File Changes for max

v501_preview to v501_preview2 (2026-07-06 to 2026-07-13) v501

• src/hg/hgLogin/hgLogin.c
  • lines changed 9, 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/hgMenubar/hgMenubar.c
  • lines changed 40, 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/hgSession/hgSession.c
  • lines changed 145, 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/hgSession/hgSession.h
  • 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/hgTracks/cds.c
  • lines changed 9, 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/hgTracks/simpleTracks.c
  • lines changed 4, 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/hgc/hgc.c
  • lines changed 9, 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
    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/trackDb/changes.html
  • lines changed 21, 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/newsarch.html
  • lines changed 14, context: html, text, full: html, text
    44a7bbc4c8aa983e1f075c25c240e6f479e99dc3 Wed Jul 8 09:24:27 2026 -0700
    gentle intro to v500 release message
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 5, 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/htdocs/style/nice_menu.css
  • lines changed 65, 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/inc/genePred.h
  • lines changed 5, 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/inc/hdb.h
  • lines changed 7, 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/js/hgTracks.js
  • lines changed 12, 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/js/makefile
  • lines changed 1, 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/js/topLinks.js
  • lines changed 383, 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/lib/cart.c
  • lines changed 4, 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.
• src/hg/lib/genePred.c
  • lines changed 13, 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/lib/hdb.c
  • lines changed 78, 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/lib/web.c
  • lines changed 58, 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/utils/genePredToProt/genePredToProt.c
  • lines changed 7, 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/inc/dnautil.h
  • lines changed 38, context: html, text, full: html, text
    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/dnautil.c
  • lines changed 207, context: html, text, full: html, text
    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
    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/tests/dnaCodonTest.c
  • lines changed 54, context: html, text, full: html, text
    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/tests/expected/dnaCodonTest
  • lines changed 10, context: html, text, full: html, text
    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/tests/makefile
  • lines changed 9, context: html, text, full: html, text
    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/oneShot/dnaGeneticCodes/dnaGeneticCodes.py
  • lines changed 80, context: html, text, full: html, text
    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/utils/qa/weeklybld/autoBuild.sh
  • lines changed 9, 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/doZip.csh
  • lines changed 44, 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/makeZip.csh
  • lines changed 14, 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.