File Changes for braney

v501_preview2 to v501_base (2026-07-13 to 2026-07-20) v501

• src/hg/hgTracks/hgTracks.c
  • lines changed 8, context: html, text, full: html, text
    b551f6c3ac801dbb5b8a436d4ae646772d4eaded Wed Jul 15 16:42:58 2026 -0700
    Revert the "0 bases" -> "1 base" ruler scale-bar change from 94f9b53d3db. At single-base zoom the base-position scale bar reads "0 bases" again, as it does on the RR. QA reviewed the dev version and preferred the existing RR behavior over the reworked ruler text, so rather than keep iterating we match the RR. This touches only computeScaleBar; the two JavaScript click-behavior fixes from 94f9b53d3db (symmetric single-click recenter and the config-strip click fix) stay in place. refs #27113
• src/hg/makeDb/scripts/hprc2X/README.txt
  • lines changed 46, context: html, text, full: html, text
    f665d4cc3b02924a8507b2f910eaf85eab54d433 Sat Jul 18 14:12:24 2026 -0700
    hprc2X: left-shifted HPRC r2 deletion analysis and external-catalog cross-reference scripts Deletion-only re-derivation of the HPRC Release 2 rearrangement track used to test left-shifting indel placement and to measure how the deletions correspond to dbSNP, DGV, ClinVar, and the previous (rel1) release. Includes the unbounded left-normalizer, the aggregation and subsampling drivers, the stability and cross-release carryover analyses, and the dbSNP rs cross-reference prototype. See README.txt for the manifest; full results and cached data live in /hive/data/genomes/hg38/bed/hprc2X. refs #37891
• src/hg/makeDb/scripts/hprc2X/buildDel.sh
  • lines changed 15, context: html, text, full: html, text
    f665d4cc3b02924a8507b2f910eaf85eab54d433 Sat Jul 18 14:12:24 2026 -0700
    hprc2X: left-shifted HPRC r2 deletion analysis and external-catalog cross-reference scripts Deletion-only re-derivation of the HPRC Release 2 rearrangement track used to test left-shifting indel placement and to measure how the deletions correspond to dbSNP, DGV, ClinVar, and the previous (rel1) release. Includes the unbounded left-normalizer, the aggregation and subsampling drivers, the stability and cross-release carryover analyses, and the dbSNP rs cross-reference prototype. See README.txt for the manifest; full results and cached data live in /hive/data/genomes/hg38/bed/hprc2X. refs #37891
• src/hg/makeDb/scripts/hprc2X/buildFullXref.sh
  • lines changed 33, context: html, text, full: html, text
    f665d4cc3b02924a8507b2f910eaf85eab54d433 Sat Jul 18 14:12:24 2026 -0700
    hprc2X: left-shifted HPRC r2 deletion analysis and external-catalog cross-reference scripts Deletion-only re-derivation of the HPRC Release 2 rearrangement track used to test left-shifting indel placement and to measure how the deletions correspond to dbSNP, DGV, ClinVar, and the previous (rel1) release. Includes the unbounded left-normalizer, the aggregation and subsampling drivers, the stability and cross-release carryover analyses, and the dbSNP rs cross-reference prototype. See README.txt for the manifest; full results and cached data live in /hive/data/genomes/hg38/bed/hprc2X. refs #37891
• src/hg/makeDb/scripts/hprc2X/buildSample.sh
  • lines changed 24, context: html, text, full: html, text
    f665d4cc3b02924a8507b2f910eaf85eab54d433 Sat Jul 18 14:12:24 2026 -0700
    hprc2X: left-shifted HPRC r2 deletion analysis and external-catalog cross-reference scripts Deletion-only re-derivation of the HPRC Release 2 rearrangement track used to test left-shifting indel placement and to measure how the deletions correspond to dbSNP, DGV, ClinVar, and the previous (rel1) release. Includes the unbounded left-normalizer, the aggregation and subsampling drivers, the stability and cross-release carryover analyses, and the dbSNP rs cross-reference prototype. See README.txt for the manifest; full results and cached data live in /hive/data/genomes/hg38/bed/hprc2X. refs #37891
