All File Changes

v500_preview to v500_preview2 (2026-06-08 to 2026-06-15) v500

• confs/asia.hg.conf
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    f75ac15d38abafacae7c01950a3c50132c8d85b0 Sun Jun 14 01:11:18 2026 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 3, context: html, text, full: html, text
    f75ac15d38abafacae7c01950a3c50132c8d85b0 Sun Jun 14 01:11:18 2026 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 3, context: html, text, full: html, text
    f75ac15d38abafacae7c01950a3c50132c8d85b0 Sun Jun 14 01:11:18 2026 -0700
    Installing updated hg.conf files from UCSC servers
• src/aladdin/aladdin/aladdin.c
  • lines changed 5, context: html, text, full: html, text
    f57fc11d951807e19b20b5960e735fa50eaea279 Fri Jun 12 13:10:00 2026 -0700
    Fix more warnings exposed by -O3 build across hg utils and errAbort Continuation of the -O3 cleanup: a full clean rebuild surfaced warnings in many programs whose objects had not been recompiled before. Most are the same mechanical patterns as the first batch (strncpy -> safecpy/memcpy, sprintf -> safef), plus a few that needed more thought: - errAbort.h: mark errAbort/vaErrAbort/errnoAbort/noWarnAbort as noreturn. They provably never return (longjmp or exit; the existing "to make compiler happy" exit(-1) in noWarnAbort confirms the intent), and this lets GCC prune the impossible null paths after an errAbort guard, fixing false-positive null-deref / overread warnings in mafAddIRows, mafAddIRowsStream and phyloPlace with no source change to those files. - altSplice.c (hgGene): real one-element stack buffer overflow. makeGrayShades writes shadesOfGray[maxShade+1], but the caller declared shadesOfGray[9] with maxShade=8. Grow the array to [10] (maxShade stays 8); behavior unchanged. - hgc.c bedPrintPos: ~60 callers pass a track-specific struct cast to (struct bed *) and read only its bed-compatible leading fields. At -O3 -Warray-bounds flags the casts because the real object is smaller than struct bed; the reads are safe by the bed-layout convention, so suppress -Warray-bounds around just that function. - mafsInRegion.c: chromFromSrc returns strchr(src,'.')+1, which GCC mis-sizes as a 0-byte region when handed to strcmp via sameString/differentString; suppress the false-positive -Wstringop-overread around extractMafs. - sanger22gtf.c, bottleneck.c: put the printf/fprintf in the else of the NULL guard so -Wformat-overflow (which runs before the noreturn-based pruning) can see the argument is non-null. safecpy/memcpy/safef conversions: basicBed already done earlier; here haplotypes (memcpy of the original pointer pun), gbToFaRa, motifSig, hgClonePos, featureBits, libScan, hgGoldGapGl, hgSoftPromoter, mafClick, mafAddQRows, hgc.c, stanToBedAndExpRecs, bedUp, faSplit, trfBig, splitFaIntoContigs, aladdin, ameme. A full clean tree now builds with no warnings at -O3. refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/ameme/ameme.c
  • lines changed 2, context: html, text, full: html, text
    f57fc11d951807e19b20b5960e735fa50eaea279 Fri Jun 12 13:10:00 2026 -0700
    Fix more warnings exposed by -O3 build across hg utils and errAbort Continuation of the -O3 cleanup: a full clean rebuild surfaced warnings in many programs whose objects had not been recompiled before. Most are the same mechanical patterns as the first batch (strncpy -> safecpy/memcpy, sprintf -> safef), plus a few that needed more thought: - errAbort.h: mark errAbort/vaErrAbort/errnoAbort/noWarnAbort as noreturn. They provably never return (longjmp or exit; the existing "to make compiler happy" exit(-1) in noWarnAbort confirms the intent), and this lets GCC prune the impossible null paths after an errAbort guard, fixing false-positive null-deref / overread warnings in mafAddIRows, mafAddIRowsStream and phyloPlace with no source change to those files. - altSplice.c (hgGene): real one-element stack buffer overflow. makeGrayShades writes shadesOfGray[maxShade+1], but the caller declared shadesOfGray[9] with maxShade=8. Grow the array to [10] (maxShade stays 8); behavior unchanged. - hgc.c bedPrintPos: ~60 callers pass a track-specific struct cast to (struct bed *) and read only its bed-compatible leading fields. At -O3 -Warray-bounds flags the casts because the real object is smaller than struct bed; the reads are safe by the bed-layout convention, so suppress -Warray-bounds around just that function. - mafsInRegion.c: chromFromSrc returns strchr(src,'.')+1, which GCC mis-sizes as a 0-byte region when handed to strcmp via sameString/differentString; suppress the false-positive -Wstringop-overread around extractMafs. - sanger22gtf.c, bottleneck.c: put the printf/fprintf in the else of the NULL guard so -Wformat-overflow (which runs before the noreturn-based pruning) can see the argument is non-null. safecpy/memcpy/safef conversions: basicBed already done earlier; here haplotypes (memcpy of the original pointer pun), gbToFaRa, motifSig, hgClonePos, featureBits, libScan, hgGoldGapGl, hgSoftPromoter, mafClick, mafAddQRows, hgc.c, stanToBedAndExpRecs, bedUp, faSplit, trfBig, splitFaIntoContigs, aladdin, ameme. A full clean tree now builds with no warnings at -O3. refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/cgilib/haplotypes.c
  • lines changed 6, context: html, text, full: html, text
    f57fc11d951807e19b20b5960e735fa50eaea279 Fri Jun 12 13:10:00 2026 -0700
    Fix more warnings exposed by -O3 build across hg utils and errAbort Continuation of the -O3 cleanup: a full clean rebuild surfaced warnings in many programs whose objects had not been recompiled before. Most are the same mechanical patterns as the first batch (strncpy -> safecpy/memcpy, sprintf -> safef), plus a few that needed more thought: - errAbort.h: mark errAbort/vaErrAbort/errnoAbort/noWarnAbort as noreturn. They provably never return (longjmp or exit; the existing "to make compiler happy" exit(-1) in noWarnAbort confirms the intent), and this lets GCC prune the impossible null paths after an errAbort guard, fixing false-positive null-deref / overread warnings in mafAddIRows, mafAddIRowsStream and phyloPlace with no source change to those files. - altSplice.c (hgGene): real one-element stack buffer overflow. makeGrayShades writes shadesOfGray[maxShade+1], but the caller declared shadesOfGray[9] with maxShade=8. Grow the array to [10] (maxShade stays 8); behavior unchanged. - hgc.c bedPrintPos: ~60 callers pass a track-specific struct cast to (struct bed *) and read only its bed-compatible leading fields. At -O3 -Warray-bounds flags the casts because the real object is smaller than struct bed; the reads are safe by the bed-layout convention, so suppress -Warray-bounds around just that function. - mafsInRegion.c: chromFromSrc returns strchr(src,'.')+1, which GCC mis-sizes as a 0-byte region when handed to strcmp via sameString/differentString; suppress the false-positive -Wstringop-overread around extractMafs. - sanger22gtf.c, bottleneck.c: put the printf/fprintf in the else of the NULL guard so -Wformat-overflow (which runs before the noreturn-based pruning) can see the argument is non-null. safecpy/memcpy/safef conversions: basicBed already done earlier; here haplotypes (memcpy of the original pointer pun), gbToFaRa, motifSig, hgClonePos, featureBits, libScan, hgGoldGapGl, hgSoftPromoter, mafClick, mafAddQRows, hgc.c, stanToBedAndExpRecs, bedUp, faSplit, trfBig, splitFaIntoContigs, aladdin, ameme. A full clean tree now builds with no warnings at -O3. refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html
  • lines changed 6, context: html, text, full: html, text
    69bc90811c9022638796c1ccde4f4a62b65fbd62 Mon Jun 8 11:44:55 2026 -0700
    Staging column Q ADGC1_Y4_Q_## 2027Q1 UCLA milestones
  • lines changed 11, context: html, text, full: html, text
    94100fbd46c1b07ed9ca5021ca7800b4c6f57084 Tue Jun 9 09:31:11 2026 -0700
    Aligning Broad/Sing timeline/milestones to Year3 -newer ADGC5
  • lines changed 1, context: html, text, full: html, text
    d11b7b685cc51f56e055a4d272b6bb22036370b5 Tue Jun 9 10:32:39 2026 -0700
    Updating year4_yale spreadsheet link to the 3/24 version (previously 3/16 verision in shared drive)
  • lines changed 7, context: html, text, full: html, text
    3db72c6a4bcb08954558ff2b77c3701dfa20cf54 Wed Jun 10 14:18:35 2026 -0700
    Adding clickable link to newest Scripps/Broad ADGC5 milestones [2026-2027]
  • lines changed 6, context: html, text, full: html, text
    e1be64ce7ec66239bea5cb253d100fbd32497766 Thu Jun 11 10:26:36 2026 -0700
    Adding shortened versions of ADGC5 Scripps/Broad 2026Q2-2027Q1 milestones for better readability.
  • lines changed 1, context: html, text, full: html, text
    a38ebe7b29e3484f08837ef481d6dc9975aad597 Sun Jun 14 14:02:24 2026 -0700
    correct Ktm5b -> Kdm5b gene name, typo in ADGC5's original document
• src/hg/featureBits/featureBits.c
  • lines changed 3, context: html, text, full: html, text
    f57fc11d951807e19b20b5960e735fa50eaea279 Fri Jun 12 13:10:00 2026 -0700
    Fix more warnings exposed by -O3 build across hg utils and errAbort Continuation of the -O3 cleanup: a full clean rebuild surfaced warnings in many programs whose objects had not been recompiled before. Most are the same mechanical patterns as the first batch (strncpy -> safecpy/memcpy, sprintf -> safef), plus a few that needed more thought: - errAbort.h: mark errAbort/vaErrAbort/errnoAbort/noWarnAbort as noreturn. They provably never return (longjmp or exit; the existing "to make compiler happy" exit(-1) in noWarnAbort confirms the intent), and this lets GCC prune the impossible null paths after an errAbort guard, fixing false-positive null-deref / overread warnings in mafAddIRows, mafAddIRowsStream and phyloPlace with no source change to those files. - altSplice.c (hgGene): real one-element stack buffer overflow. makeGrayShades writes shadesOfGray[maxShade+1], but the caller declared shadesOfGray[9] with maxShade=8. Grow the array to [10] (maxShade stays 8); behavior unchanged. - hgc.c bedPrintPos: ~60 callers pass a track-specific struct cast to (struct bed *) and read only its bed-compatible leading fields. At -O3 -Warray-bounds flags the casts because the real object is smaller than struct bed; the reads are safe by the bed-layout convention, so suppress -Warray-bounds around just that function. - mafsInRegion.c: chromFromSrc returns strchr(src,'.')+1, which GCC mis-sizes as a 0-byte region when handed to strcmp via sameString/differentString; suppress the false-positive -Wstringop-overread around extractMafs. - sanger22gtf.c, bottleneck.c: put the printf/fprintf in the else of the NULL guard so -Wformat-overflow (which runs before the noreturn-based pruning) can see the argument is non-null. safecpy/memcpy/safef conversions: basicBed already done earlier; here haplotypes (memcpy of the original pointer pun), gbToFaRa, motifSig, hgClonePos, featureBits, libScan, hgGoldGapGl, hgSoftPromoter, mafClick, mafAddQRows, hgc.c, stanToBedAndExpRecs, bedUp, faSplit, trfBig, splitFaIntoContigs, aladdin, ameme. A full clean tree now builds with no warnings at -O3. refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/gbToFaRa/gbToFaRa.c
  • lines changed 1, context: html, text, full: html, text
    f57fc11d951807e19b20b5960e735fa50eaea279 Fri Jun 12 13:10:00 2026 -0700
    Fix more warnings exposed by -O3 build across hg utils and errAbort Continuation of the -O3 cleanup: a full clean rebuild surfaced warnings in many programs whose objects had not been recompiled before. Most are the same mechanical patterns as the first batch (strncpy -> safecpy/memcpy, sprintf -> safef), plus a few that needed more thought: - errAbort.h: mark errAbort/vaErrAbort/errnoAbort/noWarnAbort as noreturn. They provably never return (longjmp or exit; the existing "to make compiler happy" exit(-1) in noWarnAbort confirms the intent), and this lets GCC prune the impossible null paths after an errAbort guard, fixing false-positive null-deref / overread warnings in mafAddIRows, mafAddIRowsStream and phyloPlace with no source change to those files. - altSplice.c (hgGene): real one-element stack buffer overflow. makeGrayShades writes shadesOfGray[maxShade+1], but the caller declared shadesOfGray[9] with maxShade=8. Grow the array to [10] (maxShade stays 8); behavior unchanged. - hgc.c bedPrintPos: ~60 callers pass a track-specific struct cast to (struct bed *) and read only its bed-compatible leading fields. At -O3 -Warray-bounds flags the casts because the real object is smaller than struct bed; the reads are safe by the bed-layout convention, so suppress -Warray-bounds around just that function. - mafsInRegion.c: chromFromSrc returns strchr(src,'.')+1, which GCC mis-sizes as a 0-byte region when handed to strcmp via sameString/differentString; suppress the false-positive -Wstringop-overread around extractMafs. - sanger22gtf.c, bottleneck.c: put the printf/fprintf in the else of the NULL guard so -Wformat-overflow (which runs before the noreturn-based pruning) can see the argument is non-null. safecpy/memcpy/safef conversions: basicBed already done earlier; here haplotypes (memcpy of the original pointer pun), gbToFaRa, motifSig, hgClonePos, featureBits, libScan, hgGoldGapGl, hgSoftPromoter, mafClick, mafAddQRows, hgc.c, stanToBedAndExpRecs, bedUp, faSplit, trfBig, splitFaIntoContigs, aladdin, ameme. A full clean tree now builds with no warnings at -O3. refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/geneBounds/motifSig/motifSig.c
  • lines changed 1, context: html, text, full: html, text
    f57fc11d951807e19b20b5960e735fa50eaea279 Fri Jun 12 13:10:00 2026 -0700
    Fix more warnings exposed by -O3 build across hg utils and errAbort Continuation of the -O3 cleanup: a full clean rebuild surfaced warnings in many programs whose objects had not been recompiled before. Most are the same mechanical patterns as the first batch (strncpy -> safecpy/memcpy, sprintf -> safef), plus a few that needed more thought: - errAbort.h: mark errAbort/vaErrAbort/errnoAbort/noWarnAbort as noreturn. They provably never return (longjmp or exit; the existing "to make compiler happy" exit(-1) in noWarnAbort confirms the intent), and this lets GCC prune the impossible null paths after an errAbort guard, fixing false-positive null-deref / overread warnings in mafAddIRows, mafAddIRowsStream and phyloPlace with no source change to those files. - altSplice.c (hgGene): real one-element stack buffer overflow. makeGrayShades writes shadesOfGray[maxShade+1], but the caller declared shadesOfGray[9] with maxShade=8. Grow the array to [10] (maxShade stays 8); behavior unchanged. - hgc.c bedPrintPos: ~60 callers pass a track-specific struct cast to (struct bed *) and read only its bed-compatible leading fields. At -O3 -Warray-bounds flags the casts because the real object is smaller than struct bed; the reads are safe by the bed-layout convention, so suppress -Warray-bounds around just that function. - mafsInRegion.c: chromFromSrc returns strchr(src,'.')+1, which GCC mis-sizes as a 0-byte region when handed to strcmp via sameString/differentString; suppress the false-positive -Wstringop-overread around extractMafs. - sanger22gtf.c, bottleneck.c: put the printf/fprintf in the else of the NULL guard so -Wformat-overflow (which runs before the noreturn-based pruning) can see the argument is non-null. safecpy/memcpy/safef conversions: basicBed already done earlier; here haplotypes (memcpy of the original pointer pun), gbToFaRa, motifSig, hgClonePos, featureBits, libScan, hgGoldGapGl, hgSoftPromoter, mafClick, mafAddQRows, hgc.c, stanToBedAndExpRecs, bedUp, faSplit, trfBig, splitFaIntoContigs, aladdin, ameme. A full clean tree now builds with no warnings at -O3. refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/hgConvert/hgConvert.c
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    f4acfa770ad691ea4bb4fc08d91d4d9d13b32a7a Fri Jun 12 08:19:18 2026 -0700
    hgConvert: avoid SIGSEGV when position missing from cart doMiddle() read the position with cartString(), which aborts via hashMustFindVal when a request arrives with a db but no position in the cart (e.g. a bot hitting hgConvert with no prior browsing). Set up the cart and database first, then read the position with the assembly's default position as a fallback, matching the pattern in hgTracks. refs #37535 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/hgGene/altSplice.c
  • lines changed 2, context: html, text, full: html, text
    f57fc11d951807e19b20b5960e735fa50eaea279 Fri Jun 12 13:10:00 2026 -0700
    Fix more warnings exposed by -O3 build across hg utils and errAbort Continuation of the -O3 cleanup: a full clean rebuild surfaced warnings in many programs whose objects had not been recompiled before. Most are the same mechanical patterns as the first batch (strncpy -> safecpy/memcpy, sprintf -> safef), plus a few that needed more thought: - errAbort.h: mark errAbort/vaErrAbort/errnoAbort/noWarnAbort as noreturn. They provably never return (longjmp or exit; the existing "to make compiler happy" exit(-1) in noWarnAbort confirms the intent), and this lets GCC prune the impossible null paths after an errAbort guard, fixing false-positive null-deref / overread warnings in mafAddIRows, mafAddIRowsStream and phyloPlace with no source change to those files. - altSplice.c (hgGene): real one-element stack buffer overflow. makeGrayShades writes shadesOfGray[maxShade+1], but the caller declared shadesOfGray[9] with maxShade=8. Grow the array to [10] (maxShade stays 8); behavior unchanged. - hgc.c bedPrintPos: ~60 callers pass a track-specific struct cast to (struct bed *) and read only its bed-compatible leading fields. At -O3 -Warray-bounds flags the casts because the real object is smaller than struct bed; the reads are safe by the bed-layout convention, so suppress -Warray-bounds around just that function. - mafsInRegion.c: chromFromSrc returns strchr(src,'.')+1, which GCC mis-sizes as a 0-byte region when handed to strcmp via sameString/differentString; suppress the false-positive -Wstringop-overread around extractMafs. - sanger22gtf.c, bottleneck.c: put the printf/fprintf in the else of the NULL guard so -Wformat-overflow (which runs before the noreturn-based pruning) can see the argument is non-null. safecpy/memcpy/safef conversions: basicBed already done earlier; here haplotypes (memcpy of the original pointer pun), gbToFaRa, motifSig, hgClonePos, featureBits, libScan, hgGoldGapGl, hgSoftPromoter, mafClick, mafAddQRows, hgc.c, stanToBedAndExpRecs, bedUp, faSplit, trfBig, splitFaIntoContigs, aladdin, ameme. A full clean tree now builds with no warnings at -O3. refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/hgLogin/hgLogin.c
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    a3cc0ea56291f64c876d1d422d432e0234638059 Fri Jun 12 11:34:25 2026 -0700
    Suppressing stack dump for bad returnto url in hgLogin, refs #37699
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 2, context: html, text, full: html, text
    7b74ff4b43a459efaadb2dc219026d522252745e Wed Jun 10 07:09:51 2026 -0700
    hgTrackUi: avoid SIGSEGV on duplicate track request not in cart A request for a dup_-prefixed track name with no matching entry in the cart passed a NULL dup to dupTdbFrom, causing a null dereference and a stack dump. This is reachable without a login and was tripped by a bot during the v499 release. errAbort with a clear message instead. refs #37743 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/hgTracks/hgTracks.c
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    d0d3ac9414a163b759edf2b028a4b50f4057dbc3 Fri Jun 12 09:02:21 2026 -0700
    hgTracks quickLift: use trash-can icon for per-track remove QA asked for the per-track remove control in a QuickLift group to match the trash-can icon already used to delete custom tracks, instead of the red 'x', so the two behave consistently. Factor the trash-can SVG into a shared printTrashIcon() helper used by both the custom-track delete and the quickLift remove, and drop the red tint so the quickLift icon matches. refs #37535 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/hgTracks/simpleTracks.c
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    bb8470a90643b057df7bbf5d0140a5b2bbf9dddd Fri Jun 12 08:44:37 2026 -0700
    quickLift: load genePreds by column name, not a fixed 15-col loader Lifting a genePred track to another assembly used genePredExtLoad15, a positional loader that assumes the extended genePred columns. Classic knownGene-format tables instead carry proteinID and alignID after the ten core columns, so the loader read proteinID as the integer score field and aborted with "invalid signed integer" (e.g. "O54946", or "" when empty). This showed up when lifting from an assembly whose knownGene is the legacy format, such as mm10 to mm39 or rheMac10. Add quickLiftGenePreds(), which loads through genePredReader so the actual set of columns in the table is honored by name (proteinID maps to name2, score defaults), matching how the tracks load when not lifted. The three call sites that hardcoded genePredExtLoad15 (hgTracks gene loading and two hgc detail handlers) now use it. The chain-walking shared with quickLiftSql is factored into quickLiftLoadChains() and quickLiftChainQueryRange(). refs #37535 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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    d08b94fcff0787dd853676e631364945c4986bfe Sun Jun 14 09:21:03 2026 -0700
    ading p. notation to mouseover, no redmine yet
• src/hg/hgc/hgc.c
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    bb8470a90643b057df7bbf5d0140a5b2bbf9dddd Fri Jun 12 08:44:37 2026 -0700
