File Changes for lrnassar
switch to commits view, user indexv504_preview to v504_preview2 (2026-09-07 to 2026-09-14) v504
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- src/hg/hgBlat/hgBlat.c
- lines changed 10, context: html, text, full: html, text
595531f894a27e59e18b32436f6cb932fa4374a0 Tue Sep 8 13:03:44 2026 -0700
BLAT form character counter: per-type limits passed through from the C constants. refs #38293
The counter showed the 75,000 DNA limit for every query type; protein and translated queries
are capped at 10,000, so an oversized protein paste looked fine until the server rejected it.
The per-sequence limits are now named constants in hgBlat.c, emitted into hgBlatFormData and
read by the counter, which keys on the Query type dropdown and recounts when it changes -
so the numbers cannot drift apart again. BLAT's guess counts against the DNA limit.
- lines changed 2, context: html, text, full: html, text
c0a6706dea55f019923332c5f51dfe64fc420dc8 Wed Sep 9 12:15:27 2026 -0700
Comment touch-ups from CR: reattach delayFraction's continuation comment, drop an imprecise history aside in the counter comment. refs #38293
- src/hg/hgc/hgc.c
- lines changed 2, context: html, text, full: html, text
c1ac48b0feb9a8ff0f0bb16d7aff15d417d6772b Tue Sep 8 12:38:42 2026 -0700
Share dialog: scope the snapshot-lifetime wording to the BLAT alignment share only. Feedback from CR. refs #37996
The softer durability text (link valid for years, save into a Session for permanence) keyed
on the generic url mode, so hgTrackUi's page-share link and the hgc item-popup share, both
plain non-expiring URLs, showed misleading copy. The wording is now behind an explicit
snapshot flag that only the BLAT alignment page's share passes; every other caller keeps
"Links never time out". Also removes a stray blank line in hgc.c from the same review.
- src/hg/htdocs/data/recTrackSets/hg38/Clinical_SNVs_hg38
- lines changed 60, context: html, text, full: html, text
dfcf312ddc1c89afe3dd518d8383ed6c2dc913b1 Tue Sep 8 14:08:19 2026 -0700
Updating the hg38 Clinical SNVs recommended track set to add the NMD Escape MANE track in pack mode. Shifts the imgOrd of the following tracks by one to place NMD escape near the top. Also picks up hide settings for tracks added since the last update and renamed track IDs (cCREs, wgEncodeReg4, GencodeV50). No RM.
- src/hg/htdocs/goldenPath/newsarch.html
- lines changed 54, context: html, text, full: html, text
808c426eb279a17a5539731811f1deda6e783e1e Wed Sep 9 17:20:31 2026 -0700
Announcing the AlphaGenome Variant Impact (AVI) score track for hg38. refs #38261
Adds the Sept. 10 news archive entry with a figure of the AVI scores across the TERT
locus, and adds the item to the front page news list, dropping the Jul. 22 entry to
keep the list at six.
- src/hg/htdocs/images/newsArchImages/alphaGenome.png
- lines changed 0, context: html, text, full: html, text
808c426eb279a17a5539731811f1deda6e783e1e Wed Sep 9 17:20:31 2026 -0700
Announcing the AlphaGenome Variant Impact (AVI) score track for hg38. refs #38261
Adds the Sept. 10 news archive entry with a figure of the AVI scores across the TERT
locus, and adds the item to the front page news list, dropping the Jul. 22 entry to
keep the list at six.
- src/hg/htdocs/indexNews.html
- lines changed 12, context: html, text, full: html, text
808c426eb279a17a5539731811f1deda6e783e1e Wed Sep 9 17:20:31 2026 -0700
Announcing the AlphaGenome Variant Impact (AVI) score track for hg38. refs #38261
Adds the Sept. 10 news archive entry with a figure of the AVI scores across the TERT
locus, and adds the item to the front page news list, dropping the Jul. 22 entry to
keep the list at six.
- src/hg/htdocs/staticStyle/gbStatic.css
- lines changed 1, context: html, text, full: html, text
2941692d3e4198ba220b16c9b791c9090aa69fbc Wed Sep 9 17:20:31 2026 -0700
Reduce the font size of image captions on static pages so they read as distinct from
body text. No RM.
p.gbsCaption had no font-size, so captions rendered at the same size as body copy.
