplate filler ("We provide documentation that indicates how..."). Title-case headings and meaningful <b> emphasis preserved. No facts/URLs/counts/versions changed. tpmi.html added as a new file (was previously uncommitted). refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/gencNcOrfs.html
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    2c38ad38c6edbcc5c71099acf373fe99386b1ecd Tue May 19 06:24:48 2026 -0700
    ncOrfs: color by Kozak strength, MANE+GENCODE intron grafting, hidden _teRgb Color: itemRgb now reflects categorical Kozak strength (Strong=golden yellow, Moderate=steel blue, Weak=medium gray, non-ATG=black, no-context =light gray) instead of the Noderer TE gradient. The TE-bin color is preserved as a hidden _teRgb field (underscore prefix => skipped by hgc) for a future second-color rendering. Every subtrack html now has its own swatch legend; the parent page legend was converted to the same style. UTRannotator intron grafting: addIntrons.py now uses MANE Select / MANE Plus Clinical as the primary donor, with the full GENCODE comprehensive set (gencodeV49) as fallback when every MANE candidate is rejected. Containment was relaxed to overlap so uORFs that extend past either end of the host transcript still get the host introns inside the overlap plus a single bridging block for the orphan portion. uORFs whose endpoint falls in a host intron are left single-block to avoid inventing exon structure. The chosen donor transcript ID is stored in intronsSource. Replaced the previous multi-database matching against gencNcOrfs/nuorfdb/metamorf/openprot. Counts on 44,435 uORFs: 5,934 MANE-grafted + 2,795 GENCODE-grafted = 8,729 spliced (was 5,318 with the old multi-db matching), 4,843 rejected for endpoint-in-intron, 143 with no host in either pool. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/metamorf.html
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    2c38ad38c6edbcc5c71099acf373fe99386b1ecd Tue May 19 06:24:48 2026 -0700
    ncOrfs: color by Kozak strength, MANE+GENCODE intron grafting, hidden _teRgb Color: itemRgb now reflects categorical Kozak strength (Strong=golden yellow, Moderate=steel blue, Weak=medium gray, non-ATG=black, no-context =light gray) instead of the Noderer TE gradient. The TE-bin color is preserved as a hidden _teRgb field (underscore prefix => skipped by hgc) for a future second-color rendering. Every subtrack html now has its own swatch legend; the parent page legend was converted to the same style. UTRannotator intron grafting: addIntrons.py now uses MANE Select / MANE Plus Clinical as the primary donor, with the full GENCODE comprehensive set (gencodeV49) as fallback when every MANE candidate is rejected. Containment was relaxed to overlap so uORFs that extend past either end of the host transcript still get the host introns inside the overlap plus a single bridging block for the orphan portion. uORFs whose endpoint falls in a host intron are left single-block to avoid inventing exon structure. The chosen donor transcript ID is stored in intronsSource. Replaced the previous multi-database matching against gencNcOrfs/nuorfdb/metamorf/openprot. Counts on 44,435 uORFs: 5,934 MANE-grafted + 2,795 GENCODE-grafted = 8,729 spliced (was 5,318 with the old multi-db matching), 4,843 rejected for endpoint-in-intron, 143 with no host in either pool. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/mpraVarDb.html
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    1525618a814bcf6eb64c4147b99c520509a55d60 Tue May 19 07:37:29 2026 -0700
    Refresh mpraVarDB to 2026-05-19 snapshot; fix hg19 pos in name field. Upstream landed the Mouri/Tewhey pvalue correction (5,092 rows with pvalue > 1 -> 0) and replaced 47,156 placeholder fdr=1.0 values with NaN. Rebuild from the new CSV; remove the temporary "pending upstream fix" note in mpraVarDb.html. Also closes the pre-existing "hg19 pos in non-rs name field" issue: mpravardbToBed.py gained a post-liftOver step that rewrites the chr:pos prefix inside non-rs names with the hg38 coordinates. 47,160 names were rewritten in this build (e.g. chr1:1403972:C>CG at hg38 chr1:1468591 now reads chr1:1468592:C>CG). itemCount preserved at 239,028. refs #37359 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/ncOrfs.html
  • lines changed 35, context: html, text, full: html, text
    2c38ad38c6edbcc5c71099acf373fe99386b1ecd Tue May 19 06:24:48 2026 -0700
    ncOrfs: color by Kozak strength, MANE+GENCODE intron grafting, hidden _teRgb Color: itemRgb now reflects categorical Kozak strength (Strong=golden yellow, Moderate=steel blue, Weak=medium gray, non-ATG=black, no-context =light gray) instead of the Noderer TE gradient. The TE-bin color is preserved as a hidden _teRgb field (underscore prefix => skipped by hgc) for a future second-color rendering. Every subtrack html now has its own swatch legend; the parent page legend was converted to the same style. UTRannotator intron grafting: addIntrons.py now uses MANE Select / MANE Plus Clinical as the primary donor, with the full GENCODE comprehensive set (gencodeV49) as fallback when every MANE candidate is rejected. Containment was relaxed to overlap so uORFs that extend past either end of the host transcript still get the host introns inside the overlap plus a single bridging block for the orphan portion. uORFs whose endpoint falls in a host intron are left single-block to avoid inventing exon structure. The chosen donor transcript ID is stored in intronsSource. Replaced the previous multi-database matching against gencNcOrfs/nuorfdb/metamorf/openprot. Counts on 44,435 uORFs: 5,934 MANE-grafted + 2,795 GENCODE-grafted = 8,729 spliced (was 5,318 with the old multi-db matching), 4,843 rejected for endpoint-in-intron, 143 with no host in either pool. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/ncOrfs.ra
