Commits for jcasper

v503_preview2 to v503_base (2026-08-24 to 2026-08-31) v503

40288931d6f7e083f7b71fd97109c03d9916bc30 Thu Aug 27 09:30:25 2026 -0700

• When memalloc fails, it calls errAbort. But if the handler is a sophisticated one, it might try to call memalloc itself, resulting in an endless loop. Better to nip that in the bud. no ticket
  • src/lib/memalloc.c - lines changed 11, context: html, text, full: html, text

ec1a4ee046073ffbd5fcf929a6bc33ea514171a2 Thu Aug 27 14:00:52 2026 -0700

• Fixing an outdated cse server reference to point to soe, no ticket
  • build/kent-core/README.md - lines changed 1, context: html, text, full: html, text

f04f1b9af06c823602c5e0ecd3b8c2059d7704d3 Thu Aug 27 14:42:31 2026 -0700

• Faceted composites now have a max display mode setting instead of a full override of child track visibilities, with accompanying support for the onlyVisibility setting. We also now include a filter block (applied to appropriate child tracks) when those settings are in place. refs #37662
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 50, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c - lines changed 32, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c - lines changed 8, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html - lines changed 12, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html - lines changed 3, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml - lines changed 60, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.json - lines changed 15, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.yaml - lines changed 37, context: html, text, full: html, text
  • src/hg/inc/hui.h - lines changed 4, context: html, text, full: html, text
  • src/hg/inc/trackDb.h - lines changed 4, context: html, text, full: html, text
  • src/hg/js/facetedComposite.js - lines changed 7, context: html, text, full: html, text
  • src/hg/lib/cart.c - lines changed 7, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 62, context: html, text, full: html, text
  • src/hg/lib/trackDbCustom.c - lines changed 9, context: html, text, full: html, text

8a2bdd70e7d5e3dd44c68f679e12e9bfe9264f6c Thu Aug 27 14:51:29 2026 -0700

• TrackDb settings for MethBase 2 DNA Methylation tracks on 31 assemblies, refs #36320
  • src/hg/makeDb/trackDb/apis/apiMel2/dnaMethylation.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/apis/apiMel2/mb2_apiMel2_colors.json - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/apis/apiMel2/mb2_apiMel2_metadata.tsv - lines changed 211, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/apis/apiMel2/methbase2.ra - lines changed 7993, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/apis/apiMel2/trackDb.ra - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/calMil/calMil1/dnaMethylation.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/calMil/calMil1/mb2_calMil1_colors.json - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/calMil/calMil1/mb2_calMil1_metadata.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/calMil/calMil1/methbase2.ra - lines changed 51, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/calMil/calMil1/trackDb.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cat/felCat9/dnaMethylation.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cat/felCat9/mb2_felCat9_colors.json - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cat/felCat9/mb2_felCat9_metadata.tsv - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cat/felCat9/methbase2.ra - lines changed 355, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cat/felCat9/trackDb.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chicken/galGal6/dnaMethylation.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chicken/galGal6/mb2_galGal6_colors.json - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chicken/galGal6/mb2_galGal6_metadata.tsv - lines changed 284, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chicken/galGal6/methbase2.ra - lines changed 10757, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chicken/galGal6/trackDb.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro6/dnaMethylation.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro6/mb2_panTro6_colors.json - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro6/mb2_panTro6_metadata.tsv - lines changed 60, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro6/methbase2.ra - lines changed 2255, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro6/trackDb.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau9/dnaMethylation.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau9/mb2_bosTau9_colors.json - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau9/mb2_bosTau9_metadata.tsv - lines changed 589, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau9/methbase2.ra - lines changed 22217, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau9/trackDb.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dog/canFam6/dnaMethylation.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dog/canFam6/mb2_canFam6_colors.json - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dog/canFam6/mb2_canFam6_metadata.tsv - lines changed 146, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dog/canFam6/methbase2.ra - lines changed 5523, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dog/canFam6/trackDb.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dolphin/turTru2/dnaMethylation.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dolphin/turTru2/mb2_turTru2_colors.json - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dolphin/turTru2/mb2_turTru2_metadata.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dolphin/turTru2/methbase2.ra - lines changed 51, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dolphin/turTru2/trackDb.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/fugu/fr3/dnaMethylation.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/fugu/fr3/mb2_fr3_colors.json - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/fugu/fr3/mb2_fr3_metadata.tsv - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/fugu/fr3/methbase2.ra - lines changed 583, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/fugu/fr3/trackDb.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gibbon/nomLeu3/dnaMethylation.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gibbon/nomLeu3/mb2_nomLeu3_colors.json - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gibbon/nomLeu3/mb2_nomLeu3_metadata.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gibbon/nomLeu3/methbase2.ra - lines changed 51, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gibbon/nomLeu3/trackDb.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gorilla/gorGor6/dnaMethylation.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gorilla/gorGor6/mb2_gorGor6_colors.json - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gorilla/gorGor6/mb2_gorGor6_metadata.tsv - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gorilla/gorGor6/methbase2.ra - lines changed 241, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gorilla/gorGor6/trackDb.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/horse/equCab3/dnaMethylation.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/horse/equCab3/mb2_equCab3_colors.json - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/horse/equCab3/mb2_equCab3_metadata.tsv - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/horse/equCab3/methbase2.ra - lines changed 127, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/horse/equCab3/trackDb.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/mb2_hg38_colors.json - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/mb2_hg38_metadata.tsv - lines changed 6512, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/methbase2.ra - lines changed 102046, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/methbase2_2.ra - lines changed 102565, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/methbase2_3.ra - lines changed 41953, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/macaca/macFas5/dnaMethylation.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/macaca/macFas5/mb2_macFas5_colors.json - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/macaca/macFas5/mb2_macFas5_metadata.tsv - lines changed 35, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/macaca/macFas5/methbase2.ra - lines changed 1295, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/macaca/macFas5/trackDb.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/medaka/oryLat2/dnaMethylation.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/medaka/oryLat2/mb2_oryLat2_colors.json - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/medaka/oryLat2/mb2_oryLat2_metadata.tsv - lines changed 23, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/medaka/oryLat2/methbase2.ra - lines changed 849, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/medaka/oryLat2/trackDb.ra - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/dnaMethylation.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/mb2_mm39_colors.json - lines changed 24, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/mb2_mm39_metadata.tsv - lines changed 6648, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/methbase2.ra - lines changed 103253, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/methbase2_2.ra - lines changed 102229, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/methbase2_3.ra - lines changed 45349, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/opossum/monDom5/dnaMethylation.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/opossum/monDom5/mb2_monDom5_colors.json - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/opossum/monDom5/mb2_monDom5_metadata.tsv - lines changed 45, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/opossum/monDom5/methbase2.ra - lines changed 1685, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/opossum/monDom5/trackDb.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/orangutan/ponAbe3/dnaMethylation.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/orangutan/ponAbe3/mb2_ponAbe3_colors.json - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/orangutan/ponAbe3/mb2_ponAbe3_metadata.tsv - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/orangutan/ponAbe3/methbase2.ra - lines changed 127, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/orangutan/ponAbe3/trackDb.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/panda/ailMel1/dnaMethylation.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/panda/ailMel1/mb2_ailMel1_colors.json - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/panda/ailMel1/mb2_ailMel1_metadata.tsv - lines changed 4, context: html, text, full: html, text
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  • src/hg/makeDb/trackDb/panda/ailMel1/trackDb.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/pig/susScr11/dnaMethylation.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/pig/susScr11/mb2_susScr11_colors.json - lines changed 24, context: html, text, full: html, text
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  • src/hg/makeDb/trackDb/platypus/ornAna2/dnaMethylation.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/platypus/ornAna2/mb2_ornAna2_colors.json - lines changed 5, context: html, text, full: html, text
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  • src/hg/makeDb/trackDb/rabbit/oryCun2/dnaMethylation.html - lines changed 4, context: html, text, full: html, text
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  • src/hg/makeDb/trackDb/rat/rn7/dnaMethylation.html - lines changed 4, context: html, text, full: html, text
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  • src/hg/makeDb/trackDb/rhesus/rheMac10/dnaMethylation.html - lines changed 4, context: html, text, full: html, text
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  • src/hg/makeDb/trackDb/sheep/oviAri4/dnaMethylation.html - lines changed 4, context: html, text, full: html, text
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  • src/hg/makeDb/trackDb/zebraFinch/taeGut2/dnaMethylation.html - lines changed 4, context: html, text, full: html, text
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  • src/hg/makeDb/trackDb/zebrafish/danRer11/dnaMethylation.html - lines changed 4, context: html, text, full: html, text
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53dff34f95bdea27e7747c8bcecb03a7ae45bdfd Thu Aug 27 14:58:41 2026 -0700