Note this is the copy of gbStatic.css under staticStyle/, which is the one the
gbPageStart includes load; the copy under style/ is not referenced by any page.
- src/hg/js/hgBlat.js
- lines changed 14, context: html, text, full: html, text
595531f894a27e59e18b32436f6cb932fa4374a0 Tue Sep 8 13:03:44 2026 -0700
BLAT form character counter: per-type limits passed through from the C constants. refs #38293
The counter showed the 75,000 DNA limit for every query type; protein and translated queries
are capped at 10,000, so an oversized protein paste looked fine until the server rejected it.
The per-sequence limits are now named constants in hgBlat.c, emitted into hgBlatFormData and
read by the counter, which keys on the Query type dropdown and recounts when it changes -
so the numbers cannot drift apart again. BLAT's guess counts against the DNA limit.
- lines changed 1, context: html, text, full: html, text
c0a6706dea55f019923332c5f51dfe64fc420dc8 Wed Sep 9 12:15:27 2026 -0700
Comment touch-ups from CR: reattach delayFraction's continuation comment, drop an imprecise history aside in the counter comment. refs #38293
- lines changed 2, context: html, text, full: html, text
e6eaaaa2b64a0ac14f17f5011f27f294d5287a23 Wed Sep 9 16:30:48 2026 -0700
Escape the ampersands in the BLAT share box and rename dialog hgSession hrefs. Feedback from CR. refs #38292
- src/hg/js/topLinks.js
- lines changed 6, context: html, text, full: html, text
c1ac48b0feb9a8ff0f0bb16d7aff15d417d6772b Tue Sep 8 12:38:42 2026 -0700
Share dialog: scope the snapshot-lifetime wording to the BLAT alignment share only. Feedback from CR. refs #37996
The softer durability text (link valid for years, save into a Session for permanence) keyed
on the generic url mode, so hgTrackUi's page-share link and the hgc item-popup share, both
plain non-expiring URLs, showed misleading copy. The wording is now behind an explicit
snapshot flag that only the BLAT alignment page's share passes; every other caller keeps
"Links never time out". Also removes a stray blank line in hgc.c from the same review.
- src/hg/makeDb/doc/hg38/alphaGenome.txt
- lines changed 10, context: html, text, full: html, text
3dd0329ee0e804f5841a9998c4e7f024d3276921 Wed Sep 9 17:20:20 2026 -0700
Releasing the AlphaGenome Variant Impact (AVI) score track for hg38. refs #38261
Moves the bigWigs to /gbdb/hg38/_alphaGenome/, the underscore convention that keeps
non-redistributable data off the download server, matching PromoterAI and PrimateAI,
and drops the alpha release tag.
Shortens the composite longLabel to fit the 85 character limit and lowercases Score
in the longLabels. Adds a New pennantIcon and points the Deleteriousness Predictions
container pennant at the Sept. 10 news post.
Corrects the median on the description page from 1.6 to 2.9. The old figure counted
the zero-filled reference base slots, which are not variants. Removes two threshold
statements that are not in the AlphaGenome Atlas preprint or any public source. Adds
the /gbdb symlink step to the makeDoc, and fixes three container page links that were
missing target=_blank.
- src/hg/makeDb/doc/mm10/mouseStrainsCactus.txt
- lines changed 79, context: html, text, full: html, text
efebc8a0a29aeef60bc470a40ced7a2aa6652efd Tue Sep 8 19:25:02 2026 -0700
Adding native mm10 track for the mouse strains Cactus alignment. refs #38308
New alpha-gated track mouseStrainsCactus exposing the Progressive Cactus
alignment of the 16 Mouse Genomes Project strain assemblies plus rat, which
until now was only reachable by attaching the mouseStrains assembly hub.
bigDataUrl, summary and frames point at the existing bigMaf files on
hgdownload rather than copying 8.8 GB into /gbdb, the same way the hg38
cactus241wayBM track is served.
Polish over the hub stanza: renamed from the generic "bigMaf", off by
default, speciesGroups splitting the strains into wild-derived, classical
laboratory and Rat/rn6, speciesLabels so side labels read 129S1/SvImJ
rather than 129S1_SvImJ, plus treeImage and speciesCodonDefault. The three
new sGroup_ tags are registered in tagTypes.tab.
