Commits for max
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v501_preview to v501_preview2 (2026-07-06 to 2026-07-13) v501
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a1489c0fc1c99793e499e3915bc346b581664ad4 Wed Jul 8 02:37:20 2026 -0700
- Add support for all NCBI alternative genetic codes to dnautil
Adds struct geneticCode plus the full set of NCBI translation tables (from
gc.prt) so DNA can be translated with any genetic code, not just the Standard
and Vertebrate Mitochondrial codes that were hardcoded.
New API: geneticCodeForId/geneticCodeForName, lookupCodonInCode,
isStopCodonInCode, dnaTranslateSomeInCode (explicit-handle, reentrant), and
setDefaultGeneticCode for the process-global default. lookupCodon and friends
are unchanged in behavior, still defaulting to the Standard code.
The genetic code data lives in the auto-generated lib/geneticCodeTable.h,
produced by oneShot/dnaGeneticCodes/dnaGeneticCodes.py from NCBI's gc.prt.
Added a unit test under lib/tests. refs #16550
- src/lib/geneticCodeTable.h - lines changed 92, context: html, text, full: html, text
- src/lib/tests/dnaCodonTest.c - lines changed 54, context: html, text, full: html, text
- src/lib/tests/expected/dnaCodonTest - lines changed 10, context: html, text, full: html, text
- src/oneShot/dnaGeneticCodes/dnaGeneticCodes.py - lines changed 80, context: html, text, full: html, text
4aa77873cb618e254b2f90d091d7bdef844947c2 Wed Jul 8 04:28:42 2026 -0700
- Let assembly hubs assign genetic codes per sequence for amino acid display
Adds a "codonTable" genomes.txt setting, e.g. "codonTable default=1
NC_017929.1=13", so an assembly hub can pick the NCBI translation table used to
show amino acids for each sequence. New hGeneticCodeForChrom(db, chrom) in
hdb.c resolves the code (per-db cached), falling back to the previous behavior:
chrM/chrMT use the vertebrate mitochondrial code, everything else the standard
code.
Wired into the two browser display paths, which both go through cds.c's
baseColorLookupCodon: the base position track three-frame translation and
codon-colored annotation tracks such as gene predictions (also PSL/BAM). Also
used for the hgc SNP amino acid details, and genePredTranslate gains a db
parameter (genePredToProt gains an optional -db flag) so command-line
translation can honor the same setting. Documented in assemblyHubHelp.html.
refs #16550
- src/hg/htdocs/goldenPath/help/assemblyHubHelp.html - lines changed 38, context: html, text, full: html, text
- src/hg/utils/genePredToProt/genePredToProt.c - lines changed 7, context: html, text, full: html, text
c5a326f3cc42beca0b59c284a2819763548c166a Wed Jul 8 05:31:13 2026 -0700
- Add top-right "Share a link" and "Login" links to the menu bar, refs #10138
New js/topLinks.js drives two links at the top-right of the menu bar on all pages:
- Login: links to the login page when logged out; when logged in it shows the
username and opens an account dialog (My Sessions / My Custom Tracks /
My Track Hubs, change password, sign out).
- Share a link: on hgTracks, one click saves the current view as a session and
shows a copyable short link, with an optional "Specify name" rename step; works
logged-in or anonymously (reserved user "l"). On hgTrackUi and the hgc/hgGene
item-details popup it instead shares the page URL with the hgsid stripped and
the db argument kept.
hgSession gains two JSON endpoints (hgS_doSaveSessionJson, hgS_doRenameSessionJson)
that reuse saveCartAsSession() and addSessionLink(). The menu bar is patched in
lib/web.c (CGI pages) and hgMenubar.c (static pages) via comment placeholders in
globalNavBar.inc. On narrow/phone screens the links collapse into a menu icon with
a dropdown so they no longer overlap the menu.