• Whoops, ensuring the MethBase2 stuff is set to alpha, and doesn't escape before review. refs #36320
  • src/hg/makeDb/trackDb/apis/apiMel2/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/calMil/calMil1/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cat/felCat9/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chicken/galGal6/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro6/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau9/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dog/canFam6/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dolphin/turTru2/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/fugu/fr3/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gibbon/nomLeu3/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gorilla/gorGor6/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/horse/equCab3/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/macaca/macFas5/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/medaka/oryLat2/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/opossum/monDom5/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/orangutan/ponAbe3/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/panda/ailMel1/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/pig/susScr11/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/platypus/ornAna2/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rabbit/oryCun2/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn7/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/rheMac10/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/sheep/oviAri4/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/stickleback/gasAcu1/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tetraodon/tetNig2/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/urchin/strPur2/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/xenTro/xenTro10/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebraFinch/taeGut2/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer11/trackDb.ra - lines changed 1, context: html, text, full: html, text

e091f937cb2d73a65e02eb56d1175db12e77f40c Thu Aug 27 15:00:34 2026 -0700

• Removing older version of MethBase2 development, refs #36320
  • src/hg/makeDb/trackDb/human/hg38/mb2.ra - lines changed 74992, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 4, context: html, text, full: html, text

90b8f880be12956b899d973bc565bffdc9b7ce89 Fri Aug 28 08:27:13 2026 -0700

• Moving sort comment on the faceted composite UI, and ading a 'hide subtracks', refs #36320
  • src/hg/hgTrackUi/hgTrackUi.c - lines changed 2, context: html, text, full: html, text
  • src/hg/htdocs/style/facetedComposite.css - lines changed 12, context: html, text, full: html, text
  • src/hg/inc/hui.h - lines changed 4, context: html, text, full: html, text
  • src/hg/js/facetedComposite.js - lines changed 4, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 43, context: html, text, full: html, text

aceb6e9fb2694e5c5bd8c2518767a04fa8c0a300 Sun Aug 30 01:11:16 2026 -0700

• Installing updated hg.conf files from UCSC servers
  • confs/hgwbeta.hg.conf - lines changed 1, context: html, text, full: html, text
  • confs/hgwdev.hg.conf - lines changed 8, context: html, text, full: html, text