  • lines changed 3, context: html, text, full: html, text
    2c38ad38c6edbcc5c71099acf373fe99386b1ecd Tue May 19 06:24:48 2026 -0700
    ncOrfs: color by Kozak strength, MANE+GENCODE intron grafting, hidden _teRgb Color: itemRgb now reflects categorical Kozak strength (Strong=golden yellow, Moderate=steel blue, Weak=medium gray, non-ATG=black, no-context =light gray) instead of the Noderer TE gradient. The TE-bin color is preserved as a hidden _teRgb field (underscore prefix => skipped by hgc) for a future second-color rendering. Every subtrack html now has its own swatch legend; the parent page legend was converted to the same style. UTRannotator intron grafting: addIntrons.py now uses MANE Select / MANE Plus Clinical as the primary donor, with the full GENCODE comprehensive set (gencodeV49) as fallback when every MANE candidate is rejected. Containment was relaxed to overlap so uORFs that extend past either end of the host transcript still get the host introns inside the overlap plus a single bridging block for the orphan portion. uORFs whose endpoint falls in a host intron are left single-block to avoid inventing exon structure. The chosen donor transcript ID is stored in intronsSource. Replaced the previous multi-database matching against gencNcOrfs/nuorfdb/metamorf/openprot. Counts on 44,435 uORFs: 5,934 MANE-grafted + 2,795 GENCODE-grafted = 8,729 spliced (was 5,318 with the old multi-db matching), 4,843 rejected for endpoint-in-intron, 143 with no host in either pool. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • lines changed 1, context: html, text, full: html, text
    ec21f46219775a5dadf6a7f4c1e8e036591fc61d Fri May 22 16:20:47 2026 -0700
    Making changes suggested by Gerardo in code review, refs #37580
• src/hg/makeDb/trackDb/human/hg38/nmd.html
  • lines changed 5, context: html, text, full: html, text
    a95508a8614511de9cb72966524ef62d8f85517c Mon May 18 07:38:56 2026 -0700
    NMDetective-AI track polish: shorter longLabels, taller bigWig, item label without gene prefix. Drop the "Veiner et al., " parenthetical from both AI subtrack longLabels, bump the AI bigWig default height to 120 px, add the AI tracks to the NMD supertrack description page (under NMDetective scores), and strip the "<gene>:" prefix from the per-variant bigBed item labels (gene symbol is still in the geneName column and the mouseover). refs #33737 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/nmd.ra
  • lines changed 3, context: html, text, full: html, text
    a95508a8614511de9cb72966524ef62d8f85517c Mon May 18 07:38:56 2026 -0700
    NMDetective-AI track polish: shorter longLabels, taller bigWig, item label without gene prefix. Drop the "Veiner et al., " parenthetical from both AI subtrack longLabels, bump the AI bigWig default height to 120 px, add the AI tracks to the NMD supertrack description page (under NMDetective scores), and strip the "<gene>:" prefix from the per-variant bigBed item labels (gene symbol is still in the geneName column and the mouseover). refs #33737 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/nuorfdb.html
  • lines changed 9, context: html, text, full: html, text
    2c38ad38c6edbcc5c71099acf373fe99386b1ecd Tue May 19 06:24:48 2026 -0700
    ncOrfs: color by Kozak strength, MANE+GENCODE intron grafting, hidden _teRgb Color: itemRgb now reflects categorical Kozak strength (Strong=golden yellow, Moderate=steel blue, Weak=medium gray, non-ATG=black, no-context =light gray) instead of the Noderer TE gradient. The TE-bin color is preserved as a hidden _teRgb field (underscore prefix => skipped by hgc) for a future second-color rendering. Every subtrack html now has its own swatch legend; the parent page legend was converted to the same style. UTRannotator intron grafting: addIntrons.py now uses MANE Select / MANE Plus Clinical as the primary donor, with the full GENCODE comprehensive set (gencodeV49) as fallback when every MANE candidate is rejected. Containment was relaxed to overlap so uORFs that extend past either end of the host transcript still get the host introns inside the overlap plus a single bridging block for the orphan portion. uORFs whose endpoint falls in a host intron are left single-block to avoid inventing exon structure. The chosen donor transcript ID is stored in intronsSource. Replaced the previous multi-database matching against gencNcOrfs/nuorfdb/metamorf/openprot. Counts on 44,435 uORFs: 5,934 MANE-grafted + 2,795 GENCODE-grafted = 8,729 spliced (was 5,318 with the old multi-db matching), 4,843 rejected for endpoint-in-intron, 143 with no host in either pool. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
  • lines changed 1, context: html, text, full: html, text
    ec21f46219775a5dadf6a7f4c1e8e036591fc61d Fri May 22 16:20:47 2026 -0700