    quickLift: load genePreds by column name, not a fixed 15-col loader Lifting a genePred track to another assembly used genePredExtLoad15, a positional loader that assumes the extended genePred columns. Classic knownGene-format tables instead carry proteinID and alignID after the ten core columns, so the loader read proteinID as the integer score field and aborted with "invalid signed integer" (e.g. "O54946", or "" when empty). This showed up when lifting from an assembly whose knownGene is the legacy format, such as mm10 to mm39 or rheMac10. Add quickLiftGenePreds(), which loads through genePredReader so the actual set of columns in the table is honored by name (proteinID maps to name2, score defaults), matching how the tracks load when not lifted. The three call sites that hardcoded genePredExtLoad15 (hgTracks gene loading and two hgc detail handlers) now use it. The chain-walking shared with quickLiftSql is factored into quickLiftLoadChains() and quickLiftChainQueryRange(). refs #37535 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
  • lines changed 11, context: html, text, full: html, text
    f57fc11d951807e19b20b5960e735fa50eaea279 Fri Jun 12 13:10:00 2026 -0700
    Fix more warnings exposed by -O3 build across hg utils and errAbort Continuation of the -O3 cleanup: a full clean rebuild surfaced warnings in many programs whose objects had not been recompiled before. Most are the same mechanical patterns as the first batch (strncpy -> safecpy/memcpy, sprintf -> safef), plus a few that needed more thought: - errAbort.h: mark errAbort/vaErrAbort/errnoAbort/noWarnAbort as noreturn. They provably never return (longjmp or exit; the existing "to make compiler happy" exit(-1) in noWarnAbort confirms the intent), and this lets GCC prune the impossible null paths after an errAbort guard, fixing false-positive null-deref / overread warnings in mafAddIRows, mafAddIRowsStream and phyloPlace with no source change to those files. - altSplice.c (hgGene): real one-element stack buffer overflow. makeGrayShades writes shadesOfGray[maxShade+1], but the caller declared shadesOfGray[9] with maxShade=8. Grow the array to [10] (maxShade stays 8); behavior unchanged. - hgc.c bedPrintPos: ~60 callers pass a track-specific struct cast to (struct bed *) and read only its bed-compatible leading fields. At -O3 -Warray-bounds flags the casts because the real object is smaller than struct bed; the reads are safe by the bed-layout convention, so suppress -Warray-bounds around just that function. - mafsInRegion.c: chromFromSrc returns strchr(src,'.')+1, which GCC mis-sizes as a 0-byte region when handed to strcmp via sameString/differentString; suppress the false-positive -Wstringop-overread around extractMafs. - sanger22gtf.c, bottleneck.c: put the printf/fprintf in the else of the NULL guard so -Wformat-overflow (which runs before the noreturn-based pruning) can see the argument is non-null. safecpy/memcpy/safef conversions: basicBed already done earlier; here haplotypes (memcpy of the original pointer pun), gbToFaRa, motifSig, hgClonePos, featureBits, libScan, hgGoldGapGl, hgSoftPromoter, mafClick, mafAddQRows, hgc.c, stanToBedAndExpRecs, bedUp, faSplit, trfBig, splitFaIntoContigs, aladdin, ameme. A full clean tree now builds with no warnings at -O3. refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/hgc/mafClick.c
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    f57fc11d951807e19b20b5960e735fa50eaea279 Fri Jun 12 13:10:00 2026 -0700
    Fix more warnings exposed by -O3 build across hg utils and errAbort Continuation of the -O3 cleanup: a full clean rebuild surfaced warnings in many programs whose objects had not been recompiled before. Most are the same mechanical patterns as the first batch (strncpy -> safecpy/memcpy, sprintf -> safef), plus a few that needed more thought: - errAbort.h: mark errAbort/vaErrAbort/errnoAbort/noWarnAbort as noreturn. They provably never return (longjmp or exit; the existing "to make compiler happy" exit(-1) in noWarnAbort confirms the intent), and this lets GCC prune the impossible null paths after an errAbort guard, fixing false-positive null-deref / overread warnings in mafAddIRows, mafAddIRowsStream and phyloPlace with no source change to those files. - altSplice.c (hgGene): real one-element stack buffer overflow. makeGrayShades writes shadesOfGray[maxShade+1], but the caller declared shadesOfGray[9] with maxShade=8. Grow the array to [10] (maxShade stays 8); behavior unchanged. - hgc.c bedPrintPos: ~60 callers pass a track-specific struct cast to (struct bed *) and read only its bed-compatible leading fields. At -O3 -Warray-bounds flags the casts because the real object is smaller than struct bed; the reads are safe by the bed-layout convention, so suppress -Warray-bounds around just that function. - mafsInRegion.c: chromFromSrc returns strchr(src,'.')+1, which GCC mis-sizes as a 0-byte region when handed to strcmp via sameString/differentString; suppress the false-positive -Wstringop-overread around extractMafs. - sanger22gtf.c, bottleneck.c: put the printf/fprintf in the else of the NULL guard so -Wformat-overflow (which runs before the noreturn-based pruning) can see the argument is non-null. safecpy/memcpy/safef conversions: basicBed already done earlier; here haplotypes (memcpy of the original pointer pun), gbToFaRa, motifSig, hgClonePos, featureBits, libScan, hgGoldGapGl, hgSoftPromoter, mafClick, mafAddQRows, hgc.c, stanToBedAndExpRecs, bedUp, faSplit, trfBig, splitFaIntoContigs, aladdin, ameme. A full clean tree now builds with no warnings at -O3. refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/hgcentralTidy/hgcentralTidy.c
  • lines changed 27, context: html, text, full: html, text
    b628620dca257848dc6e9b18ea8e09585ecaf216 Tue Jun 9 00:07:17 2026 -0700
    hgcentralTidy also needs the 64 bit sessionDb and userDb IDs refs #33554
• src/hg/htdocs/liftRequest.html
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    61272f4594c12ee485b70df7be66fa282e8b378f Wed Jun 10 07:27:54 2026 -0700
    fixup issues from claude code review refs #31811
• src/hg/htdocs/store.html
  • lines changed 2, context: html, text, full: html, text
    2a2cef743a8bf6b5b38332adbcdce72d16c5da37 Sun Jun 14 17:41:42 2026 -0700
    updating Linux versions tested for GBiC, refs #37723
• src/hg/htdocs/style/HGStyle.css
  • lines changed 1, context: html, text, full: html, text
    d0d3ac9414a163b759edf2b028a4b50f4057dbc3 Fri Jun 12 09:02:21 2026 -0700
    hgTracks quickLift: use trash-can icon for per-track remove QA asked for the per-track remove control in a QuickLift group to match the trash-can icon already used to delete custom tracks, instead of the red 'x', so the two behave consistently. Factor the trash-can SVG into a shared printTrashIcon() helper used by both the custom-track delete and the quickLift remove, and drop the red tint so the quickLift icon matches. refs #37535 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/htdocs/style/facetedComposite.css
  • lines changed 21, context: html, text, full: html, text
    6f41c6a196697c175a2cf5abcbd247ba24a2fe8e Mon Jun 15 09:22:37 2026 -0700
    Loading spinner for faceted composites (the page must first do the ajax metadata fetch, then process the result with dataTables). refs #36320
• src/hg/hubApi/tests/findGenome.README.txt
  • lines changed 159, context: html, text, full: html, text
    eb8aca4b2f05a4fac87c19f0015c0fdc830a2b09 Mon Jun 15 09:49:28 2026 -0700
    corresponding information about the use of the findGenome.sh script
• src/hg/hubApi/tests/findGenome.sh
  • lines changed 336, context: html, text, full: html, text
    847b1a96e008aecae23d9f20e250c22efd10dbe1 Mon Jun 15 09:45:56 2026 -0700
    useful script to test performance and accuracy of the "findGenome" functions, can be used before and after changes to verify functionality remains correct.
• src/hg/inc/quickLift.h
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    bb8470a90643b057df7bbf5d0140a5b2bbf9dddd Fri Jun 12 08:44:37 2026 -0700
    quickLift: load genePreds by column name, not a fixed 15-col loader Lifting a genePred track to another assembly used genePredExtLoad15, a positional loader that assumes the extended genePred columns. Classic knownGene-format tables instead carry proteinID and alignID after the ten core columns, so the loader read proteinID as the integer score field and aborted with "invalid signed integer" (e.g. "O54946", or "" when empty). This showed up when lifting from an assembly whose knownGene is the legacy format, such as mm10 to mm39 or rheMac10. Add quickLiftGenePreds(), which loads through genePredReader so the actual set of columns in the table is honored by name (proteinID maps to name2, score defaults), matching how the tracks load when not lifted. The three call sites that hardcoded genePredExtLoad15 (hgTracks gene loading and two hgc detail handlers) now use it. The chain-walking shared with quickLiftSql is factored into quickLiftLoadChains() and quickLiftChainQueryRange(). refs #37535 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/js/facetedComposite.js
  • lines changed 16, context: html, text, full: html, text
    6f41c6a196697c175a2cf5abcbd247ba24a2fe8e Mon Jun 15 09:22:37 2026 -0700
    Loading spinner for faceted composites (the page must first do the ajax metadata fetch, then process the result with dataTables). refs #36320
• src/hg/js/hgTracks.js
  • lines changed 2, context: html, text, full: html, text
    0f858fe7a83e59b83d3d034829ec6f9b09b20787 Tue Jun 9 19:34:44 2026 -0700
    hgTracks.js was looking for a myVariants form even when one didn't exist. This puts a guard on it. refs #33808
• src/hg/lib/assemblyList.sql
  • lines changed 6, context: html, text, full: html, text
    6c8386587f9dc2eb3a34db1018d8fd52361c2b4d Fri Jun 12 13:48:55 2026 -0700
    better indexes on assemblyList table to improve search performance
• src/hg/lib/bedDetail.c
  • lines changed 1, context: html, text, full: html, text
    fb50a1cca3a117bb964c43196671142484b13bf9 Fri Jun 12 12:10:47 2026 -0700
    lib jkOwnLib hg/lib: fix warnings exposed by -O3 build At -O3 GCC does more inlining and interprocedural range analysis, which surfaces several warnings that -O -g never triggered. With -Werror these break the build, so fix them ahead of switching the default to -O3. - bamFile.c: move setenv() into the else of its NULL guard so it is not reachable with a NULL argument (-Wnonnull, seen via inlining of bamFetch). - basicBed.c, wormdna.c, bedDetail.c, customFactory.c, hdb.c, qaSeq.c: replace strncpy() with safecpy() where the result must be terminated (-Wstringop-truncation). - htmshell.c: use memcpy() for the intentional exact-length, non-terminated copy (-Wstringop-truncation). - obscure.c: compute the comma groups in sprintLongWithCommas() with % 1000 so the compiler can see each %03lld argument is bounded (-Wformat-overflow). - crudeali.c: do the endian type-pun through a union so strict-aliasing analysis no longer reports the value as uninitialized (-Wuninitialized). - jksql.c: wrap a possibly-NULL database name in naForNull() before passing it to %s (-Wformat-overflow). refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/lib/cart.c
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    ca99897a163f545419d58c22e594d9608474cdb7 Tue Jun 9 19:10:23 2026 -0700
    Moving sessionDb load after captcha check so bot traffic doesn't fill up sessionDb, refs #37739
  • lines changed 3, context: html, text, full: html, text
    325cbfe133124a17017edda28f0789217e86c61f Wed Jun 10 06:17:25 2026 -0700
    just a few comments
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    6002bdaa995565598fecea8123804878062db7b1 Wed Jun 10 15:16:05 2026 -0700
    Do sessionDb and userDb load after checking captcha so that invalid bot traffic doesn't run up the id counts, refs #37739
  • lines changed 2, context: html, text, full: html, text
    596fc9e27b7266b9692723e059731fa8ff2bbd11 Fri Jun 12 11:24:40 2026 -0700
    do not need the central db connection until after the captcha verification - this appears to eliminate all SQL connection for failed robot contacts
• src/hg/lib/customFactory.c
  • lines changed 2, context: html, text, full: html, text
    fb50a1cca3a117bb964c43196671142484b13bf9 Fri Jun 12 12:10:47 2026 -0700
    lib jkOwnLib hg/lib: fix warnings exposed by -O3 build At -O3 GCC does more inlining and interprocedural range analysis, which surfaces several warnings that -O -g never triggered. With -Werror these break the build, so fix them ahead of switching the default to -O3. - bamFile.c: move setenv() into the else of its NULL guard so it is not reachable with a NULL argument (-Wnonnull, seen via inlining of bamFetch). - basicBed.c, wormdna.c, bedDetail.c, customFactory.c, hdb.c, qaSeq.c: replace strncpy() with safecpy() where the result must be terminated (-Wstringop-truncation). - htmshell.c: use memcpy() for the intentional exact-length, non-terminated copy (-Wstringop-truncation). - obscure.c: compute the comma groups in sprintLongWithCommas() with % 1000 so the compiler can see each %03lld argument is bounded (-Wformat-overflow). - crudeali.c: do the endian type-pun through a union so strict-aliasing analysis no longer reports the value as uninitialized (-Wuninitialized). - jksql.c: wrap a possibly-NULL database name in naForNull() before passing it to %s (-Wformat-overflow). refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/lib/hdb.c
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    fb50a1cca3a117bb964c43196671142484b13bf9 Fri Jun 12 12:10:47 2026 -0700
    lib jkOwnLib hg/lib: fix warnings exposed by -O3 build At -O3 GCC does more inlining and interprocedural range analysis, which surfaces several warnings that -O -g never triggered. With -Werror these break the build, so fix them ahead of switching the default to -O3. - bamFile.c: move setenv() into the else of its NULL guard so it is not reachable with a NULL argument (-Wnonnull, seen via inlining of bamFetch). - basicBed.c, wormdna.c, bedDetail.c, customFactory.c, hdb.c, qaSeq.c: replace strncpy() with safecpy() where the result must be terminated (-Wstringop-truncation). - htmshell.c: use memcpy() for the intentional exact-length, non-terminated copy (-Wstringop-truncation). - obscure.c: compute the comma groups in sprintLongWithCommas() with % 1000 so the compiler can see each %03lld argument is bounded (-Wformat-overflow). - crudeali.c: do the endian type-pun through a union so strict-aliasing analysis no longer reports the value as uninitialized (-Wuninitialized). - jksql.c: wrap a possibly-NULL database name in naForNull() before passing it to %s (-Wformat-overflow). refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/lib/jksql.c
  • lines changed 1, context: html, text, full: html, text
    fb50a1cca3a117bb964c43196671142484b13bf9 Fri Jun 12 12:10:47 2026 -0700
    lib jkOwnLib hg/lib: fix warnings exposed by -O3 build At -O3 GCC does more inlining and interprocedural range analysis, which surfaces several warnings that -O -g never triggered. With -Werror these break the build, so fix them ahead of switching the default to -O3. - bamFile.c: move setenv() into the else of its NULL guard so it is not reachable with a NULL argument (-Wnonnull, seen via inlining of bamFetch). - basicBed.c, wormdna.c, bedDetail.c, customFactory.c, hdb.c, qaSeq.c: replace strncpy() with safecpy() where the result must be terminated (-Wstringop-truncation). - htmshell.c: use memcpy() for the intentional exact-length, non-terminated copy (-Wstringop-truncation). - obscure.c: compute the comma groups in sprintLongWithCommas() with % 1000 so the compiler can see each %03lld argument is bounded (-Wformat-overflow). - crudeali.c: do the endian type-pun through a union so strict-aliasing analysis no longer reports the value as uninitialized (-Wuninitialized). - jksql.c: wrap a possibly-NULL database name in naForNull() before passing it to %s (-Wformat-overflow). refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/lib/qaSeq.c
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    fb50a1cca3a117bb964c43196671142484b13bf9 Fri Jun 12 12:10:47 2026 -0700
    lib jkOwnLib hg/lib: fix warnings exposed by -O3 build At -O3 GCC does more inlining and interprocedural range analysis, which surfaces several warnings that -O -g never triggered. With -Werror these break the build, so fix them ahead of switching the default to -O3. - bamFile.c: move setenv() into the else of its NULL guard so it is not reachable with a NULL argument (-Wnonnull, seen via inlining of bamFetch). - basicBed.c, wormdna.c, bedDetail.c, customFactory.c, hdb.c, qaSeq.c: replace strncpy() with safecpy() where the result must be terminated (-Wstringop-truncation). - htmshell.c: use memcpy() for the intentional exact-length, non-terminated copy (-Wstringop-truncation). - obscure.c: compute the comma groups in sprintLongWithCommas() with % 1000 so the compiler can see each %03lld argument is bounded (-Wformat-overflow). - crudeali.c: do the endian type-pun through a union so strict-aliasing analysis no longer reports the value as uninitialized (-Wuninitialized). - jksql.c: wrap a possibly-NULL database name in naForNull() before passing it to %s (-Wformat-overflow). refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/lib/quickLift.c
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    bb8470a90643b057df7bbf5d0140a5b2bbf9dddd Fri Jun 12 08:44:37 2026 -0700
    quickLift: load genePreds by column name, not a fixed 15-col loader Lifting a genePred track to another assembly used genePredExtLoad15, a positional loader that assumes the extended genePred columns. Classic knownGene-format tables instead carry proteinID and alignID after the ten core columns, so the loader read proteinID as the integer score field and aborted with "invalid signed integer" (e.g. "O54946", or "" when empty). This showed up when lifting from an assembly whose knownGene is the legacy format, such as mm10 to mm39 or rheMac10. Add quickLiftGenePreds(), which loads through genePredReader so the actual set of columns in the table is honored by name (proteinID maps to name2, score defaults), matching how the tracks load when not lifted. The three call sites that hardcoded genePredExtLoad15 (hgTracks gene loading and two hgc detail handlers) now use it. The chain-walking shared with quickLiftSql is factored into quickLiftLoadChains() and quickLiftChainQueryRange(). refs #37535 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/doc/hg38/gnomad.txt
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    ecc2331000637cbc2523653642d926935b5b83fc Sat Jun 13 00:42:03 2026 -0700
    gnomAD v4.1.1 bigBed variant track for hg38, refs #37351 Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
  • lines changed 57, context: html, text, full: html, text
    574399b4a7d8fc75c1745fa83564f547ddcb9e8c Sat Jun 13 00:43:54 2026 -0700
    gnomAD v4.1.1 gene constraint tracks for hg38, refs #37351 Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
• src/hg/makeDb/doc/hg38/lrSv.txt
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    ef61e73fc416622d8557ec2439df2344a1cc80c3 Tue Jun 9 15:10:01 2026 -0700
    lrSv: replace HPRC v2.0 pangenome SV track with v2.1 (hprc2v21Sv) Drop the v2.0 wave-decomposed hprc2Sv track and add hprc2v21Sv built from the HPRC v2.1 minigraph-cactus raw vg deconstruct VCFs (gref95.ro), on both hg38 (GRCh38 path, 596,063 SVs) and hs1 (T2T-CHM13 path, 608,435 SVs). The v2.1 files lack per-allele TYPE/LEN, so the new converter classifies INS/DEL by parsimony-trimming REF/ALT and the net length change. The v2.0 build recipe, converter and schema are kept but commented out in the makeDocs in case wave-decomposed VCFs are released again, refs #36258
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    cd4cf386f217a028a89e351a736e1310f0d2a5d1 Wed Jun 10 06:04:14 2026 -0700
    lrSv: document the lrSvAll merge build in the makeDoc Add a section explaining how the combined lrSvAll track is built: the databases.tsv config that lists the source bigBeds, how to run lrSvMergeAll.py, that it auto-generates lrSvAll.ra, and that the HPRC row uses the v2.1 file while the Jasmine callset is excluded, refs #36258
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    9eb4e0937782954c19d664e7d384d210bffb3b25 Sat Jun 13 16:01:42 2026 -0700
    lrSv: QA fixes from Lou's review - dedup, shared color palette, deCODE/AoU cleanup - Drop kwanhoSv (KimPD) from the lrSvAll merge in databases.tsv; it stays on dev/alpha until published, which also removes its >5 Mb breakend artifacts from the merged track. - Remove searchIndex from colorsDbSv, lrSv1kLin and lrSvAll (and the merge generator): the bigBeds were built without a name index, so by-name search never worked. - Single shared per-SV-type color palette in lrSvCommon.py (svColor), used by every converter and the merge. CPX is purple everywhere (was orange in 1kgOnt/apr/cpc1, colliding with INV's orange), colorsDb DEL is 200,0,0 like the rest, and TRA/INSDEL get their own colors. - deCODE: drop byte-identical duplicate rows and blank the fake AC=50 placeholder (AC is now a string field, omitted from the name and mouseOver). - AoU: numeric-entity-encode non-ASCII gene/trait text and drop duplicate rows. - gustafson, chirmade101, hprc2v21: drop byte-identical duplicate rows. - lrSvMergeAll.py: skip byte-identical duplicate source rows instead of summing their allele counts, which had inflated the per-database and total AC. refs #36258
• src/hg/makeDb/doc/hg38/masterMindGame.txt
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    6701d67860c32b8886b59587c9e32a4f86a8a96d Tue Jun 9 17:13:31 2026 -0700
    masterMindGame: demo bigLolly track rendering a solved game of Mastermind on hg38 Demonstrates the lolly track type by mapping a Mastermind board onto it: score field is the board row, genomic position is the peg column, itemRgb is the peg color, and the size field separates the large code pegs from the small feedback key pegs. Guesses come from a consistent-candidate solver so the black/white feedback is real. Included alpha-only.