• src/hg/makeDb/scripts/hprc2X/dbsnpStats.sh
  • lines changed 23, context: html, text, full: html, text
    f665d4cc3b02924a8507b2f910eaf85eab54d433 Sat Jul 18 14:12:24 2026 -0700
    hprc2X: left-shifted HPRC r2 deletion analysis and external-catalog cross-reference scripts Deletion-only re-derivation of the HPRC Release 2 rearrangement track used to test left-shifting indel placement and to measure how the deletions correspond to dbSNP, DGV, ClinVar, and the previous (rel1) release. Includes the unbounded left-normalizer, the aggregation and subsampling drivers, the stability and cross-release carryover analyses, and the dbSNP rs cross-reference prototype. See README.txt for the manifest; full results and cached data live in /hive/data/genomes/hg38/bed/hprc2X. refs #37891
• src/hg/makeDb/scripts/hprc2X/dumpAbsentFixed.py
  • lines changed 26, context: html, text, full: html, text
    f665d4cc3b02924a8507b2f910eaf85eab54d433 Sat Jul 18 14:12:24 2026 -0700
    hprc2X: left-shifted HPRC r2 deletion analysis and external-catalog cross-reference scripts Deletion-only re-derivation of the HPRC Release 2 rearrangement track used to test left-shifting indel placement and to measure how the deletions correspond to dbSNP, DGV, ClinVar, and the previous (rel1) release. Includes the unbounded left-normalizer, the aggregation and subsampling drivers, the stability and cross-release carryover analyses, and the dbSNP rs cross-reference prototype. See README.txt for the manifest; full results and cached data live in /hive/data/genomes/hg38/bed/hprc2X. refs #37891
• src/hg/makeDb/scripts/hprc2X/hprc2XArrange.as
  • lines changed 18, context: html, text, full: html, text
    f665d4cc3b02924a8507b2f910eaf85eab54d433 Sat Jul 18 14:12:24 2026 -0700
    hprc2X: left-shifted HPRC r2 deletion analysis and external-catalog cross-reference scripts Deletion-only re-derivation of the HPRC Release 2 rearrangement track used to test left-shifting indel placement and to measure how the deletions correspond to dbSNP, DGV, ClinVar, and the previous (rel1) release. Includes the unbounded left-normalizer, the aggregation and subsampling drivers, the stability and cross-release carryover analyses, and the dbSNP rs cross-reference prototype. See README.txt for the manifest; full results and cached data live in /hive/data/genomes/hg38/bed/hprc2X. refs #37891
• src/hg/makeDb/scripts/hprc2X/hprc2XIndelsAll.sh
  • lines changed 23, context: html, text, full: html, text
    f665d4cc3b02924a8507b2f910eaf85eab54d433 Sat Jul 18 14:12:24 2026 -0700
    hprc2X: left-shifted HPRC r2 deletion analysis and external-catalog cross-reference scripts Deletion-only re-derivation of the HPRC Release 2 rearrangement track used to test left-shifting indel placement and to measure how the deletions correspond to dbSNP, DGV, ClinVar, and the previous (rel1) release. Includes the unbounded left-normalizer, the aggregation and subsampling drivers, the stability and cross-release carryover analyses, and the dbSNP rs cross-reference prototype. See README.txt for the manifest; full results and cached data live in /hive/data/genomes/hg38/bed/hprc2X. refs #37891
• src/hg/makeDb/scripts/hprc2X/hprc2XIndelsOne.sh
  • lines changed 30, context: html, text, full: html, text
    f665d4cc3b02924a8507b2f910eaf85eab54d433 Sat Jul 18 14:12:24 2026 -0700
    hprc2X: left-shifted HPRC r2 deletion analysis and external-catalog cross-reference scripts Deletion-only re-derivation of the HPRC Release 2 rearrangement track used to test left-shifting indel placement and to measure how the deletions correspond to dbSNP, DGV, ClinVar, and the previous (rel1) release. Includes the unbounded left-normalizer, the aggregation and subsampling drivers, the stability and cross-release carryover analyses, and the dbSNP rs cross-reference prototype. See README.txt for the manifest; full results and cached data live in /hive/data/genomes/hg38/bed/hprc2X. refs #37891