    Making changes suggested by Gerardo in code review, refs #37580
• src/hg/makeDb/trackDb/human/hg38/openprot.html
  • lines changed 8, context: html, text, full: html, text
    2c38ad38c6edbcc5c71099acf373fe99386b1ecd Tue May 19 06:24:48 2026 -0700
    ncOrfs: color by Kozak strength, MANE+GENCODE intron grafting, hidden _teRgb Color: itemRgb now reflects categorical Kozak strength (Strong=golden yellow, Moderate=steel blue, Weak=medium gray, non-ATG=black, no-context =light gray) instead of the Noderer TE gradient. The TE-bin color is preserved as a hidden _teRgb field (underscore prefix => skipped by hgc) for a future second-color rendering. Every subtrack html now has its own swatch legend; the parent page legend was converted to the same style. UTRannotator intron grafting: addIntrons.py now uses MANE Select / MANE Plus Clinical as the primary donor, with the full GENCODE comprehensive set (gencodeV49) as fallback when every MANE candidate is rejected. Containment was relaxed to overlap so uORFs that extend past either end of the host transcript still get the host introns inside the overlap plus a single bridging block for the orphan portion. uORFs whose endpoint falls in a host intron are left single-block to avoid inventing exon structure. The chosen donor transcript ID is stored in intronsSource. Replaced the previous multi-database matching against gencNcOrfs/nuorfdb/metamorf/openprot. Counts on 44,435 uORFs: 5,934 MANE-grafted + 2,795 GENCODE-grafted = 8,729 spliced (was 5,318 with the old multi-db matching), 4,843 rejected for endpoint-in-intron, 143 with no host in either pool. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/utrAnnotUorfs.html
  • lines changed 24, context: html, text, full: html, text
    2c38ad38c6edbcc5c71099acf373fe99386b1ecd Tue May 19 06:24:48 2026 -0700
    ncOrfs: color by Kozak strength, MANE+GENCODE intron grafting, hidden _teRgb Color: itemRgb now reflects categorical Kozak strength (Strong=golden yellow, Moderate=steel blue, Weak=medium gray, non-ATG=black, no-context =light gray) instead of the Noderer TE gradient. The TE-bin color is preserved as a hidden _teRgb field (underscore prefix => skipped by hgc) for a future second-color rendering. Every subtrack html now has its own swatch legend; the parent page legend was converted to the same style. UTRannotator intron grafting: addIntrons.py now uses MANE Select / MANE Plus Clinical as the primary donor, with the full GENCODE comprehensive set (gencodeV49) as fallback when every MANE candidate is rejected. Containment was relaxed to overlap so uORFs that extend past either end of the host transcript still get the host introns inside the overlap plus a single bridging block for the orphan portion. uORFs whose endpoint falls in a host intron are left single-block to avoid inventing exon structure. The chosen donor transcript ID is stored in intronsSource. Replaced the previous multi-database matching against gencNcOrfs/nuorfdb/metamorf/openprot. Counts on 44,435 uORFs: 5,934 MANE-grafted + 2,795 GENCODE-grafted = 8,729 spliced (was 5,318 with the old multi-db matching), 4,843 rejected for endpoint-in-intron, 143 with no host in either pool. refs #35101 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/vgp577way.trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    ab3163d7361d2f7bcf7beb522cd947f691196bf5 Wed May 20 21:17:25 2026 -0700
    move the bigBed and bigWig files to hgdownload refs #31811
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Epigenetics.html
  • lines changed 64, context: html, text, full: html, text
    6c1fba5815103be1d60cd33c12c30b1ec26f34b7 Wed May 20 14:55:34 2026 -0700
    ENCODE4 Regulation Epigenetics (Indiv.) description page updates (hg38 and mm10): added Available Organs and Tissues table, inline assay colors in Description bullets, dropped color legend paragraph. Also raised maxCheckboxes 40 to 50 on six faceted composite .ra files (Epigenetics, TfChip, RnaSeq for both assemblies). refs #34923
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4Epigenetics.ra
  • lines changed 1, context: html, text, full: html, text
    6c1fba5815103be1d60cd33c12c30b1ec26f34b7 Wed May 20 14:55:34 2026 -0700
    ENCODE4 Regulation Epigenetics (Indiv.) description page updates (hg38 and mm10): added Available Organs and Tissues table, inline assay colors in Description bullets, dropped color legend paragraph. Also raised maxCheckboxes 40 to 50 on six faceted composite .ra files (Epigenetics, TfChip, RnaSeq for both assemblies). refs #34923
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4RnaSeq.ra
  • lines changed 1, context: html, text, full: html, text
    6c1fba5815103be1d60cd33c12c30b1ec26f34b7 Wed May 20 14:55:34 2026 -0700
    ENCODE4 Regulation Epigenetics (Indiv.) description page updates (hg38 and mm10): added Available Organs and Tissues table, inline assay colors in Description bullets, dropped color legend paragraph. Also raised maxCheckboxes 40 to 50 on six faceted composite .ra files (Epigenetics, TfChip, RnaSeq for both assemblies). refs #34923
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4TfChip.ra
  • lines changed 1, context: html, text, full: html, text
    6c1fba5815103be1d60cd33c12c30b1ec26f34b7 Wed May 20 14:55:34 2026 -0700