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    736e788b252ccc94a432bef54ac83321848560b1 Wed Jun 10 06:57:07 2026 -0700
    Revert "masterMindGame: demo bigLolly track rendering a solved game of Mastermind on hg38" This reverts commit 6701d67860c32b8886b59587c9e32a4f86a8a96d.
• src/hg/makeDb/doc/hg38/varFreqs.txt
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    af9a5b388259e680dd34bc47b2cad4ff6e3d162f Sat Jun 13 03:00:51 2026 -0700
    varFreqs: pre-release polish from comprehensive sanity check. * Sync the new combined-track shortLabels into the four description pages: "Affected/Case Individuals" -> "Disease cohorts" and "Population + Unaffected" -> "Population reference" (matches the trackdb shortLabels users now see). * Add a paragraph in the supertrack Methods section describing the pooled affectedAF / backgroundAF formulation (sum AC / sum AN) and the default_an configuration that handles AF-only cohorts. * Update the in-track Methods paragraphs on varFreqsAffected.html and varFreqsBackground.html: replace "summed/maximized" with "pooled". * Fix supertrack table downloadability column to match the underscore-prefix convention: allofus "Yes" -> "No" (description page already says license restricted); gregor "No" -> "Yes" (description page says VCF is on our download server, and the gbdb path is not underscore-prefixed). * Add a 2026-06-12 makedoc section documenting the pooled-AF rebuild, the default_an mechanism, the new affectedAN/backgroundAN columns, the before/after spot-check at APOE rs429358, and the build commands. refs #36642
• src/hg/makeDb/doc/hg38/varaico.txt
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    3030fb4a9c489593d8286b7bb469ebda3c575ad6 Wed Jun 10 12:56:44 2026 -0700
    Documenting the release 2 archive step in the Varaico makedoc and fixing a hardcoded hg38 path in the description page example, refs #37658
• src/hg/makeDb/doc/hs1/lrSv.txt
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    ef61e73fc416622d8557ec2439df2344a1cc80c3 Tue Jun 9 15:10:01 2026 -0700
    lrSv: replace HPRC v2.0 pangenome SV track with v2.1 (hprc2v21Sv) Drop the v2.0 wave-decomposed hprc2Sv track and add hprc2v21Sv built from the HPRC v2.1 minigraph-cactus raw vg deconstruct VCFs (gref95.ro), on both hg38 (GRCh38 path, 596,063 SVs) and hs1 (T2T-CHM13 path, 608,435 SVs). The v2.1 files lack per-allele TYPE/LEN, so the new converter classifies INS/DEL by parsimony-trimming REF/ALT and the net length change. The v2.0 build recipe, converter and schema are kept but commented out in the makeDocs in case wave-decomposed VCFs are released again, refs #36258
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    9eb4e0937782954c19d664e7d384d210bffb3b25 Sat Jun 13 16:01:42 2026 -0700
    lrSv: QA fixes from Lou's review - dedup, shared color palette, deCODE/AoU cleanup - Drop kwanhoSv (KimPD) from the lrSvAll merge in databases.tsv; it stays on dev/alpha until published, which also removes its >5 Mb breakend artifacts from the merged track. - Remove searchIndex from colorsDbSv, lrSv1kLin and lrSvAll (and the merge generator): the bigBeds were built without a name index, so by-name search never worked. - Single shared per-SV-type color palette in lrSvCommon.py (svColor), used by every converter and the merge. CPX is purple everywhere (was orange in 1kgOnt/apr/cpc1, colliding with INV's orange), colorsDb DEL is 200,0,0 like the rest, and TRA/INSDEL get their own colors. - deCODE: drop byte-identical duplicate rows and blank the fake AC=50 placeholder (AC is now a string field, omitted from the name and mouseOver). - AoU: numeric-entity-encode non-ASCII gene/trait text and drop duplicate rows. - gustafson, chirmade101, hprc2v21: drop byte-identical duplicate rows. - lrSvMergeAll.py: skip byte-identical duplicate source rows instead of summing their allele counts, which had inflated the per-database and total AC. refs #36258
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
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    b0e65cd4657431971b78d34a7451ec55eae082ed Tue Jun 9 16:22:13 2026 -0700
    adding a couple per user request refs #29545
• src/hg/makeDb/gnomad/combine.v4.1.1.awk
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    574399b4a7d8fc75c1745fa83564f547ddcb9e8c Sat Jun 13 00:43:54 2026 -0700
    gnomAD v4.1.1 gene constraint tracks for hg38, refs #37351 Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
• src/hg/makeDb/gnomad/gnomadVcfBedToBigBed
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    ecc2331000637cbc2523653642d926935b5b83fc Sat Jun 13 00:42:03 2026 -0700
    gnomAD v4.1.1 bigBed variant track for hg38, refs #37351 Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
• src/hg/makeDb/gnomad/missenseMetrics.v4.1.1.as
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    574399b4a7d8fc75c1745fa83564f547ddcb9e8c Sat Jun 13 00:43:54 2026 -0700
    gnomAD v4.1.1 gene constraint tracks for hg38, refs #37351 Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
• src/hg/makeDb/gnomad/pliMetrics.v4.1.1.as
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    574399b4a7d8fc75c1745fa83564f547ddcb9e8c Sat Jun 13 00:43:54 2026 -0700
    gnomAD v4.1.1 gene constraint tracks for hg38, refs #37351 Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
• src/hg/makeDb/hgClonePos/hgClonePos.c
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    f57fc11d951807e19b20b5960e735fa50eaea279 Fri Jun 12 13:10:00 2026 -0700
    Fix more warnings exposed by -O3 build across hg utils and errAbort Continuation of the -O3 cleanup: a full clean rebuild surfaced warnings in many programs whose objects had not been recompiled before. Most are the same mechanical patterns as the first batch (strncpy -> safecpy/memcpy, sprintf -> safef), plus a few that needed more thought: - errAbort.h: mark errAbort/vaErrAbort/errnoAbort/noWarnAbort as noreturn. They provably never return (longjmp or exit; the existing "to make compiler happy" exit(-1) in noWarnAbort confirms the intent), and this lets GCC prune the impossible null paths after an errAbort guard, fixing false-positive null-deref / overread warnings in mafAddIRows, mafAddIRowsStream and phyloPlace with no source change to those files. - altSplice.c (hgGene): real one-element stack buffer overflow. makeGrayShades writes shadesOfGray[maxShade+1], but the caller declared shadesOfGray[9] with maxShade=8. Grow the array to [10] (maxShade stays 8); behavior unchanged. - hgc.c bedPrintPos: ~60 callers pass a track-specific struct cast to (struct bed *) and read only its bed-compatible leading fields. At -O3 -Warray-bounds flags the casts because the real object is smaller than struct bed; the reads are safe by the bed-layout convention, so suppress -Warray-bounds around just that function. - mafsInRegion.c: chromFromSrc returns strchr(src,'.')+1, which GCC mis-sizes as a 0-byte region when handed to strcmp via sameString/differentString; suppress the false-positive -Wstringop-overread around extractMafs. - sanger22gtf.c, bottleneck.c: put the printf/fprintf in the else of the NULL guard so -Wformat-overflow (which runs before the noreturn-based pruning) can see the argument is non-null. safecpy/memcpy/safef conversions: basicBed already done earlier; here haplotypes (memcpy of the original pointer pun), gbToFaRa, motifSig, hgClonePos, featureBits, libScan, hgGoldGapGl, hgSoftPromoter, mafClick, mafAddQRows, hgc.c, stanToBedAndExpRecs, bedUp, faSplit, trfBig, splitFaIntoContigs, aladdin, ameme. A full clean tree now builds with no warnings at -O3. refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/hgGoldGapGl/hgGoldGapGl.c
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    f57fc11d951807e19b20b5960e735fa50eaea279 Fri Jun 12 13:10:00 2026 -0700
    Fix more warnings exposed by -O3 build across hg utils and errAbort Continuation of the -O3 cleanup: a full clean rebuild surfaced warnings in many programs whose objects had not been recompiled before. Most are the same mechanical patterns as the first batch (strncpy -> safecpy/memcpy, sprintf -> safef), plus a few that needed more thought: - errAbort.h: mark errAbort/vaErrAbort/errnoAbort/noWarnAbort as noreturn. They provably never return (longjmp or exit; the existing "to make compiler happy" exit(-1) in noWarnAbort confirms the intent), and this lets GCC prune the impossible null paths after an errAbort guard, fixing false-positive null-deref / overread warnings in mafAddIRows, mafAddIRowsStream and phyloPlace with no source change to those files. - altSplice.c (hgGene): real one-element stack buffer overflow. makeGrayShades writes shadesOfGray[maxShade+1], but the caller declared shadesOfGray[9] with maxShade=8. Grow the array to [10] (maxShade stays 8); behavior unchanged. - hgc.c bedPrintPos: ~60 callers pass a track-specific struct cast to (struct bed *) and read only its bed-compatible leading fields. At -O3 -Warray-bounds flags the casts because the real object is smaller than struct bed; the reads are safe by the bed-layout convention, so suppress -Warray-bounds around just that function. - mafsInRegion.c: chromFromSrc returns strchr(src,'.')+1, which GCC mis-sizes as a 0-byte region when handed to strcmp via sameString/differentString; suppress the false-positive -Wstringop-overread around extractMafs. - sanger22gtf.c, bottleneck.c: put the printf/fprintf in the else of the NULL guard so -Wformat-overflow (which runs before the noreturn-based pruning) can see the argument is non-null. safecpy/memcpy/safef conversions: basicBed already done earlier; here haplotypes (memcpy of the original pointer pun), gbToFaRa, motifSig, hgClonePos, featureBits, libScan, hgGoldGapGl, hgSoftPromoter, mafClick, mafAddQRows, hgc.c, stanToBedAndExpRecs, bedUp, faSplit, trfBig, splitFaIntoContigs, aladdin, ameme. A full clean tree now builds with no warnings at -O3. refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/outside/hgSoftPromoter/hgSoftPromoter.c
  • lines changed 1, context: html, text, full: html, text
    f57fc11d951807e19b20b5960e735fa50eaea279 Fri Jun 12 13:10:00 2026 -0700
    Fix more warnings exposed by -O3 build across hg utils and errAbort Continuation of the -O3 cleanup: a full clean rebuild surfaced warnings in many programs whose objects had not been recompiled before. Most are the same mechanical patterns as the first batch (strncpy -> safecpy/memcpy, sprintf -> safef), plus a few that needed more thought: - errAbort.h: mark errAbort/vaErrAbort/errnoAbort/noWarnAbort as noreturn. They provably never return (longjmp or exit; the existing "to make compiler happy" exit(-1) in noWarnAbort confirms the intent), and this lets GCC prune the impossible null paths after an errAbort guard, fixing false-positive null-deref / overread warnings in mafAddIRows, mafAddIRowsStream and phyloPlace with no source change to those files. - altSplice.c (hgGene): real one-element stack buffer overflow. makeGrayShades writes shadesOfGray[maxShade+1], but the caller declared shadesOfGray[9] with maxShade=8. Grow the array to [10] (maxShade stays 8); behavior unchanged. - hgc.c bedPrintPos: ~60 callers pass a track-specific struct cast to (struct bed *) and read only its bed-compatible leading fields. At -O3 -Warray-bounds flags the casts because the real object is smaller than struct bed; the reads are safe by the bed-layout convention, so suppress -Warray-bounds around just that function. - mafsInRegion.c: chromFromSrc returns strchr(src,'.')+1, which GCC mis-sizes as a 0-byte region when handed to strcmp via sameString/differentString; suppress the false-positive -Wstringop-overread around extractMafs. - sanger22gtf.c, bottleneck.c: put the printf/fprintf in the else of the NULL guard so -Wformat-overflow (which runs before the noreturn-based pruning) can see the argument is non-null. safecpy/memcpy/safef conversions: basicBed already done earlier; here haplotypes (memcpy of the original pointer pun), gbToFaRa, motifSig, hgClonePos, featureBits, libScan, hgGoldGapGl, hgSoftPromoter, mafClick, mafAddQRows, hgc.c, stanToBedAndExpRecs, bedUp, faSplit, trfBig, splitFaIntoContigs, aladdin, ameme. A full clean tree now builds with no warnings at -O3. refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/outside/sanger22gtf/sanger22gtf.c
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    f57fc11d951807e19b20b5960e735fa50eaea279 Fri Jun 12 13:10:00 2026 -0700
    Fix more warnings exposed by -O3 build across hg utils and errAbort Continuation of the -O3 cleanup: a full clean rebuild surfaced warnings in many programs whose objects had not been recompiled before. Most are the same mechanical patterns as the first batch (strncpy -> safecpy/memcpy, sprintf -> safef), plus a few that needed more thought: - errAbort.h: mark errAbort/vaErrAbort/errnoAbort/noWarnAbort as noreturn. They provably never return (longjmp or exit; the existing "to make compiler happy" exit(-1) in noWarnAbort confirms the intent), and this lets GCC prune the impossible null paths after an errAbort guard, fixing false-positive null-deref / overread warnings in mafAddIRows, mafAddIRowsStream and phyloPlace with no source change to those files. - altSplice.c (hgGene): real one-element stack buffer overflow. makeGrayShades writes shadesOfGray[maxShade+1], but the caller declared shadesOfGray[9] with maxShade=8. Grow the array to [10] (maxShade stays 8); behavior unchanged. - hgc.c bedPrintPos: ~60 callers pass a track-specific struct cast to (struct bed *) and read only its bed-compatible leading fields. At -O3 -Warray-bounds flags the casts because the real object is smaller than struct bed; the reads are safe by the bed-layout convention, so suppress -Warray-bounds around just that function. - mafsInRegion.c: chromFromSrc returns strchr(src,'.')+1, which GCC mis-sizes as a 0-byte region when handed to strcmp via sameString/differentString; suppress the false-positive -Wstringop-overread around extractMafs. - sanger22gtf.c, bottleneck.c: put the printf/fprintf in the else of the NULL guard so -Wformat-overflow (which runs before the noreturn-based pruning) can see the argument is non-null. safecpy/memcpy/safef conversions: basicBed already done earlier; here haplotypes (memcpy of the original pointer pun), gbToFaRa, motifSig, hgClonePos, featureBits, libScan, hgGoldGapGl, hgSoftPromoter, mafClick, mafAddQRows, hgc.c, stanToBedAndExpRecs, bedUp, faSplit, trfBig, splitFaIntoContigs, aladdin, ameme. A full clean tree now builds with no warnings at -O3. refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/makeDb/scripts/gnomadV4.1.1/buildGnomadV4.1.1BigBed.sh
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    ecc2331000637cbc2523653642d926935b5b83fc Sat Jun 13 00:42:03 2026 -0700
    gnomAD v4.1.1 bigBed variant track for hg38, refs #37351 Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
• src/hg/makeDb/scripts/gnomadV4.1.1/exomes.as
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    ecc2331000637cbc2523653642d926935b5b83fc Sat Jun 13 00:42:03 2026 -0700
    gnomAD v4.1.1 bigBed variant track for hg38, refs #37351 Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
• src/hg/makeDb/scripts/gnomadV4.1.1/genomes.as
  • lines changed 35, context: html, text, full: html, text
    ecc2331000637cbc2523653642d926935b5b83fc Sat Jun 13 00:42:03 2026 -0700
    gnomAD v4.1.1 bigBed variant track for hg38, refs #37351 Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
• src/hg/makeDb/scripts/gnomadV4.1.1/v4.1.1.vcfToBed.exomes.fieldList
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    ecc2331000637cbc2523653642d926935b5b83fc Sat Jun 13 00:42:03 2026 -0700
    gnomAD v4.1.1 bigBed variant track for hg38, refs #37351 Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
• src/hg/makeDb/scripts/gnomadV4.1.1/v4.1.1.vcfToBed.genomes.fieldList
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    ecc2331000637cbc2523653642d926935b5b83fc Sat Jun 13 00:42:03 2026 -0700
    gnomAD v4.1.1 bigBed variant track for hg38, refs #37351 Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
• src/hg/makeDb/scripts/lrSv/databases.tsv
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    644eae7700eb62343b142a44258ee91a944f4853 Tue Jun 9 15:17:03 2026 -0700
    lrSv: rebuild merged lrSvAll track with HPRC v2.1 data Repoint the HPRC entry in databases.tsv from the removed v2.0 hprc2.bb to the new hprc2v21.bb and re-run the merge. The combined track now holds 2,359,011 variants (was 2,694,871); the drop is the smaller v2.1 HPRC callset. Regenerated lrSvAll.ra and updated the overview table on the container page. The HPRC Jasmine track is intentionally not part of the merge, refs #36258
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    9eb4e0937782954c19d664e7d384d210bffb3b25 Sat Jun 13 16:01:42 2026 -0700
    lrSv: QA fixes from Lou's review - dedup, shared color palette, deCODE/AoU cleanup - Drop kwanhoSv (KimPD) from the lrSvAll merge in databases.tsv; it stays on dev/alpha until published, which also removes its >5 Mb breakend artifacts from the merged track. - Remove searchIndex from colorsDbSv, lrSv1kLin and lrSvAll (and the merge generator): the bigBeds were built without a name index, so by-name search never worked. - Single shared per-SV-type color palette in lrSvCommon.py (svColor), used by every converter and the merge. CPX is purple everywhere (was orange in 1kgOnt/apr/cpc1, colliding with INV's orange), colorsDb DEL is 200,0,0 like the rest, and TRA/INSDEL get their own colors. - deCODE: drop byte-identical duplicate rows and blank the fake AC=50 placeholder (AC is now a string field, omitted from the name and mouseOver). - AoU: numeric-entity-encode non-ASCII gene/trait text and drop duplicate rows. - gustafson, chirmade101, hprc2v21: drop byte-identical duplicate rows. - lrSvMergeAll.py: skip byte-identical duplicate source rows instead of summing their allele counts, which had inflated the per-database and total AC. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSv1kgOntVcfToBed.py
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    9eb4e0937782954c19d664e7d384d210bffb3b25 Sat Jun 13 16:01:42 2026 -0700
    lrSv: QA fixes from Lou's review - dedup, shared color palette, deCODE/AoU cleanup - Drop kwanhoSv (KimPD) from the lrSvAll merge in databases.tsv; it stays on dev/alpha until published, which also removes its >5 Mb breakend artifacts from the merged track. - Remove searchIndex from colorsDbSv, lrSv1kLin and lrSvAll (and the merge generator): the bigBeds were built without a name index, so by-name search never worked. - Single shared per-SV-type color palette in lrSvCommon.py (svColor), used by every converter and the merge. CPX is purple everywhere (was orange in 1kgOnt/apr/cpc1, colliding with INV's orange), colorsDb DEL is 200,0,0 like the rest, and TRA/INSDEL get their own colors. - deCODE: drop byte-identical duplicate rows and blank the fake AC=50 placeholder (AC is now a string field, omitted from the name and mouseOver). - AoU: numeric-entity-encode non-ASCII gene/trait text and drop duplicate rows. - gustafson, chirmade101, hprc2v21: drop byte-identical duplicate rows. - lrSvMergeAll.py: skip byte-identical duplicate source rows instead of summing their allele counts, which had inflated the per-database and total AC. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvAou1kCsvToBed.py