• src/hg/makeDb/scripts/hprc2X/leftNormDel.py
  • lines changed 46, context: html, text, full: html, text
    f665d4cc3b02924a8507b2f910eaf85eab54d433 Sat Jul 18 14:12:24 2026 -0700
    hprc2X: left-shifted HPRC r2 deletion analysis and external-catalog cross-reference scripts Deletion-only re-derivation of the HPRC Release 2 rearrangement track used to test left-shifting indel placement and to measure how the deletions correspond to dbSNP, DGV, ClinVar, and the previous (rel1) release. Includes the unbounded left-normalizer, the aggregation and subsampling drivers, the stability and cross-release carryover analyses, and the dbSNP rs cross-reference prototype. See README.txt for the manifest; full results and cached data live in /hive/data/genomes/hg38/bed/hprc2X. refs #37891
• src/hg/makeDb/scripts/hprc2X/normHprc.sh
  • lines changed 10, context: html, text, full: html, text
    f665d4cc3b02924a8507b2f910eaf85eab54d433 Sat Jul 18 14:12:24 2026 -0700
    hprc2X: left-shifted HPRC r2 deletion analysis and external-catalog cross-reference scripts Deletion-only re-derivation of the HPRC Release 2 rearrangement track used to test left-shifting indel placement and to measure how the deletions correspond to dbSNP, DGV, ClinVar, and the previous (rel1) release. Includes the unbounded left-normalizer, the aggregation and subsampling drivers, the stability and cross-release carryover analyses, and the dbSNP rs cross-reference prototype. See README.txt for the manifest; full results and cached data live in /hive/data/genomes/hg38/bed/hprc2X. refs #37891
• src/hg/makeDb/scripts/hprc2X/normHprc1.sh
  • lines changed 8, context: html, text, full: html, text
    f665d4cc3b02924a8507b2f910eaf85eab54d433 Sat Jul 18 14:12:24 2026 -0700
    hprc2X: left-shifted HPRC r2 deletion analysis and external-catalog cross-reference scripts Deletion-only re-derivation of the HPRC Release 2 rearrangement track used to test left-shifting indel placement and to measure how the deletions correspond to dbSNP, DGV, ClinVar, and the previous (rel1) release. Includes the unbounded left-normalizer, the aggregation and subsampling drivers, the stability and cross-release carryover analyses, and the dbSNP rs cross-reference prototype. See README.txt for the manifest; full results and cached data live in /hive/data/genomes/hg38/bed/hprc2X. refs #37891
• src/hg/makeDb/scripts/hprc2X/presentInRel2.py
  • lines changed 37, context: html, text, full: html, text
    f665d4cc3b02924a8507b2f910eaf85eab54d433 Sat Jul 18 14:12:24 2026 -0700
    hprc2X: left-shifted HPRC r2 deletion analysis and external-catalog cross-reference scripts Deletion-only re-derivation of the HPRC Release 2 rearrangement track used to test left-shifting indel placement and to measure how the deletions correspond to dbSNP, DGV, ClinVar, and the previous (rel1) release. Includes the unbounded left-normalizer, the aggregation and subsampling drivers, the stability and cross-release carryover analyses, and the dbSNP rs cross-reference prototype. See README.txt for the manifest; full results and cached data live in /hive/data/genomes/hg38/bed/hprc2X. refs #37891
• src/hg/makeDb/scripts/hprc2X/runSamples.sh
  • lines changed 8, context: html, text, full: html, text
    f665d4cc3b02924a8507b2f910eaf85eab54d433 Sat Jul 18 14:12:24 2026 -0700
    hprc2X: left-shifted HPRC r2 deletion analysis and external-catalog cross-reference scripts Deletion-only re-derivation of the HPRC Release 2 rearrangement track used to test left-shifting indel placement and to measure how the deletions correspond to dbSNP, DGV, ClinVar, and the previous (rel1) release. Includes the unbounded left-normalizer, the aggregation and subsampling drivers, the stability and cross-release carryover analyses, and the dbSNP rs cross-reference prototype. See README.txt for the manifest; full results and cached data live in /hive/data/genomes/hg38/bed/hprc2X. refs #37891