    ENCODE4 Regulation Epigenetics (Indiv.) description page updates (hg38 and mm10): added Available Organs and Tissues table, inline assay colors in Description bullets, dropped color legend paragraph. Also raised maxCheckboxes 40 to 50 on six faceted composite .ra files (Epigenetics, TfChip, RnaSeq for both assemblies). refs #34923
• src/hg/makeDb/trackDb/human/hgdp1kFreq.html
  • lines changed 8, context: html, text, full: html, text
    9bfd58221b1539193cb7f0a317b4e959c1c7e49a Thu May 21 01:00:45 2026 -0700
    varFreqs: AI generated text sounds bad, hard to read, so remove typical AI language. "humanizer" pass on all 31 varFreqs description pages — cut em dashes, copula avoidance ("serves as", "stands as"), "-ing" puffery, and boilerplate filler ("We provide documentation that indicates how..."). Title-case headings and meaningful <b> emphasis preserved. No facts/URLs/counts/versions changed. tpmi.html added as a new file (was previously uncommitted). refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hrc.html
  • lines changed 4, context: html, text, full: html, text
    9bfd58221b1539193cb7f0a317b4e959c1c7e49a Thu May 21 01:00:45 2026 -0700
    varFreqs: AI generated text sounds bad, hard to read, so remove typical AI language. "humanizer" pass on all 31 varFreqs description pages — cut em dashes, copula avoidance ("serves as", "stands as"), "-ing" puffery, and boilerplate filler ("We provide documentation that indicates how..."). Title-case headings and meaningful <b> emphasis preserved. No facts/URLs/counts/versions changed. tpmi.html added as a new file (was previously uncommitted). refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hs1/html/varFreqs.html
  • lines changed 25, context: html, text, full: html, text
    57c0c8dd69163aac91d9aa7ad7d301baf6feb584 Mon May 18 08:20:26 2026 -0700
    varFreqs: enable SweGen swefreq subtrack on hs1 with CHM13-specific supertrack description page, refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hs1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    57c0c8dd69163aac91d9aa7ad7d301baf6feb584 Mon May 18 08:20:26 2026 -0700
    varFreqs: enable SweGen swefreq subtrack on hs1 with CHM13-specific supertrack description page, refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hs1/varFreqs.ra
  • lines changed 2, context: html, text, full: html, text
    57c0c8dd69163aac91d9aa7ad7d301baf6feb584 Mon May 18 08:20:26 2026 -0700
    varFreqs: enable SweGen swefreq subtrack on hs1 with CHM13-specific supertrack description page, refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hs1/vgp577way.trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    ab3163d7361d2f7bcf7beb522cd947f691196bf5 Wed May 20 21:17:25 2026 -0700
    move the bigBed and bigWig files to hgdownload refs #31811
• src/hg/makeDb/trackDb/human/indigenomes.html
  • lines changed 3, context: html, text, full: html, text
    9bfd58221b1539193cb7f0a317b4e959c1c7e49a Thu May 21 01:00:45 2026 -0700
    varFreqs: AI generated text sounds bad, hard to read, so remove typical AI language. "humanizer" pass on all 31 varFreqs description pages — cut em dashes, copula avoidance ("serves as", "stands as"), "-ing" puffery, and boilerplate filler ("We provide documentation that indicates how..."). Title-case headings and meaningful <b> emphasis preserved. No facts/URLs/counts/versions changed. tpmi.html added as a new file (was previously uncommitted). refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/kova.html
  • lines changed 12, context: html, text, full: html, text
    9bfd58221b1539193cb7f0a317b4e959c1c7e49a Thu May 21 01:00:45 2026 -0700
    varFreqs: AI generated text sounds bad, hard to read, so remove typical AI language. "humanizer" pass on all 31 varFreqs description pages — cut em dashes, copula avoidance ("serves as", "stands as"), "-ing" puffery, and boilerplate filler ("We provide documentation that indicates how..."). Title-case headings and meaningful <b> emphasis preserved. No facts/URLs/counts/versions changed. tpmi.html added as a new file (was previously uncommitted). refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/mgrb.html
  • lines changed 9, context: html, text, full: html, text
    9bfd58221b1539193cb7f0a317b4e959c1c7e49a Thu May 21 01:00:45 2026 -0700
    varFreqs: AI generated text sounds bad, hard to read, so remove typical AI language. "humanizer" pass on all 31 varFreqs description pages — cut em dashes, copula avoidance ("serves as", "stands as"), "-ing" puffery, and boilerplate filler ("We provide documentation that indicates how..."). Title-case headings and meaningful <b> emphasis preserved. No facts/URLs/counts/versions changed. tpmi.html added as a new file (was previously uncommitted). refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/mxbFreq.html
  • lines changed 5, context: html, text, full: html, text
    9bfd58221b1539193cb7f0a317b4e959c1c7e49a Thu May 21 01:00:45 2026 -0700
    varFreqs: AI generated text sounds bad, hard to read, so remove typical AI language. "humanizer" pass on all 31 varFreqs description pages — cut em dashes, copula avoidance ("serves as", "stands as"), "-ing" puffery, and boilerplate filler ("We provide documentation that indicates how..."). Title-case headings and meaningful <b> emphasis preserved. No facts/URLs/counts/versions changed. tpmi.html added as a new file (was previously uncommitted). refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/npm.html