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    9eb4e0937782954c19d664e7d384d210bffb3b25 Sat Jun 13 16:01:42 2026 -0700
    lrSv: QA fixes from Lou's review - dedup, shared color palette, deCODE/AoU cleanup - Drop kwanhoSv (KimPD) from the lrSvAll merge in databases.tsv; it stays on dev/alpha until published, which also removes its >5 Mb breakend artifacts from the merged track. - Remove searchIndex from colorsDbSv, lrSv1kLin and lrSvAll (and the merge generator): the bigBeds were built without a name index, so by-name search never worked. - Single shared per-SV-type color palette in lrSvCommon.py (svColor), used by every converter and the merge. CPX is purple everywhere (was orange in 1kgOnt/apr/cpc1, colliding with INV's orange), colorsDb DEL is 200,0,0 like the rest, and TRA/INSDEL get their own colors. - deCODE: drop byte-identical duplicate rows and blank the fake AC=50 placeholder (AC is now a string field, omitted from the name and mouseOver). - AoU: numeric-entity-encode non-ASCII gene/trait text and drop duplicate rows. - gustafson, chirmade101, hprc2v21: drop byte-identical duplicate rows. - lrSvMergeAll.py: skip byte-identical duplicate source rows instead of summing their allele counts, which had inflated the per-database and total AC. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvAprVcfToBed.py
  • lines changed 9, context: html, text, full: html, text
    9eb4e0937782954c19d664e7d384d210bffb3b25 Sat Jun 13 16:01:42 2026 -0700
    lrSv: QA fixes from Lou's review - dedup, shared color palette, deCODE/AoU cleanup - Drop kwanhoSv (KimPD) from the lrSvAll merge in databases.tsv; it stays on dev/alpha until published, which also removes its >5 Mb breakend artifacts from the merged track. - Remove searchIndex from colorsDbSv, lrSv1kLin and lrSvAll (and the merge generator): the bigBeds were built without a name index, so by-name search never worked. - Single shared per-SV-type color palette in lrSvCommon.py (svColor), used by every converter and the merge. CPX is purple everywhere (was orange in 1kgOnt/apr/cpc1, colliding with INV's orange), colorsDb DEL is 200,0,0 like the rest, and TRA/INSDEL get their own colors. - deCODE: drop byte-identical duplicate rows and blank the fake AC=50 placeholder (AC is now a string field, omitted from the name and mouseOver). - AoU: numeric-entity-encode non-ASCII gene/trait text and drop duplicate rows. - gustafson, chirmade101, hprc2v21: drop byte-identical duplicate rows. - lrSvMergeAll.py: skip byte-identical duplicate source rows instead of summing their allele counts, which had inflated the per-database and total AC. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvChirmade101TsvToBed.py
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    9eb4e0937782954c19d664e7d384d210bffb3b25 Sat Jun 13 16:01:42 2026 -0700
    lrSv: QA fixes from Lou's review - dedup, shared color palette, deCODE/AoU cleanup - Drop kwanhoSv (KimPD) from the lrSvAll merge in databases.tsv; it stays on dev/alpha until published, which also removes its >5 Mb breakend artifacts from the merged track. - Remove searchIndex from colorsDbSv, lrSv1kLin and lrSvAll (and the merge generator): the bigBeds were built without a name index, so by-name search never worked. - Single shared per-SV-type color palette in lrSvCommon.py (svColor), used by every converter and the merge. CPX is purple everywhere (was orange in 1kgOnt/apr/cpc1, colliding with INV's orange), colorsDb DEL is 200,0,0 like the rest, and TRA/INSDEL get their own colors. - deCODE: drop byte-identical duplicate rows and blank the fake AC=50 placeholder (AC is now a string field, omitted from the name and mouseOver). - AoU: numeric-entity-encode non-ASCII gene/trait text and drop duplicate rows. - gustafson, chirmade101, hprc2v21: drop byte-identical duplicate rows. - lrSvMergeAll.py: skip byte-identical duplicate source rows instead of summing their allele counts, which had inflated the per-database and total AC. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvColorsDbSvVcfToBed.py
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    9eb4e0937782954c19d664e7d384d210bffb3b25 Sat Jun 13 16:01:42 2026 -0700
    lrSv: QA fixes from Lou's review - dedup, shared color palette, deCODE/AoU cleanup - Drop kwanhoSv (KimPD) from the lrSvAll merge in databases.tsv; it stays on dev/alpha until published, which also removes its >5 Mb breakend artifacts from the merged track. - Remove searchIndex from colorsDbSv, lrSv1kLin and lrSvAll (and the merge generator): the bigBeds were built without a name index, so by-name search never worked. - Single shared per-SV-type color palette in lrSvCommon.py (svColor), used by every converter and the merge. CPX is purple everywhere (was orange in 1kgOnt/apr/cpc1, colliding with INV's orange), colorsDb DEL is 200,0,0 like the rest, and TRA/INSDEL get their own colors. - deCODE: drop byte-identical duplicate rows and blank the fake AC=50 placeholder (AC is now a string field, omitted from the name and mouseOver). - AoU: numeric-entity-encode non-ASCII gene/trait text and drop duplicate rows. - gustafson, chirmade101, hprc2v21: drop byte-identical duplicate rows. - lrSvMergeAll.py: skip byte-identical duplicate source rows instead of summing their allele counts, which had inflated the per-database and total AC. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvCommon.py
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    9eb4e0937782954c19d664e7d384d210bffb3b25 Sat Jun 13 16:01:42 2026 -0700
    lrSv: QA fixes from Lou's review - dedup, shared color palette, deCODE/AoU cleanup - Drop kwanhoSv (KimPD) from the lrSvAll merge in databases.tsv; it stays on dev/alpha until published, which also removes its >5 Mb breakend artifacts from the merged track. - Remove searchIndex from colorsDbSv, lrSv1kLin and lrSvAll (and the merge generator): the bigBeds were built without a name index, so by-name search never worked. - Single shared per-SV-type color palette in lrSvCommon.py (svColor), used by every converter and the merge. CPX is purple everywhere (was orange in 1kgOnt/apr/cpc1, colliding with INV's orange), colorsDb DEL is 200,0,0 like the rest, and TRA/INSDEL get their own colors. - deCODE: drop byte-identical duplicate rows and blank the fake AC=50 placeholder (AC is now a string field, omitted from the name and mouseOver). - AoU: numeric-entity-encode non-ASCII gene/trait text and drop duplicate rows. - gustafson, chirmade101, hprc2v21: drop byte-identical duplicate rows. - lrSvMergeAll.py: skip byte-identical duplicate source rows instead of summing their allele counts, which had inflated the per-database and total AC. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvCpc1VcfToBed.py
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    9eb4e0937782954c19d664e7d384d210bffb3b25 Sat Jun 13 16:01:42 2026 -0700
    lrSv: QA fixes from Lou's review - dedup, shared color palette, deCODE/AoU cleanup - Drop kwanhoSv (KimPD) from the lrSvAll merge in databases.tsv; it stays on dev/alpha until published, which also removes its >5 Mb breakend artifacts from the merged track. - Remove searchIndex from colorsDbSv, lrSv1kLin and lrSvAll (and the merge generator): the bigBeds were built without a name index, so by-name search never worked. - Single shared per-SV-type color palette in lrSvCommon.py (svColor), used by every converter and the merge. CPX is purple everywhere (was orange in 1kgOnt/apr/cpc1, colliding with INV's orange), colorsDb DEL is 200,0,0 like the rest, and TRA/INSDEL get their own colors. - deCODE: drop byte-identical duplicate rows and blank the fake AC=50 placeholder (AC is now a string field, omitted from the name and mouseOver). - AoU: numeric-entity-encode non-ASCII gene/trait text and drop duplicate rows. - gustafson, chirmade101, hprc2v21: drop byte-identical duplicate rows. - lrSvMergeAll.py: skip byte-identical duplicate source rows instead of summing their allele counts, which had inflated the per-database and total AC. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvDecode.as
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    9eb4e0937782954c19d664e7d384d210bffb3b25 Sat Jun 13 16:01:42 2026 -0700
    lrSv: QA fixes from Lou's review - dedup, shared color palette, deCODE/AoU cleanup - Drop kwanhoSv (KimPD) from the lrSvAll merge in databases.tsv; it stays on dev/alpha until published, which also removes its >5 Mb breakend artifacts from the merged track. - Remove searchIndex from colorsDbSv, lrSv1kLin and lrSvAll (and the merge generator): the bigBeds were built without a name index, so by-name search never worked. - Single shared per-SV-type color palette in lrSvCommon.py (svColor), used by every converter and the merge. CPX is purple everywhere (was orange in 1kgOnt/apr/cpc1, colliding with INV's orange), colorsDb DEL is 200,0,0 like the rest, and TRA/INSDEL get their own colors. - deCODE: drop byte-identical duplicate rows and blank the fake AC=50 placeholder (AC is now a string field, omitted from the name and mouseOver). - AoU: numeric-entity-encode non-ASCII gene/trait text and drop duplicate rows. - gustafson, chirmade101, hprc2v21: drop byte-identical duplicate rows. - lrSvMergeAll.py: skip byte-identical duplicate source rows instead of summing their allele counts, which had inflated the per-database and total AC. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvDecodeVcfToBed.py
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    9eb4e0937782954c19d664e7d384d210bffb3b25 Sat Jun 13 16:01:42 2026 -0700
    lrSv: QA fixes from Lou's review - dedup, shared color palette, deCODE/AoU cleanup - Drop kwanhoSv (KimPD) from the lrSvAll merge in databases.tsv; it stays on dev/alpha until published, which also removes its >5 Mb breakend artifacts from the merged track. - Remove searchIndex from colorsDbSv, lrSv1kLin and lrSvAll (and the merge generator): the bigBeds were built without a name index, so by-name search never worked. - Single shared per-SV-type color palette in lrSvCommon.py (svColor), used by every converter and the merge. CPX is purple everywhere (was orange in 1kgOnt/apr/cpc1, colliding with INV's orange), colorsDb DEL is 200,0,0 like the rest, and TRA/INSDEL get their own colors. - deCODE: drop byte-identical duplicate rows and blank the fake AC=50 placeholder (AC is now a string field, omitted from the name and mouseOver). - AoU: numeric-entity-encode non-ASCII gene/trait text and drop duplicate rows. - gustafson, chirmade101, hprc2v21: drop byte-identical duplicate rows. - lrSvMergeAll.py: skip byte-identical duplicate source rows instead of summing their allele counts, which had inflated the per-database and total AC. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvGustafsonVcfToBed.py
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    9eb4e0937782954c19d664e7d384d210bffb3b25 Sat Jun 13 16:01:42 2026 -0700
    lrSv: QA fixes from Lou's review - dedup, shared color palette, deCODE/AoU cleanup - Drop kwanhoSv (KimPD) from the lrSvAll merge in databases.tsv; it stays on dev/alpha until published, which also removes its >5 Mb breakend artifacts from the merged track. - Remove searchIndex from colorsDbSv, lrSv1kLin and lrSvAll (and the merge generator): the bigBeds were built without a name index, so by-name search never worked. - Single shared per-SV-type color palette in lrSvCommon.py (svColor), used by every converter and the merge. CPX is purple everywhere (was orange in 1kgOnt/apr/cpc1, colliding with INV's orange), colorsDb DEL is 200,0,0 like the rest, and TRA/INSDEL get their own colors. - deCODE: drop byte-identical duplicate rows and blank the fake AC=50 placeholder (AC is now a string field, omitted from the name and mouseOver). - AoU: numeric-entity-encode non-ASCII gene/trait text and drop duplicate rows. - gustafson, chirmade101, hprc2v21: drop byte-identical duplicate rows. - lrSvMergeAll.py: skip byte-identical duplicate source rows instead of summing their allele counts, which had inflated the per-database and total AC. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvHprc2Ro.as
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    ef61e73fc416622d8557ec2439df2344a1cc80c3 Tue Jun 9 15:10:01 2026 -0700
    lrSv: replace HPRC v2.0 pangenome SV track with v2.1 (hprc2v21Sv) Drop the v2.0 wave-decomposed hprc2Sv track and add hprc2v21Sv built from the HPRC v2.1 minigraph-cactus raw vg deconstruct VCFs (gref95.ro), on both hg38 (GRCh38 path, 596,063 SVs) and hs1 (T2T-CHM13 path, 608,435 SVs). The v2.1 files lack per-allele TYPE/LEN, so the new converter classifies INS/DEL by parsimony-trimming REF/ALT and the net length change. The v2.0 build recipe, converter and schema are kept but commented out in the makeDocs in case wave-decomposed VCFs are released again, refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvHprc2RoVcfToBed.py
  • lines changed 217, context: html, text, full: html, text
    ef61e73fc416622d8557ec2439df2344a1cc80c3 Tue Jun 9 15:10:01 2026 -0700
    lrSv: replace HPRC v2.0 pangenome SV track with v2.1 (hprc2v21Sv) Drop the v2.0 wave-decomposed hprc2Sv track and add hprc2v21Sv built from the HPRC v2.1 minigraph-cactus raw vg deconstruct VCFs (gref95.ro), on both hg38 (GRCh38 path, 596,063 SVs) and hs1 (T2T-CHM13 path, 608,435 SVs). The v2.1 files lack per-allele TYPE/LEN, so the new converter classifies INS/DEL by parsimony-trimming REF/ALT and the net length change. The v2.0 build recipe, converter and schema are kept but commented out in the makeDocs in case wave-decomposed VCFs are released again, refs #36258
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    9eb4e0937782954c19d664e7d384d210bffb3b25 Sat Jun 13 16:01:42 2026 -0700
    lrSv: QA fixes from Lou's review - dedup, shared color palette, deCODE/AoU cleanup - Drop kwanhoSv (KimPD) from the lrSvAll merge in databases.tsv; it stays on dev/alpha until published, which also removes its >5 Mb breakend artifacts from the merged track. - Remove searchIndex from colorsDbSv, lrSv1kLin and lrSvAll (and the merge generator): the bigBeds were built without a name index, so by-name search never worked. - Single shared per-SV-type color palette in lrSvCommon.py (svColor), used by every converter and the merge. CPX is purple everywhere (was orange in 1kgOnt/apr/cpc1, colliding with INV's orange), colorsDb DEL is 200,0,0 like the rest, and TRA/INSDEL get their own colors. - deCODE: drop byte-identical duplicate rows and blank the fake AC=50 placeholder (AC is now a string field, omitted from the name and mouseOver). - AoU: numeric-entity-encode non-ASCII gene/trait text and drop duplicate rows. - gustafson, chirmade101, hprc2v21: drop byte-identical duplicate rows. - lrSvMergeAll.py: skip byte-identical duplicate source rows instead of summing their allele counts, which had inflated the per-database and total AC. refs #36258
• src/hg/makeDb/scripts/lrSv/lrSvMergeAll.py
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    ae2a62a18bf9750819f17f8f2237b1f7b1b9911f Sat Jun 13 10:48:41 2026 -0700
    lrSv: comment out kwanhoSv and remove all searchIndex settings. refs #36258 Per ticket: hold the preliminary/unpublished Kim PD brain track (kwanhoSv) off dev/alpha until publication (commented out; bigBed/.as/converter/makeDoc kept), and remove the searchIndex name settings that were added by mistake. searchIndex removed from colorsDbSv and lrSv1kLin in lrSv.ra, from lrSvAll.ra, and from the lrSvMergeAll.py generator so future merges do not re-add it. The pending lrSvAll rebuild will drop KimPD from databases.tsv / the merged track.
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    9eb4e0937782954c19d664e7d384d210bffb3b25 Sat Jun 13 16:01:42 2026 -0700
    lrSv: QA fixes from Lou's review - dedup, shared color palette, deCODE/AoU cleanup - Drop kwanhoSv (KimPD) from the lrSvAll merge in databases.tsv; it stays on dev/alpha until published, which also removes its >5 Mb breakend artifacts from the merged track. - Remove searchIndex from colorsDbSv, lrSv1kLin and lrSvAll (and the merge generator): the bigBeds were built without a name index, so by-name search never worked. - Single shared per-SV-type color palette in lrSvCommon.py (svColor), used by every converter and the merge. CPX is purple everywhere (was orange in 1kgOnt/apr/cpc1, colliding with INV's orange), colorsDb DEL is 200,0,0 like the rest, and TRA/INSDEL get their own colors. - deCODE: drop byte-identical duplicate rows and blank the fake AC=50 placeholder (AC is now a string field, omitted from the name and mouseOver). - AoU: numeric-entity-encode non-ASCII gene/trait text and drop duplicate rows. - gustafson, chirmade101, hprc2v21: drop byte-identical duplicate rows. - lrSvMergeAll.py: skip byte-identical duplicate source rows instead of summing their allele counts, which had inflated the per-database and total AC. refs #36258
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    02782ec9c99ef7f54699068afbc902e7dedccb93 Sun Jun 14 00:34:26 2026 -0700
    lrSv: format the lrSvAll merged-track mouseOver as multi-line HTML. refs #36258 Replace the inline mouseOver with bold-labeled lines (Var / SV len / Ins len / Sources / AF range / AC), in both the generated lrSvAll.ra and the lrSvMergeAll.py generator that writes it, so a future merge regeneration reproduces the same format.
• src/hg/makeDb/scripts/lrSv/lrSvVcfToBed.py
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    9eb4e0937782954c19d664e7d384d210bffb3b25 Sat Jun 13 16:01:42 2026 -0700
    lrSv: QA fixes from Lou's review - dedup, shared color palette, deCODE/AoU cleanup - Drop kwanhoSv (KimPD) from the lrSvAll merge in databases.tsv; it stays on dev/alpha until published, which also removes its >5 Mb breakend artifacts from the merged track. - Remove searchIndex from colorsDbSv, lrSv1kLin and lrSvAll (and the merge generator): the bigBeds were built without a name index, so by-name search never worked. - Single shared per-SV-type color palette in lrSvCommon.py (svColor), used by every converter and the merge. CPX is purple everywhere (was orange in 1kgOnt/apr/cpc1, colliding with INV's orange), colorsDb DEL is 200,0,0 like the rest, and TRA/INSDEL get their own colors. - deCODE: drop byte-identical duplicate rows and blank the fake AC=50 placeholder (AC is now a string field, omitted from the name and mouseOver). - AoU: numeric-entity-encode non-ASCII gene/trait text and drop duplicate rows. - gustafson, chirmade101, hprc2v21: drop byte-identical duplicate rows. - lrSvMergeAll.py: skip byte-identical duplicate source rows instead of summing their allele counts, which had inflated the per-database and total AC. refs #36258
• src/hg/makeDb/scripts/masterMindGame/masterMindGame.as
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    6701d67860c32b8886b59587c9e32a4f86a8a96d Tue Jun 9 17:13:31 2026 -0700
    masterMindGame: demo bigLolly track rendering a solved game of Mastermind on hg38 Demonstrates the lolly track type by mapping a Mastermind board onto it: score field is the board row, genomic position is the peg column, itemRgb is the peg color, and the size field separates the large code pegs from the small feedback key pegs. Guesses come from a consistent-candidate solver so the black/white feedback is real. Included alpha-only.