• src/hg/makeDb/scripts/hprc2X/windowMatch.py
  • lines changed 43, context: html, text, full: html, text
    f665d4cc3b02924a8507b2f910eaf85eab54d433 Sat Jul 18 14:12:24 2026 -0700
    hprc2X: left-shifted HPRC r2 deletion analysis and external-catalog cross-reference scripts Deletion-only re-derivation of the HPRC Release 2 rearrangement track used to test left-shifting indel placement and to measure how the deletions correspond to dbSNP, DGV, ClinVar, and the previous (rel1) release. Includes the unbounded left-normalizer, the aggregation and subsampling drivers, the stability and cross-release carryover analyses, and the dbSNP rs cross-reference prototype. See README.txt for the manifest; full results and cached data live in /hive/data/genomes/hg38/bed/hprc2X. refs #37891
• src/hg/makeDb/scripts/hprc2X/xrefDbSnp.sh
  • lines changed 11, context: html, text, full: html, text
    f665d4cc3b02924a8507b2f910eaf85eab54d433 Sat Jul 18 14:12:24 2026 -0700
    hprc2X: left-shifted HPRC r2 deletion analysis and external-catalog cross-reference scripts Deletion-only re-derivation of the HPRC Release 2 rearrangement track used to test left-shifting indel placement and to measure how the deletions correspond to dbSNP, DGV, ClinVar, and the previous (rel1) release. Includes the unbounded left-normalizer, the aggregation and subsampling drivers, the stability and cross-release carryover analyses, and the dbSNP rs cross-reference prototype. See README.txt for the manifest; full results and cached data live in /hive/data/genomes/hg38/bed/hprc2X. refs #37891
• src/hg/utils/automation/importTrackHub
  • lines changed 115, context: html, text, full: html, text
    943fd670e29550dee31d37fcfecd9bdfd0e53d50 Tue Jul 14 12:18:25 2026 -0700
    Remove unused importTrackHub script. It was a one-off used once in 2017 to import the Hoffman lab mappability hub (recorded in hg38.txt), is not installed by any makefile, has no callers, and even that single use fell back to a manual fetch. History retains it (added in 22740c40dcb) if it is ever needed again. refs #19154
• src/hg/utils/chainInDel/chainInDel.c
  • lines changed 103, context: html, text, full: html, text
    f977ac0a76489eb506045886eb1a1343af94818b Fri Jul 17 12:44:43 2026 -0700
    chainInDel: add optional left-normalization of indels, refs #35415 Add -t2bit and -q2bit options to left-normalize indels to their leftmost equivalent position within a repeat or homopolymer. -t2bit normalizes pure deletions using the target sequence; -q2bit additionally normalizes pure insertions and requires -t2bit. Complex indels are left untouched, and minus-strand queries are reverse-complemented into chain orientation. Without these options the output is byte-for-byte identical to before, so the existing HPRC indel build is unaffected until the options are added to it. Left-normalizing makes indel calls line up across HPRC releases even when the chain builder places the same event a few bases apart inside a repeat, which is a prerequisite for stable cross-release IDs.
• src/utils/redmineCli
  • lines changed 22, context: html, text, full: html, text
    8600f5319ad0670e63cdee1f17fe2872224bd89d Sat Jul 18 14:00:49 2026 -0700
    redmineCli: support --assemblies and --custom-field on create Trackers with required custom fields (e.g. Track requires Assemblies) 422'd on a bare create. Add a named --assemblies flag (custom field 2) and a generic repeatable --custom-field ID=VALUE, reusing the same parsing/validation as update. refs #37281 Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>