  • lines changed 8, context: html, text, full: html, text
    9bfd58221b1539193cb7f0a317b4e959c1c7e49a Thu May 21 01:00:45 2026 -0700
    varFreqs: AI generated text sounds bad, hard to read, so remove typical AI language. "humanizer" pass on all 31 varFreqs description pages — cut em dashes, copula avoidance ("serves as", "stands as"), "-ing" puffery, and boilerplate filler ("We provide documentation that indicates how..."). Title-case headings and meaningful <b> emphasis preserved. No facts/URLs/counts/versions changed. tpmi.html added as a new file (was previously uncommitted). refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/saudi.html
  • lines changed 4, context: html, text, full: html, text
    9bfd58221b1539193cb7f0a317b4e959c1c7e49a Thu May 21 01:00:45 2026 -0700
    varFreqs: AI generated text sounds bad, hard to read, so remove typical AI language. "humanizer" pass on all 31 varFreqs description pages — cut em dashes, copula avoidance ("serves as", "stands as"), "-ing" puffery, and boilerplate filler ("We provide documentation that indicates how..."). Title-case headings and meaningful <b> emphasis preserved. No facts/URLs/counts/versions changed. tpmi.html added as a new file (was previously uncommitted). refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/schema.html
  • lines changed 1, context: html, text, full: html, text
    9bfd58221b1539193cb7f0a317b4e959c1c7e49a Thu May 21 01:00:45 2026 -0700
    varFreqs: AI generated text sounds bad, hard to read, so remove typical AI language. "humanizer" pass on all 31 varFreqs description pages — cut em dashes, copula avoidance ("serves as", "stands as"), "-ing" puffery, and boilerplate filler ("We provide documentation that indicates how..."). Title-case headings and meaningful <b> emphasis preserved. No facts/URLs/counts/versions changed. tpmi.html added as a new file (was previously uncommitted). refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/sfariSparkExomes.html
  • lines changed 1, context: html, text, full: html, text
    9bfd58221b1539193cb7f0a317b4e959c1c7e49a Thu May 21 01:00:45 2026 -0700
    varFreqs: AI generated text sounds bad, hard to read, so remove typical AI language. "humanizer" pass on all 31 varFreqs description pages — cut em dashes, copula avoidance ("serves as", "stands as"), "-ing" puffery, and boilerplate filler ("We provide documentation that indicates how..."). Title-case headings and meaningful <b> emphasis preserved. No facts/URLs/counts/versions changed. tpmi.html added as a new file (was previously uncommitted). refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/sgdpFreq.html
  • lines changed 5, context: html, text, full: html, text
    9bfd58221b1539193cb7f0a317b4e959c1c7e49a Thu May 21 01:00:45 2026 -0700
    varFreqs: AI generated text sounds bad, hard to read, so remove typical AI language. "humanizer" pass on all 31 varFreqs description pages — cut em dashes, copula avoidance ("serves as", "stands as"), "-ing" puffery, and boilerplate filler ("We provide documentation that indicates how..."). Title-case headings and meaningful <b> emphasis preserved. No facts/URLs/counts/versions changed. tpmi.html added as a new file (was previously uncommitted). refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/svatalogSnv.html
  • lines changed 4, context: html, text, full: html, text
    9bfd58221b1539193cb7f0a317b4e959c1c7e49a Thu May 21 01:00:45 2026 -0700
    varFreqs: AI generated text sounds bad, hard to read, so remove typical AI language. "humanizer" pass on all 31 varFreqs description pages — cut em dashes, copula avoidance ("serves as", "stands as"), "-ing" puffery, and boilerplate filler ("We provide documentation that indicates how..."). Title-case headings and meaningful <b> emphasis preserved. No facts/URLs/counts/versions changed. tpmi.html added as a new file (was previously uncommitted). refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/swefreq.html
  • lines changed 3, context: html, text, full: html, text
    9bfd58221b1539193cb7f0a317b4e959c1c7e49a Thu May 21 01:00:45 2026 -0700
    varFreqs: AI generated text sounds bad, hard to read, so remove typical AI language. "humanizer" pass on all 31 varFreqs description pages — cut em dashes, copula avoidance ("serves as", "stands as"), "-ing" puffery, and boilerplate filler ("We provide documentation that indicates how..."). Title-case headings and meaningful <b> emphasis preserved. No facts/URLs/counts/versions changed. tpmi.html added as a new file (was previously uncommitted). refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/tishkoff180.html
  • lines changed 3, context: html, text, full: html, text
    9bfd58221b1539193cb7f0a317b4e959c1c7e49a Thu May 21 01:00:45 2026 -0700
    varFreqs: AI generated text sounds bad, hard to read, so remove typical AI language. "humanizer" pass on all 31 varFreqs description pages — cut em dashes, copula avoidance ("serves as", "stands as"), "-ing" puffery, and boilerplate filler ("We provide documentation that indicates how..."). Title-case headings and meaningful <b> emphasis preserved. No facts/URLs/counts/versions changed. tpmi.html added as a new file (was previously uncommitted). refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/tommo60kjpn.html