  • lines changed 15, context: html, text, full: html, text
    736e788b252ccc94a432bef54ac83321848560b1 Wed Jun 10 06:57:07 2026 -0700
    Revert "masterMindGame: demo bigLolly track rendering a solved game of Mastermind on hg38" This reverts commit 6701d67860c32b8886b59587c9e32a4f86a8a96d.
• src/hg/makeDb/scripts/masterMindGame/masterMindGame.py
  • lines changed 119, context: html, text, full: html, text
    6701d67860c32b8886b59587c9e32a4f86a8a96d Tue Jun 9 17:13:31 2026 -0700
    masterMindGame: demo bigLolly track rendering a solved game of Mastermind on hg38 Demonstrates the lolly track type by mapping a Mastermind board onto it: score field is the board row, genomic position is the peg column, itemRgb is the peg color, and the size field separates the large code pegs from the small feedback key pegs. Guesses come from a consistent-candidate solver so the black/white feedback is real. Included alpha-only.
  • lines changed 119, context: html, text, full: html, text
    736e788b252ccc94a432bef54ac83321848560b1 Wed Jun 10 06:57:07 2026 -0700
    Revert "masterMindGame: demo bigLolly track rendering a solved game of Mastermind on hg38" This reverts commit 6701d67860c32b8886b59587c9e32a4f86a8a96d.
• src/hg/makeDb/scripts/varFreqs/databases.tsv
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    6b285a53b036b309e3c7a9b61d3741731088a172 Fri Jun 12 02:35:01 2026 -0700
    varFreqs: switch affectedAF/backgroundAF from max-across-cohorts to pooled sum(AC)/sum(AN) so the rate matches the carrier count scale. Per-arm AN is derived as round(AC/AF) when both are reported. An optional "default_an" column was added to databases.tsv so AF-only cohorts (ABraOM, ALFA) can synthesize a denominator from their cohort size; without it those cohorts had been silently dropped from the pooled rate. New affectedAN and backgroundAN columns expose the pool denominator. The mouseOver now reads "Affected AC/AN: 33238 / 213153" so the ratio is visible. Per-arm cohorts that ship only AC and no default_an (MGRB, GREGoR AC_AFFECTED/UNAFFECTED/UNKNOWN, AllOfUs per-population) are still listed in affectedCohorts/backgroundSources but contribute 0 to the pool, preserving the invariant pool_AF <= 1. The build pipeline is unchanged: re-run vcfToBigBed.py --split-affected against the existing merged.annotated.vcf.gz. refs #36642
• src/hg/makeDb/scripts/varFreqs/vcfToBigBed.py
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    6b285a53b036b309e3c7a9b61d3741731088a172 Fri Jun 12 02:35:01 2026 -0700
    varFreqs: switch affectedAF/backgroundAF from max-across-cohorts to pooled sum(AC)/sum(AN) so the rate matches the carrier count scale. Per-arm AN is derived as round(AC/AF) when both are reported. An optional "default_an" column was added to databases.tsv so AF-only cohorts (ABraOM, ALFA) can synthesize a denominator from their cohort size; without it those cohorts had been silently dropped from the pooled rate. New affectedAN and backgroundAN columns expose the pool denominator. The mouseOver now reads "Affected AC/AN: 33238 / 213153" so the ratio is visible. Per-arm cohorts that ship only AC and no default_an (MGRB, GREGoR AC_AFFECTED/UNAFFECTED/UNKNOWN, AllOfUs per-population) are still listed in affectedCohorts/backgroundSources but contribute 0 to the pool, preserving the invariant pool_AF <= 1. The build pipeline is unchanged: re-run vcfToBigBed.py --split-affected against the existing merged.annotated.vcf.gz. refs #36642
• src/hg/makeDb/trackDb/human/aou1kSv.html
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    2e0addd016cfcbf61485b90d8980a8d75be622c2 Sun Jun 14 00:10:06 2026 -0700
    lrSv: sync description-page counts to the deduped data; drop Kim PD from the supertrack page. refs #36258 After the QA dedup, update the SV counts cited on the description pages to the unique (post-dedup) totals for the tracks served, while leaving the upstream release/paper counts in the Methods sections: decodeSv 133,886 -> 119,453 displayed gustafsonSv 113,696 -> 113,159 displayed chirmade101 87,183 -> 87,068 displayed aou1k 541,049 -> 540,155 displayed hprc2v21Sv 596,063 -> 549,649 (hg38) and 608,435 -> 541,176 (hs1), throughout (no upstream publication), incl. recomputed nested-snarl counts lrSv.html: update the Available Datasets table count cells to match, set the lrSvAll merged cell to 2,317,508 (post Kim PD removal), and remove the Kim PD Brain row, blurb and reference from the supertrack page (the track is staged on dev/alpha only, kept out of the merge and the description, and is not released).
• src/hg/makeDb/trackDb/human/chirmade101Sv.html
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    2e0addd016cfcbf61485b90d8980a8d75be622c2 Sun Jun 14 00:10:06 2026 -0700
    lrSv: sync description-page counts to the deduped data; drop Kim PD from the supertrack page. refs #36258 After the QA dedup, update the SV counts cited on the description pages to the unique (post-dedup) totals for the tracks served, while leaving the upstream release/paper counts in the Methods sections: decodeSv 133,886 -> 119,453 displayed gustafsonSv 113,696 -> 113,159 displayed chirmade101 87,183 -> 87,068 displayed aou1k 541,049 -> 540,155 displayed hprc2v21Sv 596,063 -> 549,649 (hg38) and 608,435 -> 541,176 (hs1), throughout (no upstream publication), incl. recomputed nested-snarl counts lrSv.html: update the Available Datasets table count cells to match, set the lrSvAll merged cell to 2,317,508 (post Kim PD removal), and remove the Kim PD Brain row, blurb and reference from the supertrack page (the track is staged on dev/alpha only, kept out of the merge and the description, and is not released).
• src/hg/makeDb/trackDb/human/decodeSv.html
  • lines changed 3, context: html, text, full: html, text
    2e0addd016cfcbf61485b90d8980a8d75be622c2 Sun Jun 14 00:10:06 2026 -0700
    lrSv: sync description-page counts to the deduped data; drop Kim PD from the supertrack page. refs #36258 After the QA dedup, update the SV counts cited on the description pages to the unique (post-dedup) totals for the tracks served, while leaving the upstream release/paper counts in the Methods sections: decodeSv 133,886 -> 119,453 displayed gustafsonSv 113,696 -> 113,159 displayed chirmade101 87,183 -> 87,068 displayed aou1k 541,049 -> 540,155 displayed hprc2v21Sv 596,063 -> 549,649 (hg38) and 608,435 -> 541,176 (hs1), throughout (no upstream publication), incl. recomputed nested-snarl counts lrSv.html: update the Available Datasets table count cells to match, set the lrSvAll merged cell to 2,317,508 (post Kim PD removal), and remove the Kim PD Brain row, blurb and reference from the supertrack page (the track is staged on dev/alpha only, kept out of the merge and the description, and is not released).
• src/hg/makeDb/trackDb/human/gustafsonSv.html
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    2e0addd016cfcbf61485b90d8980a8d75be622c2 Sun Jun 14 00:10:06 2026 -0700
    lrSv: sync description-page counts to the deduped data; drop Kim PD from the supertrack page. refs #36258 After the QA dedup, update the SV counts cited on the description pages to the unique (post-dedup) totals for the tracks served, while leaving the upstream release/paper counts in the Methods sections: decodeSv 133,886 -> 119,453 displayed gustafsonSv 113,696 -> 113,159 displayed chirmade101 87,183 -> 87,068 displayed aou1k 541,049 -> 540,155 displayed hprc2v21Sv 596,063 -> 549,649 (hg38) and 608,435 -> 541,176 (hs1), throughout (no upstream publication), incl. recomputed nested-snarl counts lrSv.html: update the Available Datasets table count cells to match, set the lrSvAll merged cell to 2,317,508 (post Kim PD removal), and remove the Kim PD Brain row, blurb and reference from the supertrack page (the track is staged on dev/alpha only, kept out of the merge and the description, and is not released).
• src/hg/makeDb/trackDb/human/hg38/gnomad.constraint.alpha.ra
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    574399b4a7d8fc75c1745fa83564f547ddcb9e8c Sat Jun 13 00:43:54 2026 -0700
    gnomAD v4.1.1 gene constraint tracks for hg38, refs #37351 Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
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    ecc2331000637cbc2523653642d926935b5b83fc Sat Jun 13 00:42:03 2026 -0700
    gnomAD v4.1.1 bigBed variant track for hg38, refs #37351 Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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    574399b4a7d8fc75c1745fa83564f547ddcb9e8c Sat Jun 13 00:43:54 2026 -0700
    gnomAD v4.1.1 gene constraint tracks for hg38, refs #37351 Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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    c7e37754a34c3a9406c4546225253d49b2cdf82f Sat Jun 13 01:00:41 2026 -0700
    Stage gnomad v4.1.1 bigBed as release alpha, refs #37351
• src/hg/makeDb/trackDb/human/hg38/masterMindGame.ra
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    6701d67860c32b8886b59587c9e32a4f86a8a96d Tue Jun 9 17:13:31 2026 -0700
    masterMindGame: demo bigLolly track rendering a solved game of Mastermind on hg38 Demonstrates the lolly track type by mapping a Mastermind board onto it: score field is the board row, genomic position is the peg column, itemRgb is the peg color, and the size field separates the large code pegs from the small feedback key pegs. Guesses come from a consistent-candidate solver so the black/white feedback is real. Included alpha-only.
  • lines changed 17, context: html, text, full: html, text
    736e788b252ccc94a432bef54ac83321848560b1 Wed Jun 10 06:57:07 2026 -0700
    Revert "masterMindGame: demo bigLolly track rendering a solved game of Mastermind on hg38" This reverts commit 6701d67860c32b8886b59587c9e32a4f86a8a96d.
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    6701d67860c32b8886b59587c9e32a4f86a8a96d Tue Jun 9 17:13:31 2026 -0700
    masterMindGame: demo bigLolly track rendering a solved game of Mastermind on hg38 Demonstrates the lolly track type by mapping a Mastermind board onto it: score field is the board row, genomic position is the peg column, itemRgb is the peg color, and the size field separates the large code pegs from the small feedback key pegs. Guesses come from a consistent-candidate solver so the black/white feedback is real. Included alpha-only.
  • lines changed 2, context: html, text, full: html, text
    736e788b252ccc94a432bef54ac83321848560b1 Wed Jun 10 06:57:07 2026 -0700
    Revert "masterMindGame: demo bigLolly track rendering a solved game of Mastermind on hg38" This reverts commit 6701d67860c32b8886b59587c9e32a4f86a8a96d.
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    29b2ebed5a2d7069b1abe68a3abcb44565b4dd90 Thu Jun 11 16:47:58 2026 -0700
    Releasing ENCODE4 Regulation tracks to the RR. Set the supertrack to hide by default and updated the pennantIcon to only New red. refs #34923
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg4.ra
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    29b2ebed5a2d7069b1abe68a3abcb44565b4dd90 Thu Jun 11 16:47:58 2026 -0700
    Releasing ENCODE4 Regulation tracks to the RR. Set the supertrack to hide by default and updated the pennantIcon to only New red. refs #34923
• src/hg/makeDb/trackDb/human/hprc2Sv.html
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    ef61e73fc416622d8557ec2439df2344a1cc80c3 Tue Jun 9 15:10:01 2026 -0700
    lrSv: replace HPRC v2.0 pangenome SV track with v2.1 (hprc2v21Sv) Drop the v2.0 wave-decomposed hprc2Sv track and add hprc2v21Sv built from the HPRC v2.1 minigraph-cactus raw vg deconstruct VCFs (gref95.ro), on both hg38 (GRCh38 path, 596,063 SVs) and hs1 (T2T-CHM13 path, 608,435 SVs). The v2.1 files lack per-allele TYPE/LEN, so the new converter classifies INS/DEL by parsimony-trimming REF/ALT and the net length change. The v2.0 build recipe, converter and schema are kept but commented out in the makeDocs in case wave-decomposed VCFs are released again, refs #36258
• src/hg/makeDb/trackDb/human/hprc2v21Sv.html
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    ef61e73fc416622d8557ec2439df2344a1cc80c3 Tue Jun 9 15:10:01 2026 -0700
    lrSv: replace HPRC v2.0 pangenome SV track with v2.1 (hprc2v21Sv) Drop the v2.0 wave-decomposed hprc2Sv track and add hprc2v21Sv built from the HPRC v2.1 minigraph-cactus raw vg deconstruct VCFs (gref95.ro), on both hg38 (GRCh38 path, 596,063 SVs) and hs1 (T2T-CHM13 path, 608,435 SVs). The v2.1 files lack per-allele TYPE/LEN, so the new converter classifies INS/DEL by parsimony-trimming REF/ALT and the net length change. The v2.0 build recipe, converter and schema are kept but commented out in the makeDocs in case wave-decomposed VCFs are released again, refs #36258
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    2e0addd016cfcbf61485b90d8980a8d75be622c2 Sun Jun 14 00:10:06 2026 -0700
    lrSv: sync description-page counts to the deduped data; drop Kim PD from the supertrack page. refs #36258 After the QA dedup, update the SV counts cited on the description pages to the unique (post-dedup) totals for the tracks served, while leaving the upstream release/paper counts in the Methods sections: decodeSv 133,886 -> 119,453 displayed gustafsonSv 113,696 -> 113,159 displayed chirmade101 87,183 -> 87,068 displayed aou1k 541,049 -> 540,155 displayed hprc2v21Sv 596,063 -> 549,649 (hg38) and 608,435 -> 541,176 (hs1), throughout (no upstream publication), incl. recomputed nested-snarl counts lrSv.html: update the Available Datasets table count cells to match, set the lrSvAll merged cell to 2,317,508 (post Kim PD removal), and remove the Kim PD Brain row, blurb and reference from the supertrack page (the track is staged on dev/alpha only, kept out of the merge and the description, and is not released).
• src/hg/makeDb/trackDb/human/lrSv.html
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    ef61e73fc416622d8557ec2439df2344a1cc80c3 Tue Jun 9 15:10:01 2026 -0700
    lrSv: replace HPRC v2.0 pangenome SV track with v2.1 (hprc2v21Sv) Drop the v2.0 wave-decomposed hprc2Sv track and add hprc2v21Sv built from the HPRC v2.1 minigraph-cactus raw vg deconstruct VCFs (gref95.ro), on both hg38 (GRCh38 path, 596,063 SVs) and hs1 (T2T-CHM13 path, 608,435 SVs). The v2.1 files lack per-allele TYPE/LEN, so the new converter classifies INS/DEL by parsimony-trimming REF/ALT and the net length change. The v2.0 build recipe, converter and schema are kept but commented out in the makeDocs in case wave-decomposed VCFs are released again, refs #36258
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    644eae7700eb62343b142a44258ee91a944f4853 Tue Jun 9 15:17:03 2026 -0700
    lrSv: rebuild merged lrSvAll track with HPRC v2.1 data Repoint the HPRC entry in databases.tsv from the removed v2.0 hprc2.bb to the new hprc2v21.bb and re-run the merge. The combined track now holds 2,359,011 variants (was 2,694,871); the drop is the smaller v2.1 HPRC callset. Regenerated lrSvAll.ra and updated the overview table on the container page. The HPRC Jasmine track is intentionally not part of the merge, refs #36258
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    c7e0e71c357fa4630ac2ee1fb0520a32d408a1e2 Sat Jun 13 09:33:29 2026 -0700
    lrSv QA round 2: alpha-gate unpublished subtracks, trim labels, fill dataset blurbs. refs #36258 Add "release alpha" to hprc2JasmineSv and lrSv1kLin so the two unpublished / do-not-release-yet subtracks stay on dev/alpha and do not graduate with the supertrack (both are already excluded from the lrSvAll merge via databases.tsv). Trim three longLabels to the 85-char limit: hprc2v21Sv, hprc2JasmineSv, and lrSv1kLin. lrSv.html: add the missing "Available Datasets" prose blurbs for Arab APR and CPC so all 15 datasets have a paragraph (was table-row-only).
  • lines changed 36, context: html, text, full: html, text
    2e0addd016cfcbf61485b90d8980a8d75be622c2 Sun Jun 14 00:10:06 2026 -0700
    lrSv: sync description-page counts to the deduped data; drop Kim PD from the supertrack page. refs #36258 After the QA dedup, update the SV counts cited on the description pages to the unique (post-dedup) totals for the tracks served, while leaving the upstream release/paper counts in the Methods sections: decodeSv 133,886 -> 119,453 displayed gustafsonSv 113,696 -> 113,159 displayed chirmade101 87,183 -> 87,068 displayed aou1k 541,049 -> 540,155 displayed hprc2v21Sv 596,063 -> 549,649 (hg38) and 608,435 -> 541,176 (hs1), throughout (no upstream publication), incl. recomputed nested-snarl counts lrSv.html: update the Available Datasets table count cells to match, set the lrSvAll merged cell to 2,317,508 (post Kim PD removal), and remove the Kim PD Brain row, blurb and reference from the supertrack page (the track is staged on dev/alpha only, kept out of the merge and the description, and is not released).
• src/hg/makeDb/trackDb/human/lrSv.ra
  • lines changed 8, context: html, text, full: html, text
    ef61e73fc416622d8557ec2439df2344a1cc80c3 Tue Jun 9 15:10:01 2026 -0700
    lrSv: replace HPRC v2.0 pangenome SV track with v2.1 (hprc2v21Sv) Drop the v2.0 wave-decomposed hprc2Sv track and add hprc2v21Sv built from the HPRC v2.1 minigraph-cactus raw vg deconstruct VCFs (gref95.ro), on both hg38 (GRCh38 path, 596,063 SVs) and hs1 (T2T-CHM13 path, 608,435 SVs). The v2.1 files lack per-allele TYPE/LEN, so the new converter classifies INS/DEL by parsimony-trimming REF/ALT and the net length change. The v2.0 build recipe, converter and schema are kept but commented out in the makeDocs in case wave-decomposed VCFs are released again, refs #36258
  • lines changed 5, context: html, text, full: html, text
    c7e0e71c357fa4630ac2ee1fb0520a32d408a1e2 Sat Jun 13 09:33:29 2026 -0700
    lrSv QA round 2: alpha-gate unpublished subtracks, trim labels, fill dataset blurbs. refs #36258 Add "release alpha" to hprc2JasmineSv and lrSv1kLin so the two unpublished / do-not-release-yet subtracks stay on dev/alpha and do not graduate with the supertrack (both are already excluded from the lrSvAll merge via databases.tsv). Trim three longLabels to the 85-char limit: hprc2v21Sv, hprc2JasmineSv, and lrSv1kLin. lrSv.html: add the missing "Available Datasets" prose blurbs for Arab APR and CPC so all 15 datasets have a paragraph (was table-row-only).
  • lines changed 2, context: html, text, full: html, text
    6ec6c29454ddc661b78710d1bb6de040cafaa66d Sat Jun 13 09:39:33 2026 -0700
    lrSv: remove premature per-track release tags that broke tdbQuery -strict. refs #36258 The hprc2JasmineSv and lrSv1kLin stanzas carried "release alpha", but the file is pulled in via "include lrSv.ra alpha", and tdbQuery -check -strict rejects a stanza-level release tag when the include line already supplies a release override ("Release tag in stanza with include release override"). The include-level alpha already keeps the entire supertrack on dev/alpha, so these two unpublished subtracks do not graduate regardless. Per-track release tags for the do-not-release subtracks should be added when the include line is later changed past alpha.
  • lines changed 39, context: html, text, full: html, text
    af23c5696568feae4289008ed5606a7055def77b Sat Jun 13 09:43:01 2026 -0700
    lrSv: comment out the hprc2JasmineSv stanza (test callset, not for release). refs #36258 The Jasmine-merged HPRC v2 multi-caller set is a comparison/test callset that is not slated for release, so its trackDb stanza is commented out rather than shipped on dev/alpha. The bigBed, autoSql, converter and makeDoc are retained for reference. The lrSv1kLin stanza is left in place pending confirmation.