Description page written from Lilue et al. 2018; the hub page had an empty
Description section and its Display Convention text was wigMaf boilerplate
that did not match this track. Also notes that the alignment is a poor
source for large rearrangements, since Ragout built the strain
pseudo-chromosomes against the reference and discarded most adjacencies
that disagreed with it.
Added a reciprocal relatedTracks.ra pair between this track and
mm10Strains1 ("Alternate strains"), since #38227 came in from a user who
kept landing on mm10Strains1 while looking for this alignment.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
- src/hg/makeDb/trackDb/human/alphaGenome.html
- lines changed 4, context: html, text, full: html, text
3dd0329ee0e804f5841a9998c4e7f024d3276921 Wed Sep 9 17:20:20 2026 -0700
Releasing the AlphaGenome Variant Impact (AVI) score track for hg38. refs #38261
Moves the bigWigs to /gbdb/hg38/_alphaGenome/, the underscore convention that keeps
non-redistributable data off the download server, matching PromoterAI and PrimateAI,
and drops the alpha release tag.
Shortens the composite longLabel to fit the 85 character limit and lowercases Score
in the longLabels. Adds a New pennantIcon and points the Deleteriousness Predictions
container pennant at the Sept. 10 news post.
Corrects the median on the description page from 1.6 to 2.9. The old figure counted
the zero-filled reference base slots, which are not variants. Removes two threshold
statements that are not in the AlphaGenome Atlas preprint or any public source. Adds
the /gbdb symlink step to the makeDoc, and fixes three container page links that were
missing target=_blank.
- src/hg/makeDb/trackDb/human/alphaGenome.ra
- lines changed 10, context: html, text, full: html, text
3dd0329ee0e804f5841a9998c4e7f024d3276921 Wed Sep 9 17:20:20 2026 -0700
Releasing the AlphaGenome Variant Impact (AVI) score track for hg38. refs #38261
Moves the bigWigs to /gbdb/hg38/_alphaGenome/, the underscore convention that keeps
non-redistributable data off the download server, matching PromoterAI and PrimateAI,
and drops the alpha release tag.
Shortens the composite longLabel to fit the 85 character limit and lowercases Score
in the longLabels. Adds a New pennantIcon and points the Deleteriousness Predictions
container pennant at the Sept. 10 news post.
Corrects the median on the description page from 1.6 to 2.9. The old figure counted
the zero-filled reference base slots, which are not variants. Removes two threshold
statements that are not in the AlphaGenome Atlas preprint or any public source. Adds
the /gbdb symlink step to the makeDoc, and fixes three container page links that were
missing target=_blank.
- src/hg/makeDb/trackDb/human/predictionScoresSuper.html
- lines changed 5, context: html, text, full: html, text
3dd0329ee0e804f5841a9998c4e7f024d3276921 Wed Sep 9 17:20:20 2026 -0700
Releasing the AlphaGenome Variant Impact (AVI) score track for hg38. refs #38261
Moves the bigWigs to /gbdb/hg38/_alphaGenome/, the underscore convention that keeps
non-redistributable data off the download server, matching PromoterAI and PrimateAI,
and drops the alpha release tag.
Shortens the composite longLabel to fit the 85 character limit and lowercases Score
in the longLabels. Adds a New pennantIcon and points the Deleteriousness Predictions
container pennant at the Sept. 10 news post.
Corrects the median on the description page from 1.6 to 2.9. The old figure counted
the zero-filled reference base slots, which are not variants. Removes two threshold
statements that are not in the AlphaGenome Atlas preprint or any public source. Adds
the /gbdb symlink step to the makeDoc, and fixes three container page links that were
missing target=_blank.
- src/hg/makeDb/trackDb/human/predictionScoresSuper.ra
- lines changed 2, context: html, text, full: html, text
3dd0329ee0e804f5841a9998c4e7f024d3276921 Wed Sep 9 17:20:20 2026 -0700
Releasing the AlphaGenome Variant Impact (AVI) score track for hg38. refs #38261
Moves the bigWigs to /gbdb/hg38/_alphaGenome/, the underscore convention that keeps
non-redistributable data off the download server, matching PromoterAI and PrimateAI,
and drops the alpha release tag.
Shortens the composite longLabel to fit the 85 character limit and lowercases Score
in the longLabels. Adds a New pennantIcon and points the Deleteriousness Predictions
container pennant at the Sept. 10 news post.
