v498

Code changes:

• Initial commit of myVariants feature: users can now create custom track items on the fly using a form that supports colors, descriptions, names, ref and alt alleles, custom fields, and item sharing (#33808). Chris
• hubSpace now supports assembly hub upload, limited to one assembly per hub (#37411). Chris
• Initial support for ripples recombinant search in usher-sampled-server on hgPhyloPlace. Angie
• Replace subtrackUrl setting for faceted composites with subtrackUrls, supporting outlinks in multiple fields (#36320). Jonathan
• Limit the amount of setting data that can be added to a cart in a single POST request to mitigate cart-stuffing robots (#37452). Jonathan
• Fix mdbSearch URL construction so the Advanced tab in track search makes valid hgApi queries (#37421). Jonathan
• Push trackDbHub anchor jumps below the search box so the first content under the anchor is no longer hidden. Jonathan
• On-going development of the lift-over user request system (#31811). Hiram
• Reset the assembly request form to verify user authentication with the Cloudflare credentials (#31811). Hiram
• Fortify the GenArk build system for use with cron jobs (#31811). Hiram
• Fix bug in maf track item clicks to correctly link out to the other assemblies in the alignment when they are GenArk browsers (#34370). Hiram
• Render the filter UI on track-collection configuration pages with Submit and Reset to defaults; fix a pre-existing bigGenePred duplicate-filter bug surfaced during the work (#37426). Max
• Reduce the gap between the Filters heading and the first filter row on track-collection configuration pages (#37426). Gerardo
• Composite hgTrackUi: the global [-] button now hides the composite dropdown, and [-]/[+] remembers previous visibility instead of reverting to pack (#37182). Max
• Fixup zoom to exon/codon right-click option for genePreds, bigGenePreds, and bigBeds (#37521). Chris
• Add simpleTracks mouseover exon length (#37439). Max
• Restructure the /docs/ landing page for new users with a sticky sidebar table of contents (#36894). Lou
• Add a chromAlias info icon next to the chromosome position, with mouseover usage description and docs link (#29201). Lou
• Added chainToMaf command. Mark
• Switch GENCODE versions in all.joiner to use macros instead of growing every release (#37436). Mark
• New mafToBigMafSummary utility producing bed3+4 input for bedToBigBed -as=mafSummary.as, replacing the documented hgLoadMafSummary -test | cut -f2- | sort hack; also fixes errAbort on plain hg38.chrY-style master src names (#37404). Braney
• Make assumesHub-from-assembly-hub session portability work across hosts: remap db cart variable and db-keyed cart vars alongside the hub_<id>_* track settings that were already being renamed (#34986). Braney
• Make quickLifted GENCODE tracks usable: click details, position links, Get DNA flow, and coding/non-coding coloring (#36059). Braney
• Make quickLifted refGene and NCBI RefSeq clicks fully functional: rich RefSeq fields, Predicted Protein and CDS FASTA links, Ctrl/Cmd+drag zoom, and "Select all subtracks" before quickLifting; also keep hidden composite siblings in the lift hub (#36125). Braney
• hgGene clicks on quickLifted knownGene items no longer segfault: all sections, GeneReviews, and Methods page render (#36370). Braney
• Remap bigBed search hits from source to destination coordinates on quickLifted hub tracks so search result links resolve correctly (#36340). Braney
• hgc bigBed click: skip intervals that fail quickLift remap instead of errAborting the page, and only emit BR / set found after passing filters (#36335). Braney
• Populate the quickLift source track description on details and config pages when the source assembly is a hub or GenArk (#37389). Braney
• Let quickLift tracks join the hgTracks parallel-fetch worker pool, saving roughly 5 seconds of serial main-thread time per track (#37470). Braney
• Route parallel-loaded bigDataUrls through hReplaceGbdb so gbdbLoc1/gbdbLoc2 rewrites apply to bigBed, bigWig, and bamWig tracks (#37479). Braney
• hgTracks no longer SIGBUSes mid-render when /dev/shm is full (notably under Docker's 64 MB default tmpfs); the Docker image now stores the trackDb cache on a persistent path outside /dev/shm (#37475). Braney
• Resolve the $D macro in quickLifted ClinVar dataVersion paths, rather than displaying the literal $D on the config page (#37489). Braney
• hgConvert "failed to lift" composite warning now lists only user-visible non-liftable subtracks, while still bringing hidden liftable siblings across (#37491, #36125). Braney
• Exclude quickLifted tracks from hgTables and hgIntegrator output paths where they would produce wrong results: block hgTables output, hide QuickLift groups from both dropdowns, avoid SQL connect to the hub assembly, and stop the hgIntegrator "Choose fields" hang (#37519). Braney
• New quickLiftBench harness: saved-session comparisons, per-phase timing, parallel-fetch regression case with phase assertions; hgTracks also emits per-track timing on the trackImgOnly=1 fast path (#37445, #37470, #37488). Braney
• Move the parseQuickLiftLogs log-crawl helper into the kent source tree. Braney
• redmineCli: add --file-list-add to append paths idempotently (#35059). Max
• redmineCli: let create accept --tracker and --status by name; fix --status integer-default crash in the resolver. Braney