  • lines changed 49, context: html, text, full: html, text
    ae2a62a18bf9750819f17f8f2237b1f7b1b9911f Sat Jun 13 10:48:41 2026 -0700
    lrSv: comment out kwanhoSv and remove all searchIndex settings. refs #36258 Per ticket: hold the preliminary/unpublished Kim PD brain track (kwanhoSv) off dev/alpha until publication (commented out; bigBed/.as/converter/makeDoc kept), and remove the searchIndex name settings that were added by mistake. searchIndex removed from colorsDbSv and lrSv1kLin in lrSv.ra, from lrSvAll.ra, and from the lrSvMergeAll.py generator so future merges do not re-add it. The pending lrSvAll rebuild will drop KimPD from databases.tsv / the merged track.
  • lines changed 15, context: html, text, full: html, text
    f09028646c6429d692a80cc38d214e805724e7fa Sat Jun 13 10:51:38 2026 -0700
    lrSv: default all subtracks to hide except lrSvAll (pack), add lrSvAll desc page. refs #36258 Set the 15 released lrSv subtracks to "visibility hide" so the supertrack opens with only the merged overview visible; lrSvAll stays "visibility pack". Add the missing lrSvAll.html description page (Description, Display Conventions, Methods, Data Access, Credits) describing the position-merged combined track.
  • lines changed 10, context: html, text, full: html, text
    9eb4e0937782954c19d664e7d384d210bffb3b25 Sat Jun 13 16:01:42 2026 -0700
    lrSv: QA fixes from Lou's review - dedup, shared color palette, deCODE/AoU cleanup - Drop kwanhoSv (KimPD) from the lrSvAll merge in databases.tsv; it stays on dev/alpha until published, which also removes its >5 Mb breakend artifacts from the merged track. - Remove searchIndex from colorsDbSv, lrSv1kLin and lrSvAll (and the merge generator): the bigBeds were built without a name index, so by-name search never worked. - Single shared per-SV-type color palette in lrSvCommon.py (svColor), used by every converter and the merge. CPX is purple everywhere (was orange in 1kgOnt/apr/cpc1, colliding with INV's orange), colorsDb DEL is 200,0,0 like the rest, and TRA/INSDEL get their own colors. - deCODE: drop byte-identical duplicate rows and blank the fake AC=50 placeholder (AC is now a string field, omitted from the name and mouseOver). - AoU: numeric-entity-encode non-ASCII gene/trait text and drop duplicate rows. - gustafson, chirmade101, hprc2v21: drop byte-identical duplicate rows. - lrSvMergeAll.py: skip byte-identical duplicate source rows instead of summing their allele counts, which had inflated the per-database and total AC. refs #36258
  • lines changed 55, context: html, text, full: html, text
    4a1651999514d41b9ed33cbd8ee7ceee08df21eb Sat Jun 13 23:28:59 2026 -0700
    removing kim
• src/hg/makeDb/trackDb/human/lrSvAll.html
  • lines changed 81, context: html, text, full: html, text
    f09028646c6429d692a80cc38d214e805724e7fa Sat Jun 13 10:51:38 2026 -0700
    lrSv: default all subtracks to hide except lrSvAll (pack), add lrSvAll desc page. refs #36258 Set the 15 released lrSv subtracks to "visibility hide" so the supertrack opens with only the merged overview visible; lrSvAll stays "visibility pack". Add the missing lrSvAll.html description page (Description, Display Conventions, Methods, Data Access, Credits) describing the position-merged combined track.
• src/hg/makeDb/trackDb/human/lrSvAll.ra
  • lines changed 1, context: html, text, full: html, text
    644eae7700eb62343b142a44258ee91a944f4853 Tue Jun 9 15:17:03 2026 -0700
    lrSv: rebuild merged lrSvAll track with HPRC v2.1 data Repoint the HPRC entry in databases.tsv from the removed v2.0 hprc2.bb to the new hprc2v21.bb and re-run the merge. The combined track now holds 2,359,011 variants (was 2,694,871); the drop is the smaller v2.1 HPRC callset. Regenerated lrSvAll.ra and updated the overview table on the container page. The HPRC Jasmine track is intentionally not part of the merge, refs #36258
  • lines changed 1, context: html, text, full: html, text
    ae2a62a18bf9750819f17f8f2237b1f7b1b9911f Sat Jun 13 10:48:41 2026 -0700
    lrSv: comment out kwanhoSv and remove all searchIndex settings. refs #36258 Per ticket: hold the preliminary/unpublished Kim PD brain track (kwanhoSv) off dev/alpha until publication (commented out; bigBed/.as/converter/makeDoc kept), and remove the searchIndex name settings that were added by mistake. searchIndex removed from colorsDbSv and lrSv1kLin in lrSv.ra, from lrSvAll.ra, and from the lrSvMergeAll.py generator so future merges do not re-add it. The pending lrSvAll rebuild will drop KimPD from databases.tsv / the merged track.
  • lines changed 3, context: html, text, full: html, text
    9eb4e0937782954c19d664e7d384d210bffb3b25 Sat Jun 13 16:01:42 2026 -0700
    lrSv: QA fixes from Lou's review - dedup, shared color palette, deCODE/AoU cleanup - Drop kwanhoSv (KimPD) from the lrSvAll merge in databases.tsv; it stays on dev/alpha until published, which also removes its >5 Mb breakend artifacts from the merged track. - Remove searchIndex from colorsDbSv, lrSv1kLin and lrSvAll (and the merge generator): the bigBeds were built without a name index, so by-name search never worked. - Single shared per-SV-type color palette in lrSvCommon.py (svColor), used by every converter and the merge. CPX is purple everywhere (was orange in 1kgOnt/apr/cpc1, colliding with INV's orange), colorsDb DEL is 200,0,0 like the rest, and TRA/INSDEL get their own colors. - deCODE: drop byte-identical duplicate rows and blank the fake AC=50 placeholder (AC is now a string field, omitted from the name and mouseOver). - AoU: numeric-entity-encode non-ASCII gene/trait text and drop duplicate rows. - gustafson, chirmade101, hprc2v21: drop byte-identical duplicate rows. - lrSvMergeAll.py: skip byte-identical duplicate source rows instead of summing their allele counts, which had inflated the per-database and total AC. refs #36258
  • lines changed 1, context: html, text, full: html, text
    02782ec9c99ef7f54699068afbc902e7dedccb93 Sun Jun 14 00:34:26 2026 -0700
    lrSv: format the lrSvAll merged-track mouseOver as multi-line HTML. refs #36258 Replace the inline mouseOver with bold-labeled lines (Var / SV len / Ins len / Sources / AF range / AC), in both the generated lrSvAll.ra and the lrSvMergeAll.py generator that writes it, so a future merge regeneration reproduces the same format.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 36, context: html, text, full: html, text
    4f34ad1308512a42b91b2a164e8c73d40dc18135 Wed Jun 10 12:03:40 2026 -0700
    Staging the Varaico release 3 tracks, removing test tracks, and adding Updated pennantIcon to the superTrack and Varaico tracks, refs #37658
  • lines changed 1, context: html, text, full: html, text
    fa29b7e72d8fb2a9519bf14f1122feccfd79eca2 Thu Jun 11 04:46:21 2026 -0700
    Retire mastermind track by gating it to alpha and noting retirement on the varsInPubs description page. refs #37753 The Genomenon Mastermind track no longer updates and the provider asked us to take it down. Added release alpha to the mastermind subtrack so it stays on dev/sandbox but is removed from beta and public for both hg38 and hg19, and updated the varsInPubs.html bullet to note the track has been retired.
  • lines changed 1, context: html, text, full: html, text
    e211864299ad6f9570a6e28a1d4cc9044d85ec26 Sun Jun 14 00:13:00 2026 -0700
    Silent release of the variant frequencies track, refs #36642
• src/hg/makeDb/trackDb/human/varFreqs.html
  • lines changed 3, context: html, text, full: html, text
    f0d9b9d7a69a43e62c52d80b18ef06ba1bf335ed Fri Jun 12 02:40:53 2026 -0700
    varFreqs: add "tableBrowser off" to every subtrack whose bigDataUrl points into an underscore-prefixed /gbdb dir (the rsync-exclusion convention for non-redistributable cohorts). Covers varFreqsAffected, varFreqsBackground, varFreqsArray, and genomeindia which were missing it. Also fix the "Downloadable from UCSC" column on the supertrack page for TOPMed, FinnGen and GenomeIndia (table said "Yes" but their gbdb paths are underscore-prefixed, so they aren't actually downloadable from us). refs #36642
  • lines changed 45, context: html, text, full: html, text
    af9a5b388259e680dd34bc47b2cad4ff6e3d162f Sat Jun 13 03:00:51 2026 -0700
    varFreqs: pre-release polish from comprehensive sanity check. * Sync the new combined-track shortLabels into the four description pages: "Affected/Case Individuals" -> "Disease cohorts" and "Population + Unaffected" -> "Population reference" (matches the trackdb shortLabels users now see). * Add a paragraph in the supertrack Methods section describing the pooled affectedAF / backgroundAF formulation (sum AC / sum AN) and the default_an configuration that handles AF-only cohorts. * Update the in-track Methods paragraphs on varFreqsAffected.html and varFreqsBackground.html: replace "summed/maximized" with "pooled". * Fix supertrack table downloadability column to match the underscore-prefix convention: allofus "Yes" -> "No" (description page already says license restricted); gregor "No" -> "Yes" (description page says VCF is on our download server, and the gbdb path is not underscore-prefixed). * Add a 2026-06-12 makedoc section documenting the pooled-AF rebuild, the default_an mechanism, the new affectedAN/backgroundAN columns, the before/after spot-check at APOE rs429358, and the build commands. refs #36642
  • lines changed 111, context: html, text, full: html, text
    d4951d6de0335238ce124b3fb9703d82d329b1ab Sat Jun 13 06:35:27 2026 -0700
    html updates to varFreqs, refs #36642
• src/hg/makeDb/trackDb/human/varFreqs.ra
  • lines changed 2, context: html, text, full: html, text
    dce21104b16337c132dea98bc763d74313381101 Fri Jun 12 01:05:02 2026 -0700
    varFreqs: rename combined-track shortLabels per the conversation with Max on the ticket. varFreqsAffected -> "Disease cohorts" (was "Affected/Case Individuals"); varFreqsBackground -> "Population reference" (was "Population + Unaffected"). longLabels unchanged. refs #36642
  • lines changed 14, context: html, text, full: html, text
    6b285a53b036b309e3c7a9b61d3741731088a172 Fri Jun 12 02:35:01 2026 -0700
    varFreqs: switch affectedAF/backgroundAF from max-across-cohorts to pooled sum(AC)/sum(AN) so the rate matches the carrier count scale. Per-arm AN is derived as round(AC/AF) when both are reported. An optional "default_an" column was added to databases.tsv so AF-only cohorts (ABraOM, ALFA) can synthesize a denominator from their cohort size; without it those cohorts had been silently dropped from the pooled rate. New affectedAN and backgroundAN columns expose the pool denominator. The mouseOver now reads "Affected AC/AN: 33238 / 213153" so the ratio is visible. Per-arm cohorts that ship only AC and no default_an (MGRB, GREGoR AC_AFFECTED/UNAFFECTED/UNKNOWN, AllOfUs per-population) are still listed in affectedCohorts/backgroundSources but contribute 0 to the pool, preserving the invariant pool_AF <= 1. The build pipeline is unchanged: re-run vcfToBigBed.py --split-affected against the existing merged.annotated.vcf.gz. refs #36642
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    f0d9b9d7a69a43e62c52d80b18ef06ba1bf335ed Fri Jun 12 02:40:53 2026 -0700
    varFreqs: add "tableBrowser off" to every subtrack whose bigDataUrl points into an underscore-prefixed /gbdb dir (the rsync-exclusion convention for non-redistributable cohorts). Covers varFreqsAffected, varFreqsBackground, varFreqsArray, and genomeindia which were missing it. Also fix the "Downloadable from UCSC" column on the supertrack page for TOPMed, FinnGen and GenomeIndia (table said "Yes" but their gbdb paths are underscore-prefixed, so they aren't actually downloadable from us). refs #36642
  • lines changed 31, context: html, text, full: html, text
    21e8af7d071bb2294f0cf682ac871c63a5a5332d Sat Jun 13 05:00:09 2026 -0700
    varFreqs: reorder subtrack priorities A-Z by shortLabel. Combined tracks keep their order: Population reference (0.1), Disease cohorts (0.11), Genotyping Array Databases Combined (0.2). The 32 per-project subtracks get integer priorities 1..32 sorted alphabetically by shortLabel (case-insensitive). Adds explicit priority to the 9 subtracks that lacked one (abraom, gasp, gaspIndel, hrc, indigenomes, kova, mgrb, npm, saudi). refs #36642
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    c6c684b4d0ec1926eb07485b899b0f48496f7063 Sat Jun 13 05:30:17 2026 -0700
    varFreqs: add a "New" pennantIcon to the supertrack as a placeholder pointing to newsarch.html#TBD. Once the release news post lands, update the anchor and tooltip with the actual date. refs #36642
• src/hg/makeDb/trackDb/human/varFreqsAffected.html
  • lines changed 19, context: html, text, full: html, text
    6b285a53b036b309e3c7a9b61d3741731088a172 Fri Jun 12 02:35:01 2026 -0700
    varFreqs: switch affectedAF/backgroundAF from max-across-cohorts to pooled sum(AC)/sum(AN) so the rate matches the carrier count scale. Per-arm AN is derived as round(AC/AF) when both are reported. An optional "default_an" column was added to databases.tsv so AF-only cohorts (ABraOM, ALFA) can synthesize a denominator from their cohort size; without it those cohorts had been silently dropped from the pooled rate. New affectedAN and backgroundAN columns expose the pool denominator. The mouseOver now reads "Affected AC/AN: 33238 / 213153" so the ratio is visible. Per-arm cohorts that ship only AC and no default_an (MGRB, GREGoR AC_AFFECTED/UNAFFECTED/UNKNOWN, AllOfUs per-population) are still listed in affectedCohorts/backgroundSources but contribute 0 to the pool, preserving the invariant pool_AF <= 1. The build pipeline is unchanged: re-run vcfToBigBed.py --split-affected against the existing merged.annotated.vcf.gz. refs #36642
  • lines changed 7, context: html, text, full: html, text
    af9a5b388259e680dd34bc47b2cad4ff6e3d162f Sat Jun 13 03:00:51 2026 -0700
    varFreqs: pre-release polish from comprehensive sanity check. * Sync the new combined-track shortLabels into the four description pages: "Affected/Case Individuals" -> "Disease cohorts" and "Population + Unaffected" -> "Population reference" (matches the trackdb shortLabels users now see). * Add a paragraph in the supertrack Methods section describing the pooled affectedAF / backgroundAF formulation (sum AC / sum AN) and the default_an configuration that handles AF-only cohorts. * Update the in-track Methods paragraphs on varFreqsAffected.html and varFreqsBackground.html: replace "summed/maximized" with "pooled". * Fix supertrack table downloadability column to match the underscore-prefix convention: allofus "Yes" -> "No" (description page already says license restricted); gregor "No" -> "Yes" (description page says VCF is on our download server, and the gbdb path is not underscore-prefixed). * Add a 2026-06-12 makedoc section documenting the pooled-AF rebuild, the default_an mechanism, the new affectedAN/backgroundAN columns, the before/after spot-check at APOE rs429358, and the build commands. refs #36642
• src/hg/makeDb/trackDb/human/varFreqsArray.html
  • lines changed 5, context: html, text, full: html, text
    af9a5b388259e680dd34bc47b2cad4ff6e3d162f Sat Jun 13 03:00:51 2026 -0700
    varFreqs: pre-release polish from comprehensive sanity check. * Sync the new combined-track shortLabels into the four description pages: "Affected/Case Individuals" -> "Disease cohorts" and "Population + Unaffected" -> "Population reference" (matches the trackdb shortLabels users now see). * Add a paragraph in the supertrack Methods section describing the pooled affectedAF / backgroundAF formulation (sum AC / sum AN) and the default_an configuration that handles AF-only cohorts. * Update the in-track Methods paragraphs on varFreqsAffected.html and varFreqsBackground.html: replace "summed/maximized" with "pooled". * Fix supertrack table downloadability column to match the underscore-prefix convention: allofus "Yes" -> "No" (description page already says license restricted); gregor "No" -> "Yes" (description page says VCF is on our download server, and the gbdb path is not underscore-prefixed). * Add a 2026-06-12 makedoc section documenting the pooled-AF rebuild, the default_an mechanism, the new affectedAN/backgroundAN columns, the before/after spot-check at APOE rs429358, and the build commands. refs #36642
• src/hg/makeDb/trackDb/human/varFreqsBackground.html
  • lines changed 23, context: html, text, full: html, text
    6b285a53b036b309e3c7a9b61d3741731088a172 Fri Jun 12 02:35:01 2026 -0700
    varFreqs: switch affectedAF/backgroundAF from max-across-cohorts to pooled sum(AC)/sum(AN) so the rate matches the carrier count scale. Per-arm AN is derived as round(AC/AF) when both are reported. An optional "default_an" column was added to databases.tsv so AF-only cohorts (ABraOM, ALFA) can synthesize a denominator from their cohort size; without it those cohorts had been silently dropped from the pooled rate. New affectedAN and backgroundAN columns expose the pool denominator. The mouseOver now reads "Affected AC/AN: 33238 / 213153" so the ratio is visible. Per-arm cohorts that ship only AC and no default_an (MGRB, GREGoR AC_AFFECTED/UNAFFECTED/UNKNOWN, AllOfUs per-population) are still listed in affectedCohorts/backgroundSources but contribute 0 to the pool, preserving the invariant pool_AF <= 1. The build pipeline is unchanged: re-run vcfToBigBed.py --split-affected against the existing merged.annotated.vcf.gz. refs #36642
  • lines changed 6, context: html, text, full: html, text
    af9a5b388259e680dd34bc47b2cad4ff6e3d162f Sat Jun 13 03:00:51 2026 -0700
    varFreqs: pre-release polish from comprehensive sanity check. * Sync the new combined-track shortLabels into the four description pages: "Affected/Case Individuals" -> "Disease cohorts" and "Population + Unaffected" -> "Population reference" (matches the trackdb shortLabels users now see). * Add a paragraph in the supertrack Methods section describing the pooled affectedAF / backgroundAF formulation (sum AC / sum AN) and the default_an configuration that handles AF-only cohorts. * Update the in-track Methods paragraphs on varFreqsAffected.html and varFreqsBackground.html: replace "summed/maximized" with "pooled". * Fix supertrack table downloadability column to match the underscore-prefix convention: allofus "Yes" -> "No" (description page already says license restricted); gregor "No" -> "Yes" (description page says VCF is on our download server, and the gbdb path is not underscore-prefixed). * Add a 2026-06-12 makedoc section documenting the pooled-AF rebuild, the default_an mechanism, the new affectedAN/backgroundAN columns, the before/after spot-check at APOE rs429358, and the build commands. refs #36642
• src/hg/makeDb/trackDb/human/varaico.html
  • lines changed 1, context: html, text, full: html, text
    3030fb4a9c489593d8286b7bb469ebda3c575ad6 Wed Jun 10 12:56:44 2026 -0700
    Documenting the release 2 archive step in the Varaico makedoc and fixing a hardcoded hg38 path in the description page example, refs #37658
• src/hg/makeDb/trackDb/human/varsInPubs.html
  • lines changed 3, context: html, text, full: html, text
    fa29b7e72d8fb2a9519bf14f1122feccfd79eca2 Thu Jun 11 04:46:21 2026 -0700
    Retire mastermind track by gating it to alpha and noting retirement on the varsInPubs description page. refs #37753 The Genomenon Mastermind track no longer updates and the provider asked us to take it down. Added release alpha to the mastermind subtrack so it stays on dev/sandbox but is removed from beta and public for both hg38 and hg19, and updated the varsInPubs.html bullet to note the track has been retired.