Corrects the median on the description page from 1.6 to 2.9. The old figure counted
the zero-filled reference base slots, which are not variants. Removes two threshold
statements that are not in the AlphaGenome Atlas preprint or any public source. Adds
the /gbdb symlink step to the makeDoc, and fixes three container page links that were
missing target=_blank.
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 1, context: html, text, full: html, text
74bea0582059450e508b0f69a6b70c072ac1d3a2 Wed Sep 9 16:29:28 2026 -0700
List the newest deprecated transcript first for a deprecated NP_ search, per CR feedback.
When a superseded protein accession maps to several deprecated transcript
versions, the search returns all of them, but they were listed in table order so
the oldest came first. Order the xrefQuery newest-first, matching the choice the
HGVS protein path already makes. Sort by length before value so .10 beats .9
rather than losing a string comparison. refs #38292
- src/hg/makeDb/trackDb/mouse/mm10/mouseStrainsCactus.html
- lines changed 236, context: html, text, full: html, text
efebc8a0a29aeef60bc470a40ced7a2aa6652efd Tue Sep 8 19:25:02 2026 -0700
Adding native mm10 track for the mouse strains Cactus alignment. refs #38308
New alpha-gated track mouseStrainsCactus exposing the Progressive Cactus
alignment of the 16 Mouse Genomes Project strain assemblies plus rat, which
until now was only reachable by attaching the mouseStrains assembly hub.
bigDataUrl, summary and frames point at the existing bigMaf files on
hgdownload rather than copying 8.8 GB into /gbdb, the same way the hg38
cactus241wayBM track is served.
Polish over the hub stanza: renamed from the generic "bigMaf", off by
default, speciesGroups splitting the strains into wild-derived, classical
laboratory and Rat/rn6, speciesLabels so side labels read 129S1/SvImJ
rather than 129S1_SvImJ, plus treeImage and speciesCodonDefault. The three
new sGroup_ tags are registered in tagTypes.tab.
Description page written from Lilue et al. 2018; the hub page had an empty
Description section and its Display Convention text was wigMaf boilerplate
that did not match this track. Also notes that the alignment is a poor
source for large rearrangements, since Ragout built the strain
pseudo-chromosomes against the reference and discarded most adjacencies
that disagreed with it.
Added a reciprocal relatedTracks.ra pair between this track and
mm10Strains1 ("Alternate strains"), since #38227 came in from a user who
kept landing on mm10Strains1 while looking for this alignment.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
- src/hg/makeDb/trackDb/mouse/mm10/mouseStrainsCactus.ra
- lines changed 20, context: html, text, full: html, text
efebc8a0a29aeef60bc470a40ced7a2aa6652efd Tue Sep 8 19:25:02 2026 -0700
Adding native mm10 track for the mouse strains Cactus alignment. refs #38308
New alpha-gated track mouseStrainsCactus exposing the Progressive Cactus
alignment of the 16 Mouse Genomes Project strain assemblies plus rat, which
until now was only reachable by attaching the mouseStrains assembly hub.
bigDataUrl, summary and frames point at the existing bigMaf files on
hgdownload rather than copying 8.8 GB into /gbdb, the same way the hg38
cactus241wayBM track is served.
Polish over the hub stanza: renamed from the generic "bigMaf", off by
default, speciesGroups splitting the strains into wild-derived, classical
laboratory and Rat/rn6, speciesLabels so side labels read 129S1/SvImJ
rather than 129S1_SvImJ, plus treeImage and speciesCodonDefault. The three
new sGroup_ tags are registered in tagTypes.tab.
Description page written from Lilue et al. 2018; the hub page had an empty
Description section and its Display Convention text was wigMaf boilerplate
that did not match this track. Also notes that the alignment is a poor
source for large rearrangements, since Ragout built the strain
pseudo-chromosomes against the reference and discarded most adjacencies
that disagreed with it.
Added a reciprocal relatedTracks.ra pair between this track and
mm10Strains1 ("Alternate strains"), since #38227 came in from a user who
kept landing on mm10Strains1 while looking for this alignment.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
- lines changed 1, context: html, text, full: html, text
efebc8a0a29aeef60bc470a40ced7a2aa6652efd Tue Sep 8 19:25:02 2026 -0700
Adding native mm10 track for the mouse strains Cactus alignment. refs #38308
New alpha-gated track mouseStrainsCactus exposing the Progressive Cactus
alignment of the 16 Mouse Genomes Project strain assemblies plus rat, which
until now was only reachable by attaching the mouseStrains assembly hub.
bigDataUrl, summary and frames point at the existing bigMaf files on
hgdownload rather than copying 8.8 GB into /gbdb, the same way the hg38
cactus241wayBM track is served.