  • lines changed 3, context: html, text, full: html, text
    9bfd58221b1539193cb7f0a317b4e959c1c7e49a Thu May 21 01:00:45 2026 -0700
    varFreqs: AI generated text sounds bad, hard to read, so remove typical AI language. "humanizer" pass on all 31 varFreqs description pages — cut em dashes, copula avoidance ("serves as", "stands as"), "-ing" puffery, and boilerplate filler ("We provide documentation that indicates how..."). Title-case headings and meaningful <b> emphasis preserved. No facts/URLs/counts/versions changed. tpmi.html added as a new file (was previously uncommitted). refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/topmed.html
  • lines changed 1, context: html, text, full: html, text
    9bfd58221b1539193cb7f0a317b4e959c1c7e49a Thu May 21 01:00:45 2026 -0700
    varFreqs: AI generated text sounds bad, hard to read, so remove typical AI language. "humanizer" pass on all 31 varFreqs description pages — cut em dashes, copula avoidance ("serves as", "stands as"), "-ing" puffery, and boilerplate filler ("We provide documentation that indicates how..."). Title-case headings and meaningful <b> emphasis preserved. No facts/URLs/counts/versions changed. tpmi.html added as a new file (was previously uncommitted). refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/tpmi.html
  • lines changed 135, context: html, text, full: html, text
    9bfd58221b1539193cb7f0a317b4e959c1c7e49a Thu May 21 01:00:45 2026 -0700
    varFreqs: AI generated text sounds bad, hard to read, so remove typical AI language. "humanizer" pass on all 31 varFreqs description pages — cut em dashes, copula avoidance ("serves as", "stands as"), "-ing" puffery, and boilerplate filler ("We provide documentation that indicates how..."). Title-case headings and meaningful <b> emphasis preserved. No facts/URLs/counts/versions changed. tpmi.html added as a new file (was previously uncommitted). refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/ukbb.html
  • lines changed 6, context: html, text, full: html, text
    9bfd58221b1539193cb7f0a317b4e959c1c7e49a Thu May 21 01:00:45 2026 -0700
    varFreqs: AI generated text sounds bad, hard to read, so remove typical AI language. "humanizer" pass on all 31 varFreqs description pages — cut em dashes, copula avoidance ("serves as", "stands as"), "-ing" puffery, and boilerplate filler ("We provide documentation that indicates how..."). Title-case headings and meaningful <b> emphasis preserved. No facts/URLs/counts/versions changed. tpmi.html added as a new file (was previously uncommitted). refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/varFreqs.html
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    9bfd58221b1539193cb7f0a317b4e959c1c7e49a Thu May 21 01:00:45 2026 -0700
    varFreqs: AI generated text sounds bad, hard to read, so remove typical AI language. "humanizer" pass on all 31 varFreqs description pages — cut em dashes, copula avoidance ("serves as", "stands as"), "-ing" puffery, and boilerplate filler ("We provide documentation that indicates how..."). Title-case headings and meaningful <b> emphasis preserved. No facts/URLs/counts/versions changed. tpmi.html added as a new file (was previously uncommitted). refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/varFreqs.ra
  • lines changed 41, context: html, text, full: html, text
    af9d8fe39e88f7b7cec3792ea797dab44f1416b0 Tue May 19 04:36:02 2026 -0700
    varFreqs: rebuild varFreqsAll with WBBC/TPMI/ChinaMAP/GenomeIndia, drop IndiGen, harden build pipeline Rebuilds /gbdb/hg38/varFreqs/_all/varFreqsAll.bb to fold in the four new subtracks registered earlier in May (WBBC 78.6M, TPMI 672k, ChinaMAP 147M, GenomeIndia 130M) and to drop IndiGen, which ships only a VRT bit and contributed an always-empty AC/AF column. New bb is 47 GB / 147 fields / 1.34 billion items (was 44 GB / 133 / 1.22B). Two pipeline fixes were necessary mid-rebuild: - bcftools 1.22 csq is stricter than earlier versions. Added --unify-chr-names chr,-,chr (Ensembl GFF3 uses bare "1" while merged VCF + FASTA use "chr1") and --force (5 SCHEMA alt contigs end up in the merge but aren't annotated in the GFF3) to the csq invocation in mergeAndAnnotate.sh. Four follow-up cleanups to the build scripts (no track change, just safer next rebuild): - mergeAndAnnotate.sh now reads VCF paths directly from databases.tsv in both the per-VCF strip+norm step and the merge step. The previous "files.txt + find normalized/" model could silently re-merge stale norm cache entries after a database was dropped from databases.tsv. - vcfToBigBed.py concat step streams sort stdout straight to disk instead of capture_output=True, which buffered the whole sorted chromosome (~24 GB for chr1) in Python RAM. - vcfToBigBed.py generate_trackdb_fragment() now emits the three customizations that used to have to be added on top of the auto-fragment by hand: filterType.consequence multipleListOr, the expanded consequence buckets (3_prime_utr, 5_prime_utr, non_coding, others), and skipEmptyFields on. - trackDb/human/varFreqs.ra updated to match the new bb columns (WBBC/TPMI/ChinaMAP/GenomeIndia AC+AF filters, WBBC 4-region population filters, IndiGen filter removed). refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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    0ef7d0ffeea25371b4828fc23051cdd27598439f Wed May 20 14:57:51 2026 -0700