Data changes:

• Released PrimateAI-3D and PromoterAI tracks to beta and RR (#37274, #37278). Lou
• New ClinPred missense pathogenicity score track on hg19 and hg38 (#37510). Lou
• New TP53 VCEP track hub (#37399). Lou
• Expanded dbVar tracks to expose all six nstd186 source studies and add new Somatic and Other composites on hg19 and hg38 (#37406). Lou
• New goat (ARS1.2) liftOver chain files added across the AsmHub clades (#37380). Jairo
• New SSREV phyloP subtrack content on cons30way and cactus447way, with updated labels, view limits, and references (#28259). Jairo
• Restore the longReadVariants track on the RR by fixing its bigDataUrl (#36258). Jairo
• Shortened ncOrfs labels and cleaned up GENCODE references on related description pages (#35101). Jairo
• Long-read SV track collection: added doc pages and converters for CoLoRSdb, GA4K, Gustafson, HGSVC2, HPRC2, 1KG 3202 SR comparator, and tommoJpCnv; restricted CPC1 to its 58 samples; flagged Kim PD as preliminary; rebuilt CoLoRSdb with float AF and insLen; harmonized shortLabels; added human-readable svType labels; added an hs1 HPRC2 build; added the new merged lrSvAll track (2.69M unique SVs across 15 subtracks); added Coverage column and sample-overlap note to the overview (#36258, #36642). Max
• Short-read SV track collection: split abelSv, onekg3202Sr, and tommoJpCnv out of lrSv into a sibling track collection with mirrored filter fields (dev only) (#36258). Max
• varFreqs allele-frequency tracks: added SVatalog 101, Tishkoff 180, ChinaMap, China Westlake, NPM Singapore subtracks; lifted GenomeAsia (gasp/gaspIndel) from hg19 to hg38; added GenomesIndia (#36642). Max
• New gnomAD MPC v4.1.1 composite track on hg38 (four per-ALT bigWigs plus a per-transcript bigBed); added an hg19 warning page (#37434, #37478). Max
• New mei track collection on hg38 and hs1 for mobile element insertions, cross-linked to lrSv (#37524). Max
• New CHORI/NCBI BAC clone-end placements on danRer11 with CH73, CH211, and CH1073 subtracks; modernized BAC description pages (#35059). Max
• NMD Escape: added a MANE Select Plus Clinical 1.5 subtrack with its own autoSql; fixed the Rule 1 over-paint bug on single-CDS-exon transcripts with 3'UTR introns (#33737). Max
• rnaMod track collection: added a DRACH motif sites track (MANE Select v1.5 projected via pslMap) and an m6A-Atlas v2 sites track (Liang 2024) (dev only) (#36613). Max
• ncOrfs: added Kozak strengths to the trackDb stanza and to all bigBeds with a generic tool that adds Kozak strength to bigGenePred files (#35101). Max
• Correct dataVersion statement on ClinVar (#37467). Max
• Dev-only dbVar non-redundant subtrack stanza for future comparison work. Max
• Fix ClinVar submission_summary corruption: strip a trailing backslash before tab, so MySQL LOAD DATA doesn't eat the field separator, with a follow-up to use a Python r-prefix so perl sees the intended regex (#37477). Braney
• clinVarToBed: remove a stray non-ASCII character. Braney