Commits for braney
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v495_base to v496_preview (2026-03-09 to 2026-03-16) v496
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1bbbf05971f950d48fcd67ac9e8e6d395bae9761 Tue Mar 10 09:29:23 2026 -0700
- fix problem with composites with only one child and noParentConfig on (refs #37130)
36e79dca2dc1ba9ef65c7ea13424ff8475e2bc72 Tue Mar 10 10:43:50 2026 -0700
- hubCheck: validate sequence names in 2bit files for illegal characters (refs #37174)
Add check that sequence names contain only [A-Za-z0-9._-], start with
a letter or digit, and are at most 254 characters. Warns per sequence
with the offending character and suggests chromAlias. New -noSeqNameCheck
flag disables the check.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- src/hg/utils/hubCheck/hubCheck.c - lines changed 45, context: html, text, full: html, text
71b7edde11d143446fcc9e72c14c8f213e74c900 Tue Mar 10 10:49:54 2026 -0700
- hubCheck: add unit tests for sequence name validation (refs #37174)
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- src/hg/utils/hubCheck/tests/expected/noSeqNameCheck.output.txt - lines changed 3, context: html, text, full: html, text
- src/hg/utils/hubCheck/tests/expected/seqNameCheck.output.txt - lines changed 7, context: html, text, full: html, text
- src/hg/utils/hubCheck/tests/input/seqNameGenomes.txt - lines changed 7, context: html, text, full: html, text
- src/hg/utils/hubCheck/tests/input/seqNameHub.txt - lines changed 5, context: html, text, full: html, text
- src/hg/utils/hubCheck/tests/input/seqNameTest.2bit - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/hg/utils/hubCheck/tests/input/seqNameTrackDb.txt - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
- src/hg/utils/hubCheck/tests/makefile - lines changed 9, context: html, text, full: html, text
a71215bcc4a26e1641770d82127dc57ced1842c8 Tue Mar 10 12:37:04 2026 -0700
- Detect tracks that list themselves as their own parent, preventing infinite loop refs #35986
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- src/hg/lib/trackDbCustom.c - lines changed 7, context: html, text, full: html, text
- src/hg/utils/hubCheck/tests/expected/selfParent.output.txt - lines changed 3, context: html, text, full: html, text
- src/hg/utils/hubCheck/tests/input/selfParent.txt - lines changed 14, context: html, text, full: html, text
- src/hg/utils/hubCheck/tests/makefile - lines changed 5, context: html, text, full: html, text
8bf67a4375f3d5f15a109bea5a33a782c602fe67 Tue Mar 10 13:07:00 2026 -0700
- hubCheck: warn about periods in track names refs #37223
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- src/hg/utils/hubCheck/hubCheck.c - lines changed 14, context: html, text, full: html, text
- src/hg/utils/hubCheck/tests/expected/dotInName.output.txt - lines changed 8, context: html, text, full: html, text
- src/hg/utils/hubCheck/tests/expected/manyErrors.output.txt - lines changed 3, context: html, text, full: html, text
- src/hg/utils/hubCheck/tests/input/dotInName.txt - lines changed 27, context: html, text, full: html, text
- src/hg/utils/hubCheck/tests/makefile - lines changed 5, context: html, text, full: html, text
0529f8de2a72011dfcea8f9a1221b6d227341743 Tue Mar 10 17:34:58 2026 -0700
- hgc MAF click: use mafFrag to show only selected species with inserts removed
Change the hgc MAF detail page to use hgMafFrag/hgBigMafFrag instead of
displaying raw MAF blocks. This stitches alignments into a single continuous
display in reference coordinates, filtering to only selected species and
removing insertion columns where the reference has gaps.
Key changes:
- mafClick.c: rewrite mafOrAxtClick2 to build species orderList from
trackDb settings (speciesOrder, speciesGroup, speciesUseFile) respecting
speciesDefaultOff and cart on/off state via cartUsualBooleanClosestToHome,
matching the hgTracks species selection logic in newSpeciesItems().
Add mafStripRefGaps() to remove insertion columns from mafFrag output.
Show spaces instead of dots for matching bases in diff mode.