• src/hg/makeDb/trackDb/mouse/mm10/encode4Reg.ra
  • lines changed 2, context: html, text, full: html, text
    29b2ebed5a2d7069b1abe68a3abcb44565b4dd90 Thu Jun 11 16:47:58 2026 -0700
    Releasing ENCODE4 Regulation tracks to the RR. Set the supertrack to hide by default and updated the pennantIcon to only New red. refs #34923
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.encode3.ra
  • lines changed 1, context: html, text, full: html, text
    1ccc5efb8d6678d29201fa8248d7f32733864ab8 Sat Jun 13 10:53:01 2026 -0700
    Setting the mm10 ENCODE3 Regulation supertrack to be on by default on the RR. refs #37729
  • lines changed 1, context: html, text, full: html, text
    d5a3ad4f5ea1e13e1aa62681b4728edbdfe450ee Sun Jun 14 09:19:26 2026 -0700
    Changing the mm10 ENCODE3 Regulation supertrack back to hidden by default, refs #37729
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    29b2ebed5a2d7069b1abe68a3abcb44565b4dd90 Thu Jun 11 16:47:58 2026 -0700
    Releasing ENCODE4 Regulation tracks to the RR. Set the supertrack to hide by default and updated the pennantIcon to only New red. refs #34923
• src/hg/makeDb/trackDb/relatedTracks.ra
  • lines changed 6, context: html, text, full: html, text
    d4951d6de0335238ce124b3fb9703d82d329b1ab Sat Jun 13 06:35:27 2026 -0700
    html updates to varFreqs, refs #36642
• src/hg/mouseStuff/libScan/libScan.c
  • lines changed 3, context: html, text, full: html, text
    f57fc11d951807e19b20b5960e735fa50eaea279 Fri Jun 12 13:10:00 2026 -0700
    Fix more warnings exposed by -O3 build across hg utils and errAbort Continuation of the -O3 cleanup: a full clean rebuild surfaced warnings in many programs whose objects had not been recompiled before. Most are the same mechanical patterns as the first batch (strncpy -> safecpy/memcpy, sprintf -> safef), plus a few that needed more thought: - errAbort.h: mark errAbort/vaErrAbort/errnoAbort/noWarnAbort as noreturn. They provably never return (longjmp or exit; the existing "to make compiler happy" exit(-1) in noWarnAbort confirms the intent), and this lets GCC prune the impossible null paths after an errAbort guard, fixing false-positive null-deref / overread warnings in mafAddIRows, mafAddIRowsStream and phyloPlace with no source change to those files. - altSplice.c (hgGene): real one-element stack buffer overflow. makeGrayShades writes shadesOfGray[maxShade+1], but the caller declared shadesOfGray[9] with maxShade=8. Grow the array to [10] (maxShade stays 8); behavior unchanged. - hgc.c bedPrintPos: ~60 callers pass a track-specific struct cast to (struct bed *) and read only its bed-compatible leading fields. At -O3 -Warray-bounds flags the casts because the real object is smaller than struct bed; the reads are safe by the bed-layout convention, so suppress -Warray-bounds around just that function. - mafsInRegion.c: chromFromSrc returns strchr(src,'.')+1, which GCC mis-sizes as a 0-byte region when handed to strcmp via sameString/differentString; suppress the false-positive -Wstringop-overread around extractMafs. - sanger22gtf.c, bottleneck.c: put the printf/fprintf in the else of the NULL guard so -Wformat-overflow (which runs before the noreturn-based pruning) can see the argument is non-null. safecpy/memcpy/safef conversions: basicBed already done earlier; here haplotypes (memcpy of the original pointer pun), gbToFaRa, motifSig, hgClonePos, featureBits, libScan, hgGoldGapGl, hgSoftPromoter, mafClick, mafAddQRows, hgc.c, stanToBedAndExpRecs, bedUp, faSplit, trfBig, splitFaIntoContigs, aladdin, ameme. A full clean tree now builds with no warnings at -O3. refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/nci60/stanToBedAndExpRecs.c
  • lines changed 1, context: html, text, full: html, text
    f57fc11d951807e19b20b5960e735fa50eaea279 Fri Jun 12 13:10:00 2026 -0700
    Fix more warnings exposed by -O3 build across hg utils and errAbort Continuation of the -O3 cleanup: a full clean rebuild surfaced warnings in many programs whose objects had not been recompiled before. Most are the same mechanical patterns as the first batch (strncpy -> safecpy/memcpy, sprintf -> safef), plus a few that needed more thought: - errAbort.h: mark errAbort/vaErrAbort/errnoAbort/noWarnAbort as noreturn. They provably never return (longjmp or exit; the existing "to make compiler happy" exit(-1) in noWarnAbort confirms the intent), and this lets GCC prune the impossible null paths after an errAbort guard, fixing false-positive null-deref / overread warnings in mafAddIRows, mafAddIRowsStream and phyloPlace with no source change to those files. - altSplice.c (hgGene): real one-element stack buffer overflow. makeGrayShades writes shadesOfGray[maxShade+1], but the caller declared shadesOfGray[9] with maxShade=8. Grow the array to [10] (maxShade stays 8); behavior unchanged. - hgc.c bedPrintPos: ~60 callers pass a track-specific struct cast to (struct bed *) and read only its bed-compatible leading fields. At -O3 -Warray-bounds flags the casts because the real object is smaller than struct bed; the reads are safe by the bed-layout convention, so suppress -Warray-bounds around just that function. - mafsInRegion.c: chromFromSrc returns strchr(src,'.')+1, which GCC mis-sizes as a 0-byte region when handed to strcmp via sameString/differentString; suppress the false-positive -Wstringop-overread around extractMafs. - sanger22gtf.c, bottleneck.c: put the printf/fprintf in the else of the NULL guard so -Wformat-overflow (which runs before the noreturn-based pruning) can see the argument is non-null. safecpy/memcpy/safef conversions: basicBed already done earlier; here haplotypes (memcpy of the original pointer pun), gbToFaRa, motifSig, hgClonePos, featureBits, libScan, hgGoldGapGl, hgSoftPromoter, mafClick, mafAddQRows, hgc.c, stanToBedAndExpRecs, bedUp, faSplit, trfBig, splitFaIntoContigs, aladdin, ameme. A full clean tree now builds with no warnings at -O3. refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/ratStuff/mafAddQRows/mafAddQRows.c
  • lines changed 1, context: html, text, full: html, text
    f57fc11d951807e19b20b5960e735fa50eaea279 Fri Jun 12 13:10:00 2026 -0700
    Fix more warnings exposed by -O3 build across hg utils and errAbort Continuation of the -O3 cleanup: a full clean rebuild surfaced warnings in many programs whose objects had not been recompiled before. Most are the same mechanical patterns as the first batch (strncpy -> safecpy/memcpy, sprintf -> safef), plus a few that needed more thought: - errAbort.h: mark errAbort/vaErrAbort/errnoAbort/noWarnAbort as noreturn. They provably never return (longjmp or exit; the existing "to make compiler happy" exit(-1) in noWarnAbort confirms the intent), and this lets GCC prune the impossible null paths after an errAbort guard, fixing false-positive null-deref / overread warnings in mafAddIRows, mafAddIRowsStream and phyloPlace with no source change to those files. - altSplice.c (hgGene): real one-element stack buffer overflow. makeGrayShades writes shadesOfGray[maxShade+1], but the caller declared shadesOfGray[9] with maxShade=8. Grow the array to [10] (maxShade stays 8); behavior unchanged. - hgc.c bedPrintPos: ~60 callers pass a track-specific struct cast to (struct bed *) and read only its bed-compatible leading fields. At -O3 -Warray-bounds flags the casts because the real object is smaller than struct bed; the reads are safe by the bed-layout convention, so suppress -Warray-bounds around just that function. - mafsInRegion.c: chromFromSrc returns strchr(src,'.')+1, which GCC mis-sizes as a 0-byte region when handed to strcmp via sameString/differentString; suppress the false-positive -Wstringop-overread around extractMafs. - sanger22gtf.c, bottleneck.c: put the printf/fprintf in the else of the NULL guard so -Wformat-overflow (which runs before the noreturn-based pruning) can see the argument is non-null. safecpy/memcpy/safef conversions: basicBed already done earlier; here haplotypes (memcpy of the original pointer pun), gbToFaRa, motifSig, hgClonePos, featureBits, libScan, hgGoldGapGl, hgSoftPromoter, mafClick, mafAddQRows, hgc.c, stanToBedAndExpRecs, bedUp, faSplit, trfBig, splitFaIntoContigs, aladdin, ameme. A full clean tree now builds with no warnings at -O3. refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/ratStuff/mafsInRegion/mafsInRegion.c
  • lines changed 8, context: html, text, full: html, text
    f57fc11d951807e19b20b5960e735fa50eaea279 Fri Jun 12 13:10:00 2026 -0700
    Fix more warnings exposed by -O3 build across hg utils and errAbort Continuation of the -O3 cleanup: a full clean rebuild surfaced warnings in many programs whose objects had not been recompiled before. Most are the same mechanical patterns as the first batch (strncpy -> safecpy/memcpy, sprintf -> safef), plus a few that needed more thought: - errAbort.h: mark errAbort/vaErrAbort/errnoAbort/noWarnAbort as noreturn. They provably never return (longjmp or exit; the existing "to make compiler happy" exit(-1) in noWarnAbort confirms the intent), and this lets GCC prune the impossible null paths after an errAbort guard, fixing false-positive null-deref / overread warnings in mafAddIRows, mafAddIRowsStream and phyloPlace with no source change to those files. - altSplice.c (hgGene): real one-element stack buffer overflow. makeGrayShades writes shadesOfGray[maxShade+1], but the caller declared shadesOfGray[9] with maxShade=8. Grow the array to [10] (maxShade stays 8); behavior unchanged. - hgc.c bedPrintPos: ~60 callers pass a track-specific struct cast to (struct bed *) and read only its bed-compatible leading fields. At -O3 -Warray-bounds flags the casts because the real object is smaller than struct bed; the reads are safe by the bed-layout convention, so suppress -Warray-bounds around just that function. - mafsInRegion.c: chromFromSrc returns strchr(src,'.')+1, which GCC mis-sizes as a 0-byte region when handed to strcmp via sameString/differentString; suppress the false-positive -Wstringop-overread around extractMafs. - sanger22gtf.c, bottleneck.c: put the printf/fprintf in the else of the NULL guard so -Wformat-overflow (which runs before the noreturn-based pruning) can see the argument is non-null. safecpy/memcpy/safef conversions: basicBed already done earlier; here haplotypes (memcpy of the original pointer pun), gbToFaRa, motifSig, hgClonePos, featureBits, libScan, hgGoldGapGl, hgSoftPromoter, mafClick, mafAddQRows, hgc.c, stanToBedAndExpRecs, bedUp, faSplit, trfBig, splitFaIntoContigs, aladdin, ameme. A full clean tree now builds with no warnings at -O3. refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/recycleDb/bedUp/bedUp.c
  • lines changed 2, context: html, text, full: html, text
    f57fc11d951807e19b20b5960e735fa50eaea279 Fri Jun 12 13:10:00 2026 -0700
    Fix more warnings exposed by -O3 build across hg utils and errAbort Continuation of the -O3 cleanup: a full clean rebuild surfaced warnings in many programs whose objects had not been recompiled before. Most are the same mechanical patterns as the first batch (strncpy -> safecpy/memcpy, sprintf -> safef), plus a few that needed more thought: - errAbort.h: mark errAbort/vaErrAbort/errnoAbort/noWarnAbort as noreturn. They provably never return (longjmp or exit; the existing "to make compiler happy" exit(-1) in noWarnAbort confirms the intent), and this lets GCC prune the impossible null paths after an errAbort guard, fixing false-positive null-deref / overread warnings in mafAddIRows, mafAddIRowsStream and phyloPlace with no source change to those files. - altSplice.c (hgGene): real one-element stack buffer overflow. makeGrayShades writes shadesOfGray[maxShade+1], but the caller declared shadesOfGray[9] with maxShade=8. Grow the array to [10] (maxShade stays 8); behavior unchanged. - hgc.c bedPrintPos: ~60 callers pass a track-specific struct cast to (struct bed *) and read only its bed-compatible leading fields. At -O3 -Warray-bounds flags the casts because the real object is smaller than struct bed; the reads are safe by the bed-layout convention, so suppress -Warray-bounds around just that function. - mafsInRegion.c: chromFromSrc returns strchr(src,'.')+1, which GCC mis-sizes as a 0-byte region when handed to strcmp via sameString/differentString; suppress the false-positive -Wstringop-overread around extractMafs. - sanger22gtf.c, bottleneck.c: put the printf/fprintf in the else of the NULL guard so -Wformat-overflow (which runs before the noreturn-based pruning) can see the argument is non-null. safecpy/memcpy/safef conversions: basicBed already done earlier; here haplotypes (memcpy of the original pointer pun), gbToFaRa, motifSig, hgClonePos, featureBits, libScan, hgGoldGapGl, hgSoftPromoter, mafClick, mafAddQRows, hgc.c, stanToBedAndExpRecs, bedUp, faSplit, trfBig, splitFaIntoContigs, aladdin, ameme. A full clean tree now builds with no warnings at -O3. refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/splitFaIntoContigs/splitFaIntoContigs.c
  • lines changed 2, context: html, text, full: html, text
    f57fc11d951807e19b20b5960e735fa50eaea279 Fri Jun 12 13:10:00 2026 -0700
    Fix more warnings exposed by -O3 build across hg utils and errAbort Continuation of the -O3 cleanup: a full clean rebuild surfaced warnings in many programs whose objects had not been recompiled before. Most are the same mechanical patterns as the first batch (strncpy -> safecpy/memcpy, sprintf -> safef), plus a few that needed more thought: - errAbort.h: mark errAbort/vaErrAbort/errnoAbort/noWarnAbort as noreturn. They provably never return (longjmp or exit; the existing "to make compiler happy" exit(-1) in noWarnAbort confirms the intent), and this lets GCC prune the impossible null paths after an errAbort guard, fixing false-positive null-deref / overread warnings in mafAddIRows, mafAddIRowsStream and phyloPlace with no source change to those files. - altSplice.c (hgGene): real one-element stack buffer overflow. makeGrayShades writes shadesOfGray[maxShade+1], but the caller declared shadesOfGray[9] with maxShade=8. Grow the array to [10] (maxShade stays 8); behavior unchanged. - hgc.c bedPrintPos: ~60 callers pass a track-specific struct cast to (struct bed *) and read only its bed-compatible leading fields. At -O3 -Warray-bounds flags the casts because the real object is smaller than struct bed; the reads are safe by the bed-layout convention, so suppress -Warray-bounds around just that function. - mafsInRegion.c: chromFromSrc returns strchr(src,'.')+1, which GCC mis-sizes as a 0-byte region when handed to strcmp via sameString/differentString; suppress the false-positive -Wstringop-overread around extractMafs. - sanger22gtf.c, bottleneck.c: put the printf/fprintf in the else of the NULL guard so -Wformat-overflow (which runs before the noreturn-based pruning) can see the argument is non-null. safecpy/memcpy/safef conversions: basicBed already done earlier; here haplotypes (memcpy of the original pointer pun), gbToFaRa, motifSig, hgClonePos, featureBits, libScan, hgGoldGapGl, hgSoftPromoter, mafClick, mafAddQRows, hgc.c, stanToBedAndExpRecs, bedUp, faSplit, trfBig, splitFaIntoContigs, aladdin, ameme. A full clean tree now builds with no warnings at -O3. refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/trfBig/trfBig.c
  • lines changed 1, context: html, text, full: html, text
    f57fc11d951807e19b20b5960e735fa50eaea279 Fri Jun 12 13:10:00 2026 -0700
    Fix more warnings exposed by -O3 build across hg utils and errAbort Continuation of the -O3 cleanup: a full clean rebuild surfaced warnings in many programs whose objects had not been recompiled before. Most are the same mechanical patterns as the first batch (strncpy -> safecpy/memcpy, sprintf -> safef), plus a few that needed more thought: - errAbort.h: mark errAbort/vaErrAbort/errnoAbort/noWarnAbort as noreturn. They provably never return (longjmp or exit; the existing "to make compiler happy" exit(-1) in noWarnAbort confirms the intent), and this lets GCC prune the impossible null paths after an errAbort guard, fixing false-positive null-deref / overread warnings in mafAddIRows, mafAddIRowsStream and phyloPlace with no source change to those files. - altSplice.c (hgGene): real one-element stack buffer overflow. makeGrayShades writes shadesOfGray[maxShade+1], but the caller declared shadesOfGray[9] with maxShade=8. Grow the array to [10] (maxShade stays 8); behavior unchanged. - hgc.c bedPrintPos: ~60 callers pass a track-specific struct cast to (struct bed *) and read only its bed-compatible leading fields. At -O3 -Warray-bounds flags the casts because the real object is smaller than struct bed; the reads are safe by the bed-layout convention, so suppress -Warray-bounds around just that function. - mafsInRegion.c: chromFromSrc returns strchr(src,'.')+1, which GCC mis-sizes as a 0-byte region when handed to strcmp via sameString/differentString; suppress the false-positive -Wstringop-overread around extractMafs. - sanger22gtf.c, bottleneck.c: put the printf/fprintf in the else of the NULL guard so -Wformat-overflow (which runs before the noreturn-based pruning) can see the argument is non-null. safecpy/memcpy/safef conversions: basicBed already done earlier; here haplotypes (memcpy of the original pointer pun), gbToFaRa, motifSig, hgClonePos, featureBits, libScan, hgGoldGapGl, hgSoftPromoter, mafClick, mafAddQRows, hgc.c, stanToBedAndExpRecs, bedUp, faSplit, trfBig, splitFaIntoContigs, aladdin, ameme. A full clean tree now builds with no warnings at -O3. refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/hg/utils/automation/kegAlign.json.ga
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    31734e42148b0358ee38a154aa343e2d1c0b258f Thu Jun 11 17:20:55 2026 -0700
    kegAlign updated to accept scoring matrix refs #31811
• src/hg/utils/otto/genArk/addAssemblyList.sh
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    01f8a6872a8d3679c29e63adac60c59f6a86c0c9 Fri Jun 12 15:14:45 2026 -0700
    correctly reloading assemblyList table with new indexes and no interference with the running system
• src/hg/utils/otto/otto.crontab
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    6e13fa20c66e496bcd2200d52235e093bd26d240 Sat Jun 13 22:41:40 2026 -0700
    explicity use a read-only kent mirror script
• src/hg/utils/otto/readOnlyKentMirror
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    95364ad664672b64da007a4fc25b0c51e9f23a30 Sat Jun 13 22:40:07 2026 -0700
    script to keep otto source tree up to date
  • lines changed 19, context: html, text, full: html, text
    12b69accc1d28a01e01c1cf7444d3b97e752aa82 Sat Jun 13 22:55:19 2026 -0700
    correct typo error and check for all error condition exits
• src/hg/utils/otto/sandboxupdate
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    13d2aa231f56c354b17528b8d72c541b1f98b2e6 Fri Jun 12 15:30:36 2026 -0700
    existing script in the otto user account HOME/bin/
  • lines changed 26, context: html, text, full: html, text
    3b97fd6c57d705abd88608cc5b277d264dae31ef Fri Jun 12 15:50:57 2026 -0700
    correct fetch update of the otto user sandbox
  • lines changed 26, context: html, text, full: html, text
    0b81e64efebcdb9ce7dc37f00868010ddcf70d56 Sat Jun 13 22:46:52 2026 -0700
    restore the original meaning of this script
  • lines changed 7, context: html, text, full: html, text
    a5d8d437fd8a70311ca85fb0f9ce8b27fbe1c459 Sat Jun 13 22:58:10 2026 -0700
    correct email address for error message
• src/hg/utils/otto/userRequests/asmRequestWatch.sh
  • lines changed 133, context: html, text, full: html, text
    87aafb03635a2e1ea4821bb1a2e41b640c867799 Mon Jun 8 13:11:17 2026 -0700
    initial script for assembly watch refs #31811
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    7133bbf60ed53ab306628d72050c9379ee74a9f1 Mon Jun 8 14:23:43 2026 -0700
    watch for an assembly build to have begun refs #31811
  • lines changed 28, context: html, text, full: html, text
    9ffda9e5b601497b1ddcda75d5bbf377c1156713 Mon Jun 8 14:32:29 2026 -0700
    watch for a build to have completed refs #31811
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    c54bbc1b2596adbb4bf4fcd278a531224c1d4624 Mon Jun 8 15:23:59 2026 -0700
    add checking for the files to go through the system refs #31811
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    90297a90d259da8b7e7d48e7bf8600994e6a09a6 Wed Jun 10 07:23:05 2026 -0700
    minor fixups per claude code review refs #31811
  • lines changed 1, context: html, text, full: html, text
    862b3b53dd2a3e4011560f989ac1c18310d4ffc4 Thu Jun 11 15:55:44 2026 -0700
    better email subject construction refs #31811
• src/hg/utils/otto/userRequests/ottoLib.py
  • lines changed 18, context: html, text, full: html, text
    bbbd8958d58ef4d08410683f00b476095fda53cc Fri Jun 12 16:05:30 2026 -0700
    improved source tree update refs #31811
• src/hg/utils/otto/userRequests/ottoRequestView.cgi
  • lines changed 28, context: html, text, full: html, text
    b8e0ec67d7da42dbdd9837bb11833cdc6b761b31 Mon Jun 8 14:50:45 2026 -0700
    eliminate the checkIp and reset STATUS_NAMES to liftStatus refs #31811
  • lines changed 20, context: html, text, full: html, text
    77f91b38ab166f2adfefbdff3c2cbd50c2591cd0 Mon Jun 8 15:21:14 2026 -0700
    correct status labels to differeniate liftOver vs. assembly status refs #31811
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    90297a90d259da8b7e7d48e7bf8600994e6a09a6 Wed Jun 10 07:23:05 2026 -0700
    minor fixups per claude code review refs #31811
  • lines changed 1, context: html, text, full: html, text
    8d11236cb4e555b9cbd549b86a097e7817682e49 Sat Jun 13 23:05:30 2026 -0700
    grammer correction per claude code review refs #31811
• src/hg/utils/otto/userRequests/ottoRequestWatch.sh
  • lines changed 3, context: html, text, full: html, text
    862b3b53dd2a3e4011560f989ac1c18310d4ffc4 Thu Jun 11 15:55:44 2026 -0700
    better email subject construction refs #31811
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    e14c4963bf3ad0f67e9ecf82a081acae159d821b Sat Jun 13 23:03:16 2026 -0700
    restore the galaxy cleanup step refs #31811
• src/inc/common.h
  • lines changed 10, context: html, text, full: html, text
    b628620dca257848dc6e9b18ea8e09585ecaf216 Tue Jun 9 00:07:17 2026 -0700
    hgcentralTidy also needs the 64 bit sessionDb and userDb IDs refs #33554
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    5437603957fb22ab9ffb254c2978c2a02439b2e9 Wed Jun 10 07:14:01 2026 -0700
    fixup comments per claud code review refs #33554
• src/inc/common.mk
  • lines changed 1, context: html, text, full: html, text
    a4ac71abc9e7bc32f98fd7c60ff8a48cba1ff056 Fri Jun 12 10:51:15 2026 -0700
    common.mk: default COPT to -O3 instead of -O -g Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
  • lines changed 1, context: html, text, full: html, text
    a7d7f0965efb3593fa74de84e7d9265dd8d0b05a Fri Jun 12 11:02:29 2026 -0700
    Revert "common.mk: default COPT to -O3 instead of -O -g" This reverts commit a4ac71abc9e7bc32f98fd7c60ff8a48cba1ff056.