Polish over the hub stanza: renamed from the generic "bigMaf", off by
default, speciesGroups splitting the strains into wild-derived, classical
laboratory and Rat/rn6, speciesLabels so side labels read 129S1/SvImJ
rather than 129S1_SvImJ, plus treeImage and speciesCodonDefault. The three
new sGroup_ tags are registered in tagTypes.tab.
Description page written from Lilue et al. 2018; the hub page had an empty
Description section and its Display Convention text was wigMaf boilerplate
that did not match this track. Also notes that the alignment is a poor
source for large rearrangements, since Ragout built the strain
pseudo-chromosomes against the reference and discarded most adjacencies
that disagreed with it.
Added a reciprocal relatedTracks.ra pair between this track and
mm10Strains1 ("Alternate strains"), since #38227 came in from a user who
kept landing on mm10Strains1 while looking for this alignment.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
- src/hg/makeDb/trackDb/relatedTracks.ra
- lines changed 4, context: html, text, full: html, text
efebc8a0a29aeef60bc470a40ced7a2aa6652efd Tue Sep 8 19:25:02 2026 -0700
Adding native mm10 track for the mouse strains Cactus alignment. refs #38308
New alpha-gated track mouseStrainsCactus exposing the Progressive Cactus
alignment of the 16 Mouse Genomes Project strain assemblies plus rat, which
until now was only reachable by attaching the mouseStrains assembly hub.
bigDataUrl, summary and frames point at the existing bigMaf files on
hgdownload rather than copying 8.8 GB into /gbdb, the same way the hg38
cactus241wayBM track is served.
Polish over the hub stanza: renamed from the generic "bigMaf", off by
default, speciesGroups splitting the strains into wild-derived, classical
laboratory and Rat/rn6, speciesLabels so side labels read 129S1/SvImJ
rather than 129S1_SvImJ, plus treeImage and speciesCodonDefault. The three
new sGroup_ tags are registered in tagTypes.tab.
Description page written from Lilue et al. 2018; the hub page had an empty
Description section and its Display Convention text was wigMaf boilerplate
that did not match this track. Also notes that the alignment is a poor
source for large rearrangements, since Ragout built the strain
pseudo-chromosomes against the reference and discarded most adjacencies
that disagreed with it.
Added a reciprocal relatedTracks.ra pair between this track and
mm10Strains1 ("Alternate strains"), since #38227 came in from a user who
kept landing on mm10Strains1 while looking for this alignment.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
- src/hg/makeDb/trackDb/tagTypes.tab
- lines changed 3, context: html, text, full: html, text
efebc8a0a29aeef60bc470a40ced7a2aa6652efd Tue Sep 8 19:25:02 2026 -0700
Adding native mm10 track for the mouse strains Cactus alignment. refs #38308
New alpha-gated track mouseStrainsCactus exposing the Progressive Cactus
alignment of the 16 Mouse Genomes Project strain assemblies plus rat, which
until now was only reachable by attaching the mouseStrains assembly hub.
bigDataUrl, summary and frames point at the existing bigMaf files on
hgdownload rather than copying 8.8 GB into /gbdb, the same way the hg38
cactus241wayBM track is served.
Polish over the hub stanza: renamed from the generic "bigMaf", off by
default, speciesGroups splitting the strains into wild-derived, classical
laboratory and Rat/rn6, speciesLabels so side labels read 129S1/SvImJ
rather than 129S1_SvImJ, plus treeImage and speciesCodonDefault. The three
new sGroup_ tags are registered in tagTypes.tab.
Description page written from Lilue et al. 2018; the hub page had an empty
Description section and its Display Convention text was wigMaf boilerplate
that did not match this track. Also notes that the alignment is a poor
source for large rearrangements, since Ragout built the strain
pseudo-chromosomes against the reference and discarded most adjacencies
that disagreed with it.
Added a reciprocal relatedTracks.ra pair between this track and
mm10Strains1 ("Alternate strains"), since #38227 came in from a user who
kept landing on mm10Strains1 while looking for this alignment.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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