    varFreqs: add Genome of the Netherlands (GoNL) subtrack on hg38, GRCh38 re-analysis v1.0, 498 unrelated parents (250 fathers + 248 mothers), 36.4M biallelic records after dropping decoy/EBV contigs and bcftools norm split+left-align, refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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    5c88f2b10f443d95e3f9c8e4bbc81534b78d9222 Thu May 21 00:40:38 2026 -0700
    varFreqs: rename supertrack to "SNV Frequencies"; add GoNL (Netherlands, ~13x SR) to databases.tsv and to the varFreqsAll filter UI so the next combined-track rebuild picks it up. refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/varFreqsAll.html
  • lines changed 7, context: html, text, full: html, text
    9bfd58221b1539193cb7f0a317b4e959c1c7e49a Thu May 21 01:00:45 2026 -0700
    varFreqs: AI generated text sounds bad, hard to read, so remove typical AI language. "humanizer" pass on all 31 varFreqs description pages — cut em dashes, copula avoidance ("serves as", "stands as"), "-ing" puffery, and boilerplate filler ("We provide documentation that indicates how..."). Title-case headings and meaningful <b> emphasis preserved. No facts/URLs/counts/versions changed. tpmi.html added as a new file (was previously uncommitted). refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/wbbc.html
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    9bfd58221b1539193cb7f0a317b4e959c1c7e49a Thu May 21 01:00:45 2026 -0700
    varFreqs: AI generated text sounds bad, hard to read, so remove typical AI language. "humanizer" pass on all 31 varFreqs description pages — cut em dashes, copula avoidance ("serves as", "stands as"), "-ing" puffery, and boilerplate filler ("We provide documentation that indicates how..."). Title-case headings and meaningful <b> emphasis preserved. No facts/URLs/counts/versions changed. tpmi.html added as a new file (was previously uncommitted). refs #36642 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.html
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    6c1fba5815103be1d60cd33c12c30b1ec26f34b7 Wed May 20 14:55:34 2026 -0700
    ENCODE4 Regulation Epigenetics (Indiv.) description page updates (hg38 and mm10): added Available Organs and Tissues table, inline assay colors in Description bullets, dropped color legend paragraph. Also raised maxCheckboxes 40 to 50 on six faceted composite .ra files (Epigenetics, TfChip, RnaSeq for both assemblies). refs #34923
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegEpigenetics.ra
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    6c1fba5815103be1d60cd33c12c30b1ec26f34b7 Wed May 20 14:55:34 2026 -0700
    ENCODE4 Regulation Epigenetics (Indiv.) description page updates (hg38 and mm10): added Available Organs and Tissues table, inline assay colors in Description bullets, dropped color legend paragraph. Also raised maxCheckboxes 40 to 50 on six faceted composite .ra files (Epigenetics, TfChip, RnaSeq for both assemblies). refs #34923
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegRnaSeq.ra
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    6c1fba5815103be1d60cd33c12c30b1ec26f34b7 Wed May 20 14:55:34 2026 -0700
    ENCODE4 Regulation Epigenetics (Indiv.) description page updates (hg38 and mm10): added Available Organs and Tissues table, inline assay colors in Description bullets, dropped color legend paragraph. Also raised maxCheckboxes 40 to 50 on six faceted composite .ra files (Epigenetics, TfChip, RnaSeq for both assemblies). refs #34923
• src/hg/makeDb/trackDb/mouse/mm10/encode4RegTfChip.ra
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    6c1fba5815103be1d60cd33c12c30b1ec26f34b7 Wed May 20 14:55:34 2026 -0700
    ENCODE4 Regulation Epigenetics (Indiv.) description page updates (hg38 and mm10): added Available Organs and Tissues table, inline assay colors in Description bullets, dropped color legend paragraph. Also raised maxCheckboxes 40 to 50 on six faceted composite .ra files (Epigenetics, TfChip, RnaSeq for both assemblies). refs #34923
• src/hg/makeDb/trackDb/mouse/mm10/mouseDevTimecourse.ra
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    c9a1cccc385263cc62a9e3a4af30481fbf8e9158 Sat May 23 15:35:44 2026 -0700
    Per author request, updated the mouseDevTimecourse subtrack longLabels and added the He et al. 2020 Nature paper to the references. refs #37001
• src/hg/makeDb/trackDb/mouse/mm39/mouseDevTimecourse.ra
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    c9a1cccc385263cc62a9e3a4af30481fbf8e9158 Sat May 23 15:35:44 2026 -0700
    Per author request, updated the mouseDevTimecourse subtrack longLabels and added the He et al. 2020 Nature paper to the references. refs #37001
• src/hg/makeDb/trackDb/mouse/mm39/vgp577way.trackDb.ra
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    ab3163d7361d2f7bcf7beb522cd947f691196bf5 Wed May 20 21:17:25 2026 -0700
    move the bigBed and bigWig files to hgdownload refs #31811
• src/hg/makeDb/trackDb/mouseDevTimecourseCreditsAndReferences.shared.html
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    c9a1cccc385263cc62a9e3a4af30481fbf8e9158 Sat May 23 15:35:44 2026 -0700
