Commits for mspeir
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v504_preview2 to v504_base (2026-09-14 to 2026-09-21) v504
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f5dc9662ac04c32e82c97b1d0ac4b856beb1938d Wed Sep 16 11:32:25 2026 -0700
- hprc2annot: say what summary.tsv actually retains instead of claiming near-lossless counts for every track, refs #35415
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
- src/hg/makeDb/doc/contrib/hprc2annot/hprc2annot.txt - lines changed 7, context: html, text, full: html, text
0a6c6ae0e873e8c95fc1d6a941a26b50d7e92f36 Wed Sep 16 11:40:45 2026 -0700
- Add a blank line after the horizontal rules in the gb101 and gateway tutorials, no Redmine
These two pages put a bare --- rule directly above the next heading or div.
Pandoc reads a line of dashes as either a horizontal rule or a table rule
depending on what follows it, so the parse can flip when the block underneath
changes. It resolves to a rule today, but converting the divs on these pages to
fenced divs was enough to turn 5 sections of gb101 into tables and drop every
<hr>. The blank line removes the ambiguity. The built HTML is byte-identical
before and after.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
- docs/tutorials/gatewayTutorial.md - lines changed 2, context: html, text, full: html, text
- docs/tutorials/gb101.md - lines changed 10, context: html, text, full: html, text
f164d5cd5b9cfecc0c35f7e08350a2a768e46457 Wed Sep 16 11:40:45 2026 -0700
- Sort attributes in staticPage.lua so the docs build is reproducible, no Redmine
attributes() walked the attribute table with pairs(), which has no defined
order, so any element with two or more attributes came out in a different order
from one build to the next. Eight identical builds of gb101.md produced two
distinct outputs. It renders the same either way, but it makes the install
rsync re-push files nobody edited and makes a byte comparison of any docs change
meaningless. Sorting the keys fixes it; no page changes semantically.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
fec6f772c9613d436f976c315673bfb5f4ce3262 Thu Sep 17 14:45:58 2026 -0700
- relatedTracks.ra: put back the hg19 ensGene entry, refs #38016
The audit commit dropped three ensGene lines but only justified two. Ensembl
Genes is retired on hg38 and mm10, but it is still a live track on hg19: the
table has 204,940 rows and hgTrackUi?db=hg19&g=ensGene renders on the RR.
knownGene is public on hg19 too, so the entry met the commit's own test and
should have stayed. Its removal took a working related-track pointer off the
hg19 Ensembl Genes page.
Found in the v504 code review, #38354.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
- src/hg/makeDb/trackDb/relatedTracks.ra - lines changed 1, context: html, text, full: html, text
157d7eb9f2765db7651e12c14233c56fa7205e96 Thu Sep 17 14:46:12 2026 -0700
- VCF help: add the two settings the sweep missed, and fix a value order, refs #38010
The earlier commit left out sampleMetadataFile and showHardyWeinberg on the
grounds that nothing in the tree reads them. Both are read: hgc/vcfClick.c
loads the metadata file in vcfGenotypeTable, and reads showHardyWeinberg with
cartOrTdbBoolean in vcfGenotypesDetails. Neither call is gated on track type,
so both also apply to vcfPhasedTrio, which tagTypes.tab had not allowed; that
is corrected here too.
sampleColorFile and showHardyWeinberg had no entry in trackDbLibrary.shtml, so
they were missing from the trackDb doc pages as well. Both get a blurb, a row
in trackDbDoc.html and trackDbHub.v3.html, and a changes.html note.
sampleColorFile is the last VCF setting that was recognized but undocumented.
vcf.html and the three trackDb doc files listed vcfPhasedColorBy as
mendelDiff|deNovo|function|noColor. vcfUi.c prints the radio buttons in the
opposite order, so the lists now read noColor|function|deNovo|mendelDiff, the
way hapClusterColorBy already matches its own buttons.
trackDbSettings.yaml and .json are regenerated. They also pick up minAc,
vcfDoMinAc and vcfPhasedColorBy, which were documented earlier in this series
without a regen.
Found in the v504 code review, #38354.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
- src/hg/htdocs/goldenPath/help/trackDb/changes.html - lines changed 14, context: html, text, full: html, text
- src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html - lines changed 7, context: html, text, full: html, text
- src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html - lines changed 7, context: html, text, full: html, text
- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml - lines changed 41, context: html, text, full: html, text
- src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.json - lines changed 77, context: html, text, full: html, text
- src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.yaml - lines changed 98, context: html, text, full: html, text
- src/hg/htdocs/goldenPath/help/vcf.html - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/trackDb/tagTypes.tab - lines changed 2, context: html, text, full: html, text
f78e12e52a1bc47b7a69246a1f184d78900eab51 Thu Sep 17 14:46:18 2026 -0700
- hgSessionHelp.html: give the second duplicate anchor its own name, refs #38062
The page carried two <a name="Create"> anchors, one on "Creating a session" and
one on "Opening a saved session". Nine pages link to #Create meaning the first
one, and they land there only because it comes first in the document. The
second is now OpenSaved. Nothing linked to it, and the separate #Open anchor
further down belongs to "Opening a shared session", a different section.
Found in the v504 code review, #38354.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
- src/hg/htdocs/goldenPath/help/hgSessionHelp.html - lines changed 1, context: html, text, full: html, text
69f4ef65bd1f1d15304c3fe0a47e701d58d6e688 Fri Sep 18 13:05:49 2026 -0700
- trackLists: take the otto assembly counts from the jobs, and quiet the weekly mail. refs #38295
Code review feedback from Lou on the mirror track lists page.
The Assemblies column counted every assembly with a table matching the job's
keyword, not the assemblies the job rebuilds, so NCBI RefSeq read 84 where
ottoNcbiRefSeq.sh runs four and GRC Incident read 61 where runUpdate.sh works
through ten. Each job now carries the list it actually builds, read out of its
script; UniProt keeps the trackDb count because doUniprot chooses its assemblies
at run time. A run reports either way the list and trackDb disagree.
An otto job the keyword table did not recognize vanished from the page without
a word, which is how STRchive went missing from it. STRchive is described now,
and anything else unrecognized is named on the page and in the cron mail.
The weekly mail was the whole progress log with the reachable restricted files
buried in it, because every note() went to stderr and the "updated" line fired
every run. Progress now goes to stdout and on to lastRun.log; stderr carries
only what needs a person, so mail from this cron line means something is wrong.
The "every file marked as restricted is correctly blocked" line could print on
a run where no fetch got an answer, and covered only the 39 of 58 rows that
name a file. It now says how many were tried and stays quiet about blocking
when the check could not finish.
Four rows reading "Mutation: A" through "Mutation: T" sat under M in the
restricted table, nowhere near AlphaGenome. A subtrack of a listed track now
sorts directly under that track, keeping its own row, since each of these is a
separate file a mirror cannot have. A track named after its container is
labelled with the container as well, so varFreqsBackground reads "SNV
Frequencies: Population reference" rather than "Population reference".
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
- src/hg/utils/otto/otto.crontab - lines changed 3, context: html, text, full: html, text
- src/hg/utils/otto/trackLists/README.txt - lines changed 37, context: html, text, full: html, text
- src/hg/utils/otto/trackLists/collect.py - lines changed 178, context: html, text, full: html, text
- src/hg/utils/otto/trackLists/mkPage.py - lines changed 87, context: html, text, full: html, text
- src/hg/utils/otto/trackLists/trackLists.sh - lines changed 16, context: html, text, full: html, text
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