- hgMaf.h/hgMaf.c: add hgMafFragFromMafList() public wrapper for
pre-loaded mafLists (AXT/custom mafFile support). Change hgMafFragHelper
to skip species not in orderList instead of errAbort. Track per-species
source coordinates (src, start, end, srcSize, strand) in struct oneOrg
so browser/DNA links work correctly in mafFrag output.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- src/hg/hgc/mafClick.c - lines changed 185, context: html, text, full: html, text
2f032b790bd3d0354f1d61de5dcadb2e469c1817 Tue Mar 10 17:42:42 2026 -0700
- Add unit tests for mafFrag tool
Add test suite with 5 tests covering basic extraction, reverse strand,
custom outName, small region, and larger multi-block region using
hg38 multiz100way. Replace broken old test target that referenced
a missing expected.maf file.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- src/hg/ratStuff/mafFrag/makefile - lines changed 5, context: html, text, full: html, text
- src/hg/ratStuff/mafFrag/tests/expected/basic.maf - lines changed 5, context: html, text, full: html, text
- src/hg/ratStuff/mafFrag/tests/expected/larger.maf - lines changed 29, context: html, text, full: html, text
- src/hg/ratStuff/mafFrag/tests/expected/outName.maf - lines changed 5, context: html, text, full: html, text
- src/hg/ratStuff/mafFrag/tests/expected/revStrand.maf - lines changed 5, context: html, text, full: html, text
- src/hg/ratStuff/mafFrag/tests/expected/small.maf - lines changed 5, context: html, text, full: html, text
- src/hg/ratStuff/mafFrag/tests/makefile - lines changed 35, context: html, text, full: html, text
46ab7629ec58dbef76d6d8c09d687875efa7af01 Tue Mar 10 17:53:21 2026 -0700
- Merge branch 'master' into mafClickMafFrag
2da16dce988cd42c7d97019eebd9660bfe20b68b Tue Mar 10 17:55:26 2026 -0700
- Update mafFrag test expected outputs for source coordinate tracking
Regenerate expected files to reflect hgMafFragHelper now preserving
full source (db.chrom), start, size, srcSize, and strand for
non-reference species instead of placeholder values.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- src/hg/ratStuff/mafFrag/tests/expected/basic.maf - lines changed 1, context: html, text, full: html, text
- src/hg/ratStuff/mafFrag/tests/expected/larger.maf - lines changed 25, context: html, text, full: html, text
- src/hg/ratStuff/mafFrag/tests/expected/outName.maf - lines changed 1, context: html, text, full: html, text
- src/hg/ratStuff/mafFrag/tests/expected/revStrand.maf - lines changed 1, context: html, text, full: html, text
- src/hg/ratStuff/mafFrag/tests/expected/small.maf - lines changed 1, context: html, text, full: html, text
4d91bce1e029162895c6acde3100bd375ceee24e Tue Mar 10 18:14:44 2026 -0700
- Gate new mafFrag MAF click display behind hg.conf mafClickMafFrag setting
The new stitched mafFrag display (species filtering, insertion removal,
space-for-match in diff mode) is now controlled by the hg.conf boolean
mafClickMafFrag. When off (default), the original block-by-block display
is used. Set mafClickMafFrag=on to enable the new behavior.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- src/hg/hgc/mafClick.c - lines changed 145, context: html, text, full: html, text
715e2acf2dd9ef6106cc42ce79c724e1e52ad62e Thu Mar 12 09:14:28 2026 -0700
- NoDots MAF alignment display for hgc mafClick, with i-row preservation and mafFrag -noDots flag
hgMaf.c: add hgMafFragHelperNoDots and public wrappers (hgMafFragNoDots,
hgBigMafFragNoDots, hgMafFragFromMafListNoDots) that return a list of maf
blocks containing only species with actual sequence — no dot-filled rows.
Blocks are broken when the species set changes; gaps between same-species
blocks are filled with native sequence for the reference and dashes for
others. Preserve i-row data (leftStatus/rightStatus/leftLen/rightLen)
through the NoDots path so insert annotations appear in emitted blocks.
hgMaf.h: declare the new NoDots public functions.
mafClick.c: use NoDots path when mafClickMafFrag is enabled. Fix block
numbering (aliIx was never incremented in useMafFrag path). Use full
textSize for NoDots line width. Use dots instead of spaces in diff mode
for both paths. Fix species label width computation to check labelHash
consistently so long assembly names don't misalign sequences. Strip
ref gap columns where no other species has sequence.
mafFrag: add -noDots option to invoke hgMafFragNoDots from the command line,
with 4 new tests (noDots, noDotsRev, noDotsOutName, noDotsLarger).
refs #21477
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
- src/hg/ratStuff/mafFrag/mafFrag.c - lines changed 27, context: html, text, full: html, text
- src/hg/ratStuff/mafFrag/tests/expected/noDots.maf - lines changed 6, context: html, text, full: html, text
- src/hg/ratStuff/mafFrag/tests/expected/noDotsLarger.maf - lines changed 254, context: html, text, full: html, text
- src/hg/ratStuff/mafFrag/tests/expected/noDotsOutName.maf - lines changed 6, context: html, text, full: html, text
- src/hg/ratStuff/mafFrag/tests/expected/noDotsRev.maf - lines changed 6, context: html, text, full: html, text
- src/hg/ratStuff/mafFrag/tests/makefile - lines changed 17, context: html, text, full: html, text
147740e133aa59c5aa7938ef68f1b66f3696c701 Fri Mar 13 15:29:49 2026 -0700
- Revert noDots mafClick/mafFrag work from master, refs #21477
Remove the mafClickMafFrag/noDots code path from mafClick.c, hgMaf.c,
hgMaf.h, and mafFrag.c. Also remove mafFrag unit tests added as part
of this work. The code is preserved on the mafFragNoDots and
mafClickMafFrag branches.
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
- src/hg/hgc/mafClick.c - lines changed 205, context: html, text, full: html, text
- src/hg/ratStuff/mafFrag/mafFrag.c - lines changed 27, context: html, text, full: html, text
- src/hg/ratStuff/mafFrag/makefile - lines changed 5, context: html, text, full: html, text
- src/hg/ratStuff/mafFrag/tests/expected/basic.maf - lines changed 5, context: html, text, full: html, text
- src/hg/ratStuff/mafFrag/tests/expected/larger.maf - lines changed 29, context: html, text, full: html, text
- src/hg/ratStuff/mafFrag/tests/expected/noDots.maf - lines changed 6, context: html, text, full: html, text
- src/hg/ratStuff/mafFrag/tests/expected/noDotsLarger.maf - lines changed 254, context: html, text, full: html, text
- src/hg/ratStuff/mafFrag/tests/expected/noDotsOutName.maf - lines changed 6, context: html, text, full: html, text
- src/hg/ratStuff/mafFrag/tests/expected/noDotsRev.maf - lines changed 6, context: html, text, full: html, text
- src/hg/ratStuff/mafFrag/tests/expected/outName.maf - lines changed 5, context: html, text, full: html, text
- src/hg/ratStuff/mafFrag/tests/expected/revStrand.maf - lines changed 5, context: html, text, full: html, text
- src/hg/ratStuff/mafFrag/tests/expected/small.maf - lines changed 5, context: html, text, full: html, text
- src/hg/ratStuff/mafFrag/tests/makefile - lines changed 51, context: html, text, full: html, text
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