- src/hg/hgMenubar/hgMenubar.c - lines changed 40, context: html, text, full: html, text
- src/hg/hgSession/hgSession.c - lines changed 145, context: html, text, full: html, text
- src/hg/hgSession/hgSession.h - lines changed 7, context: html, text, full: html, text
- src/hg/htdocs/inc/globalNavBar.inc - lines changed 5, context: html, text, full: html, text
- src/hg/htdocs/style/nice_menu.css - lines changed 65, context: html, text, full: html, text
- src/hg/js/topLinks.js - lines changed 383, context: html, text, full: html, text
32d8c9cb1c107f4bee849bdbf0db07b6bfb2a94d Wed Jul 8 05:35:07 2026 -0700
- hgLogin: require new user names to be at least two characters, refs #10138
Single-character user names are now reserved ("l" is used internally for anonymous shared-session links), so signup() rejects them. The check is only in the account-creation path, so existing accounts -- including any single-character ones -- keep working for login and sessions.
- src/hg/hgLogin/hgLogin.c - lines changed 9, context: html, text, full: html, text
c60812dd154dc99e8045db2d617ea969c26a28a2 Wed Jul 8 08:07:55 2026 -0700
- cart: treat an empty position value the same as unset, refs #37794
cartGetPosition only fell back to the assembly default position when the
cart position was NULL or the literal string "default". A stale empty
"position=" value (e.g. hgTracks?position=, or a position carried over from
a different assembly via a db= link) is returned verbatim as "" by
cartUsualString, so it slipped past that check and made hgTracks abort with
"Please go back and enter a coordinate range...". Treat an empty string like
unset so we fall back to the default position instead of crashing.
44a7bbc4c8aa983e1f075c25c240e6f479e99dc3 Wed Jul 8 09:24:27 2026 -0700
- gentle intro to v500 release message
- src/hg/htdocs/goldenPath/newsarch.html - lines changed 14, context: html, text, full: html, text
aac2d475d4e656e52e1b56fc7a1891d56b513220 Wed Jul 8 10:01:35 2026 -0700
- Log codonTable and chromAuthority genomes.txt settings in trackDb changes.html
These are assembly hub genome-stanza (genomes.txt) settings, not track
settings, so each row is flagged accordingly and links to assemblyHubHelp.html.
refs #16550
- src/hg/htdocs/goldenPath/help/trackDb/changes.html - lines changed 21, context: html, text, full: html, text
3126025a52d8ee7cd03a13869722f78f996063ad Fri Jul 10 04:52:16 2026 -0700
- Fix codon mouseover protein position: 1-based single p. and singular label
The zoomed-in codon mouseover printed the protein position as a 0-based
two-position range, e.g. the first codon read c.1-3 (p.0-1). A codon is a
single amino acid, and p. should be 1-based to match the adjacent c.
numbering, so it now reads c.1-3 (p.1). Also corrected the label from the
plural Codons to Codon since each mouseover covers one codon.
refs #37773
- src/hg/hgTracks/simpleTracks.c - lines changed 4, context: html, text, full: html, text
88f4f3286f2b21c8fb65b3502adbbc2e7eaf60f1 Fri Jul 10 06:14:13 2026 -0700
- Automate GitHub source-archive upload with submodules, refs #37741
makeZip.csh now also builds jksrc.vNN.tar.gz next to the zip (both from the
recurse-submodules clone, so both include the htslib submodule). doZip.csh
hardlinks these to kent.src.zip / kent.src.tar.gz and uploads them to the
GitHub release (creating it if needed). This works around git-archive omitting
submodule contents, which is why GitHub's own auto-generated source archives are
not buildable. autoBuild.sh now runs release-markdown before the zip step so the
release doZip creates carries the real notes.
- src/utils/qa/weeklybld/autoBuild.sh - lines changed 9, context: html, text, full: html, text
- src/utils/qa/weeklybld/doZip.csh - lines changed 44, context: html, text, full: html, text
- src/utils/qa/weeklybld/makeZip.csh - lines changed 14, context: html, text, full: html, text
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