    Per author request, updated the mouseDevTimecourse subtrack longLabels and added the He et al. 2020 Nature paper to the references. refs #37001
• src/hg/makeDb/trackDb/mouseDevTimecourseDisplay.shared.html
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    4eb8ce4c1204debcf7cf81f1de5af5a3dd9343d3 Fri May 22 17:27:25 2026 -0700
    The author requested updating the per-tissue colors to gradients. Updated the mouseDevTimecourse legend HTML to match the new colors and documented the data file update in the mm10 and mm39 makedocs. refs #37001
• src/hg/makeDb/trackDb/publicGenArk.txt
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    a1ca00e26cc02777d80ab7b1e1c9c87d14a249eb Sat May 23 08:55:38 2026 -0700
    allow vgp577way HPRCv2 and lowelab to become official public tracks
• src/hg/utils/automation/asmHubChainNetTrackDb.sh
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    ab84356e6829bc2a0d2939f232dadb6acdd92e2f Thu May 21 15:35:01 2026 -0700
    correctly get the "query" short and longLabel in the track statement refs #37380
• src/hg/utils/automation/asmHubTOGA.pl
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    55d9b1b7504ff9c43ad1173ae981a27d9212d773 Thu May 21 11:48:01 2026 -0700
    cron job safe full path names to kent commands refs #31811
• src/hg/utils/otto/userRequests/ottoLib.py
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    6ddaedca96e314bcd1607e69bcfa8fb228d22a3c Thu May 21 21:53:56 2026 -0700
    common functions moved to ottoLib.py and shared with ottoBuildGenArkHub.py and fixup the legacy clade situation refs #31811
• src/hg/utils/otto/userRequests/ottoRequestPush.py
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    cff0574d507c40d5bd01f091ccf8edf75ef5e892 Thu May 21 19:33:26 2026 -0700
    need to receive error message in cron stderr when something does not push correctly refs #31811
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    b82f144c8a3db1f34a7ffb2d453515b76bb84bd7 Thu May 21 19:41:57 2026 -0700
    must run as umask 002 while making files to avoid write permissions by other users in our group refs #31811
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    6ddaedca96e314bcd1607e69bcfa8fb228d22a3c Thu May 21 21:53:56 2026 -0700
    common functions moved to ottoLib.py and shared with ottoBuildGenArkHub.py and fixup the legacy clade situation refs #31811
• src/hg/utils/otto/userRequests/ottoRequestView.cgi
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    b8c37065aeee89c5c9d074112afe9351dd72a3ad Thu May 21 19:56:22 2026 -0700
    show the cron times in the page refs #31811
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    785e9cccf3daee25d9e7c2fcfd0284b68323374d Sat May 23 18:20:53 2026 -0700
    add the otto user cron tab times refs #31811
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    9e84b6fc13d60a1beb638f18050cb1fed5835410 Sun May 24 12:04:05 2026 -0700
    add a "hide/show completed" toggle and no longer need to protect via VPN IP with .htaccess now refs #31811
• src/hg/utils/otto/userRequests/ottoRequestWatch.sh
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    70e3a28ad9458ae12f69bf99db04ad4d3e857792 Thu May 21 10:18:45 2026 -0700
    send failed doTrackDb logs to stderr email to cron refs #31811
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    19f16e7908a8bca3aedae90340d499bce4ae8535 Thu May 21 11:48:50 2026 -0700
    reentrant save log files for the doTrackDb steps refs #31811
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    8f801f0b7d0b28d3adbc5f26fc7cb8976ac2830f Fri May 22 13:48:48 2026 -0700
    add the featureBits measurements to the user notification email refs #31811
• src/hg/utils/otto/userRequests/verifyChainTables.py
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    9fac381fd49318efc76d205caddc9e3146b8541e Thu May 21 11:51:06 2026 -0700
    housekeeping script to verify liftOverChain and quickLiftChain tables are in synchronization - they should have the same pairs of fromDb and toDb refs #31811
• src/utils/hubtools/hubtools
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    03a7221f2973a860ee4363183fc5c582ce0d6178 Tue May 19 10:25:26 2026 -0700
    tons of changes to hubtools, committing now for chris
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    cc99fd8cda2d90b8f6fd95b2f926fc19704d0a90 Fri May 22 13:33:25 2026 -0700
    hubtools: fix upload to match hubspace hooks, add to user-apps, refs #36790 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/utils/makefile
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    cc99fd8cda2d90b8f6fd95b2f926fc19704d0a90 Fri May 22 13:33:25 2026 -0700
    hubtools: fix upload to match hubspace hooks, add to user-apps, refs #36790 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/utils/qa/quickLiftBench/cases.yaml
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    a92eac84f90b5eea841e25edcb8398f6183cf591 Fri May 22 15:29:39 2026 -0700
    quickLiftBench: add Mode A case (hgwbeta saved-session pair), refs #37445 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
• src/utils/redmineCli
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    7fbdfb4c6e5566f9590c6e8ab9ddbd723d329a45 Mon May 18 13:17:51 2026 -0700
    redmineCli: add --private flag to comment/update/attach for Redmine private notes. refs #37281

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