  • lines changed 1, context: html, text, full: html, text
    556a70d62db277decca5aeda7ca157d35b73188b Fri Jun 12 12:11:03 2026 -0700
    common.mk: default COPT to -O3 instead of -O -g Re-apply now that the -O3 build warnings are fixed (this was reverted in a7d7f0965ef because the fixes had not landed yet). -O3 renders the bigSpeedTest1 hgTracks session about 1.5x faster than -O -g. refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
  • lines changed 6, context: html, text, full: html, text
    37ea1c69ef1e3101a3fea67043162744ea57666d Fri Jun 12 14:10:17 2026 -0700
    common.mk: add -fno-strict-aliasing The tree has long-standing type-punning idioms that violate strict aliasing, notably the dlList sentinel trick in lib/dlist.c (which overlays struct dlNode on struct dlList). These were harmless under the old -O -g (-O1) default because GCC does not enable -fstrict-aliasing until -O2. With the -O3 default they get miscompiled: blat, which uses dlList for stitching, silently produced fragmented alignments and failed blat/test until -fno-strict-aliasing was added. dlist is unlikely to be the only such violation, so disable the optimization tree-wide rather than patch individual idioms. refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/inc/errAbort.h
  • lines changed 12, context: html, text, full: html, text
    f57fc11d951807e19b20b5960e735fa50eaea279 Fri Jun 12 13:10:00 2026 -0700
    Fix more warnings exposed by -O3 build across hg utils and errAbort Continuation of the -O3 cleanup: a full clean rebuild surfaced warnings in many programs whose objects had not been recompiled before. Most are the same mechanical patterns as the first batch (strncpy -> safecpy/memcpy, sprintf -> safef), plus a few that needed more thought: - errAbort.h: mark errAbort/vaErrAbort/errnoAbort/noWarnAbort as noreturn. They provably never return (longjmp or exit; the existing "to make compiler happy" exit(-1) in noWarnAbort confirms the intent), and this lets GCC prune the impossible null paths after an errAbort guard, fixing false-positive null-deref / overread warnings in mafAddIRows, mafAddIRowsStream and phyloPlace with no source change to those files. - altSplice.c (hgGene): real one-element stack buffer overflow. makeGrayShades writes shadesOfGray[maxShade+1], but the caller declared shadesOfGray[9] with maxShade=8. Grow the array to [10] (maxShade stays 8); behavior unchanged. - hgc.c bedPrintPos: ~60 callers pass a track-specific struct cast to (struct bed *) and read only its bed-compatible leading fields. At -O3 -Warray-bounds flags the casts because the real object is smaller than struct bed; the reads are safe by the bed-layout convention, so suppress -Warray-bounds around just that function. - mafsInRegion.c: chromFromSrc returns strchr(src,'.')+1, which GCC mis-sizes as a 0-byte region when handed to strcmp via sameString/differentString; suppress the false-positive -Wstringop-overread around extractMafs. - sanger22gtf.c, bottleneck.c: put the printf/fprintf in the else of the NULL guard so -Wformat-overflow (which runs before the noreturn-based pruning) can see the argument is non-null. safecpy/memcpy/safef conversions: basicBed already done earlier; here haplotypes (memcpy of the original pointer pun), gbToFaRa, motifSig, hgClonePos, featureBits, libScan, hgGoldGapGl, hgSoftPromoter, mafClick, mafAddQRows, hgc.c, stanToBedAndExpRecs, bedUp, faSplit, trfBig, splitFaIntoContigs, aladdin, ameme. A full clean tree now builds with no warnings at -O3. refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/jkOwnLib/crudeali.c
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    fb50a1cca3a117bb964c43196671142484b13bf9 Fri Jun 12 12:10:47 2026 -0700
    lib jkOwnLib hg/lib: fix warnings exposed by -O3 build At -O3 GCC does more inlining and interprocedural range analysis, which surfaces several warnings that -O -g never triggered. With -Werror these break the build, so fix them ahead of switching the default to -O3. - bamFile.c: move setenv() into the else of its NULL guard so it is not reachable with a NULL argument (-Wnonnull, seen via inlining of bamFetch). - basicBed.c, wormdna.c, bedDetail.c, customFactory.c, hdb.c, qaSeq.c: replace strncpy() with safecpy() where the result must be terminated (-Wstringop-truncation). - htmshell.c: use memcpy() for the intentional exact-length, non-terminated copy (-Wstringop-truncation). - obscure.c: compute the comma groups in sprintLongWithCommas() with % 1000 so the compiler can see each %03lld argument is bounded (-Wformat-overflow). - crudeali.c: do the endian type-pun through a union so strict-aliasing analysis no longer reports the value as uninitialized (-Wuninitialized). - jksql.c: wrap a possibly-NULL database name in naForNull() before passing it to %s (-Wformat-overflow). refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/lib/bamFile.c
  • lines changed 1, context: html, text, full: html, text
    fb50a1cca3a117bb964c43196671142484b13bf9 Fri Jun 12 12:10:47 2026 -0700
    lib jkOwnLib hg/lib: fix warnings exposed by -O3 build At -O3 GCC does more inlining and interprocedural range analysis, which surfaces several warnings that -O -g never triggered. With -Werror these break the build, so fix them ahead of switching the default to -O3. - bamFile.c: move setenv() into the else of its NULL guard so it is not reachable with a NULL argument (-Wnonnull, seen via inlining of bamFetch). - basicBed.c, wormdna.c, bedDetail.c, customFactory.c, hdb.c, qaSeq.c: replace strncpy() with safecpy() where the result must be terminated (-Wstringop-truncation). - htmshell.c: use memcpy() for the intentional exact-length, non-terminated copy (-Wstringop-truncation). - obscure.c: compute the comma groups in sprintLongWithCommas() with % 1000 so the compiler can see each %03lld argument is bounded (-Wformat-overflow). - crudeali.c: do the endian type-pun through a union so strict-aliasing analysis no longer reports the value as uninitialized (-Wuninitialized). - jksql.c: wrap a possibly-NULL database name in naForNull() before passing it to %s (-Wformat-overflow). refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/lib/basicBed.c
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    fb50a1cca3a117bb964c43196671142484b13bf9 Fri Jun 12 12:10:47 2026 -0700
    lib jkOwnLib hg/lib: fix warnings exposed by -O3 build At -O3 GCC does more inlining and interprocedural range analysis, which surfaces several warnings that -O -g never triggered. With -Werror these break the build, so fix them ahead of switching the default to -O3. - bamFile.c: move setenv() into the else of its NULL guard so it is not reachable with a NULL argument (-Wnonnull, seen via inlining of bamFetch). - basicBed.c, wormdna.c, bedDetail.c, customFactory.c, hdb.c, qaSeq.c: replace strncpy() with safecpy() where the result must be terminated (-Wstringop-truncation). - htmshell.c: use memcpy() for the intentional exact-length, non-terminated copy (-Wstringop-truncation). - obscure.c: compute the comma groups in sprintLongWithCommas() with % 1000 so the compiler can see each %03lld argument is bounded (-Wformat-overflow). - crudeali.c: do the endian type-pun through a union so strict-aliasing analysis no longer reports the value as uninitialized (-Wuninitialized). - jksql.c: wrap a possibly-NULL database name in naForNull() before passing it to %s (-Wformat-overflow). refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/lib/common.c
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    b628620dca257848dc6e9b18ea8e09585ecaf216 Tue Jun 9 00:07:17 2026 -0700
    hgcentralTidy also needs the 64 bit sessionDb and userDb IDs refs #33554
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    5437603957fb22ab9ffb254c2978c2a02439b2e9 Wed Jun 10 07:14:01 2026 -0700
    fixup comments per claud code review refs #33554
• src/lib/htmshell.c
  • lines changed 1, context: html, text, full: html, text
    fb50a1cca3a117bb964c43196671142484b13bf9 Fri Jun 12 12:10:47 2026 -0700
    lib jkOwnLib hg/lib: fix warnings exposed by -O3 build At -O3 GCC does more inlining and interprocedural range analysis, which surfaces several warnings that -O -g never triggered. With -Werror these break the build, so fix them ahead of switching the default to -O3. - bamFile.c: move setenv() into the else of its NULL guard so it is not reachable with a NULL argument (-Wnonnull, seen via inlining of bamFetch). - basicBed.c, wormdna.c, bedDetail.c, customFactory.c, hdb.c, qaSeq.c: replace strncpy() with safecpy() where the result must be terminated (-Wstringop-truncation). - htmshell.c: use memcpy() for the intentional exact-length, non-terminated copy (-Wstringop-truncation). - obscure.c: compute the comma groups in sprintLongWithCommas() with % 1000 so the compiler can see each %03lld argument is bounded (-Wformat-overflow). - crudeali.c: do the endian type-pun through a union so strict-aliasing analysis no longer reports the value as uninitialized (-Wuninitialized). - jksql.c: wrap a possibly-NULL database name in naForNull() before passing it to %s (-Wformat-overflow). refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/lib/obscure.c
  • lines changed 39, context: html, text, full: html, text
    fb50a1cca3a117bb964c43196671142484b13bf9 Fri Jun 12 12:10:47 2026 -0700
    lib jkOwnLib hg/lib: fix warnings exposed by -O3 build At -O3 GCC does more inlining and interprocedural range analysis, which surfaces several warnings that -O -g never triggered. With -Werror these break the build, so fix them ahead of switching the default to -O3. - bamFile.c: move setenv() into the else of its NULL guard so it is not reachable with a NULL argument (-Wnonnull, seen via inlining of bamFetch). - basicBed.c, wormdna.c, bedDetail.c, customFactory.c, hdb.c, qaSeq.c: replace strncpy() with safecpy() where the result must be terminated (-Wstringop-truncation). - htmshell.c: use memcpy() for the intentional exact-length, non-terminated copy (-Wstringop-truncation). - obscure.c: compute the comma groups in sprintLongWithCommas() with % 1000 so the compiler can see each %03lld argument is bounded (-Wformat-overflow). - crudeali.c: do the endian type-pun through a union so strict-aliasing analysis no longer reports the value as uninitialized (-Wuninitialized). - jksql.c: wrap a possibly-NULL database name in naForNull() before passing it to %s (-Wformat-overflow). refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/lib/tests/mmHashTest.c
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    dd59061711dca60f7fe8f430411b8c5eb7559d4a Fri Jun 12 14:48:21 2026 -0700
    lib/tests: fix -O3 format-overflow in mmHashTest Put the fprintf in the else of the NULL guard so -Wformat-overflow (which runs before the noreturn-based pruning) sees the value is non-null. Same pattern as the earlier sanger22gtf/bottleneck fixes. This surfaced only now because make clean does not clean most test directories, so the test programs kept reusing stale -O -g objects until a forced rebuild recompiled them at -O3. refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/lib/wormdna.c
  • lines changed 2, context: html, text, full: html, text
    fb50a1cca3a117bb964c43196671142484b13bf9 Fri Jun 12 12:10:47 2026 -0700
    lib jkOwnLib hg/lib: fix warnings exposed by -O3 build At -O3 GCC does more inlining and interprocedural range analysis, which surfaces several warnings that -O -g never triggered. With -Werror these break the build, so fix them ahead of switching the default to -O3. - bamFile.c: move setenv() into the else of its NULL guard so it is not reachable with a NULL argument (-Wnonnull, seen via inlining of bamFetch). - basicBed.c, wormdna.c, bedDetail.c, customFactory.c, hdb.c, qaSeq.c: replace strncpy() with safecpy() where the result must be terminated (-Wstringop-truncation). - htmshell.c: use memcpy() for the intentional exact-length, non-terminated copy (-Wstringop-truncation). - obscure.c: compute the comma groups in sprintLongWithCommas() with % 1000 so the compiler can see each %03lld argument is bounded (-Wformat-overflow). - crudeali.c: do the endian type-pun through a union so strict-aliasing analysis no longer reports the value as uninitialized (-Wuninitialized). - jksql.c: wrap a possibly-NULL database name in naForNull() before passing it to %s (-Wformat-overflow). refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/submodules/submoduleSetup
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    e617d8fcfd4f783bfe7e3b569c620532ab43858d Wed Jun 10 01:32:09 2026 -0700
    fix #37741 Source zip (jksrc.zip) build broken: htslib submodule not included by git archive
• src/userApps/fetchKentSource.sh
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    edb6fc7755da47df33f2dce4af4fd0017385b7fc Thu Jun 11 12:55:46 2026 -0700
    hacking in the submodules for the htslib no redmine
• src/utils/faSplit/faSplit.c
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    f57fc11d951807e19b20b5960e735fa50eaea279 Fri Jun 12 13:10:00 2026 -0700
    Fix more warnings exposed by -O3 build across hg utils and errAbort Continuation of the -O3 cleanup: a full clean rebuild surfaced warnings in many programs whose objects had not been recompiled before. Most are the same mechanical patterns as the first batch (strncpy -> safecpy/memcpy, sprintf -> safef), plus a few that needed more thought: - errAbort.h: mark errAbort/vaErrAbort/errnoAbort/noWarnAbort as noreturn. They provably never return (longjmp or exit; the existing "to make compiler happy" exit(-1) in noWarnAbort confirms the intent), and this lets GCC prune the impossible null paths after an errAbort guard, fixing false-positive null-deref / overread warnings in mafAddIRows, mafAddIRowsStream and phyloPlace with no source change to those files. - altSplice.c (hgGene): real one-element stack buffer overflow. makeGrayShades writes shadesOfGray[maxShade+1], but the caller declared shadesOfGray[9] with maxShade=8. Grow the array to [10] (maxShade stays 8); behavior unchanged. - hgc.c bedPrintPos: ~60 callers pass a track-specific struct cast to (struct bed *) and read only its bed-compatible leading fields. At -O3 -Warray-bounds flags the casts because the real object is smaller than struct bed; the reads are safe by the bed-layout convention, so suppress -Warray-bounds around just that function. - mafsInRegion.c: chromFromSrc returns strchr(src,'.')+1, which GCC mis-sizes as a 0-byte region when handed to strcmp via sameString/differentString; suppress the false-positive -Wstringop-overread around extractMafs. - sanger22gtf.c, bottleneck.c: put the printf/fprintf in the else of the NULL guard so -Wformat-overflow (which runs before the noreturn-based pruning) can see the argument is non-null. safecpy/memcpy/safef conversions: basicBed already done earlier; here haplotypes (memcpy of the original pointer pun), gbToFaRa, motifSig, hgClonePos, featureBits, libScan, hgGoldGapGl, hgSoftPromoter, mafClick, mafAddQRows, hgc.c, stanToBedAndExpRecs, bedUp, faSplit, trfBig, splitFaIntoContigs, aladdin, ameme. A full clean tree now builds with no warnings at -O3. refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
• src/utils/qa/weeklybld/coBranch.csh
  • lines changed 7, context: html, text, full: html, text
    e617d8fcfd4f783bfe7e3b569c620532ab43858d Wed Jun 10 01:32:09 2026 -0700
    fix #37741 Source zip (jksrc.zip) build broken: htslib submodule not included by git archive
• src/utils/qa/weeklybld/makeZip.csh
  • lines changed 50, context: html, text, full: html, text
    e617d8fcfd4f783bfe7e3b569c620532ab43858d Wed Jun 10 01:32:09 2026 -0700
    fix #37741 Source zip (jksrc.zip) build broken: htslib submodule not included by git archive
• src/weblet/bottleneck/bottleneck.c
  • lines changed 1, context: html, text, full: html, text
    f57fc11d951807e19b20b5960e735fa50eaea279 Fri Jun 12 13:10:00 2026 -0700
    Fix more warnings exposed by -O3 build across hg utils and errAbort Continuation of the -O3 cleanup: a full clean rebuild surfaced warnings in many programs whose objects had not been recompiled before. Most are the same mechanical patterns as the first batch (strncpy -> safecpy/memcpy, sprintf -> safef), plus a few that needed more thought: - errAbort.h: mark errAbort/vaErrAbort/errnoAbort/noWarnAbort as noreturn. They provably never return (longjmp or exit; the existing "to make compiler happy" exit(-1) in noWarnAbort confirms the intent), and this lets GCC prune the impossible null paths after an errAbort guard, fixing false-positive null-deref / overread warnings in mafAddIRows, mafAddIRowsStream and phyloPlace with no source change to those files. - altSplice.c (hgGene): real one-element stack buffer overflow. makeGrayShades writes shadesOfGray[maxShade+1], but the caller declared shadesOfGray[9] with maxShade=8. Grow the array to [10] (maxShade stays 8); behavior unchanged. - hgc.c bedPrintPos: ~60 callers pass a track-specific struct cast to (struct bed *) and read only its bed-compatible leading fields. At -O3 -Warray-bounds flags the casts because the real object is smaller than struct bed; the reads are safe by the bed-layout convention, so suppress -Warray-bounds around just that function. - mafsInRegion.c: chromFromSrc returns strchr(src,'.')+1, which GCC mis-sizes as a 0-byte region when handed to strcmp via sameString/differentString; suppress the false-positive -Wstringop-overread around extractMafs. - sanger22gtf.c, bottleneck.c: put the printf/fprintf in the else of the NULL guard so -Wformat-overflow (which runs before the noreturn-based pruning) can see the argument is non-null. safecpy/memcpy/safef conversions: basicBed already done earlier; here haplotypes (memcpy of the original pointer pun), gbToFaRa, motifSig, hgClonePos, featureBits, libScan, hgGoldGapGl, hgSoftPromoter, mafClick, mafAddQRows, hgc.c, stanToBedAndExpRecs, bedUp, faSplit, trfBig, splitFaIntoContigs, aladdin, ameme. A full clean tree now builds with no warnings at -O3. refs #37761 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

• lines changed: 4960
• files changed: 204