Commits for hiram

v497_preview2 to v497_base (2026-04-13 to 2026-04-20) v497

38549bf61d05dc874b81c0d33c2e27a620e51d52 Mon Apr 13 13:39:20 2026 -0700

• initial view of the VGP 577-way cactus alignment refs #34370
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/vgp577way.trackDb.ra - lines changed 48, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/vgp577way.trackDb.ra - lines changed 48, context: html, text, full: html, text

4b55654dd73a403c1f30eeefbe37489a3bb4153f Mon Apr 13 13:41:50 2026 -0700

• initial view of the VGP 577-way cactus alignment refs #34370
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 11, context: html, text, full: html, text

9de971b5871aa13f6aaac9928fcb456b75a8359c Mon Apr 13 15:55:21 2026 -0700

• initial shell to run galaxy kegAlign lastz - to be cleaned up refs #31811
  • src/hg/utils/automation/kegAlignLastz.sh - lines changed 693, context: html, text, full: html, text

f08a32f711b71809d508587d53612a3d701b8749 Mon Apr 13 16:23:53 2026 -0700

• adding processing of the result into bigBed files and in the usual lastz output locations refs #31811
  • src/hg/utils/automation/kegAlignLastz.sh - lines changed 110, context: html, text, full: html, text

2cbbc4621cd9e83ffd450178330665df5ae36fe0 Wed Apr 15 16:56:37 2026 -0700

• closing in on a galaxy lastz workflow that may be useful refs #31811
  • src/hg/utils/automation/kegAlign.json.ga - lines changed 2353, context: html, text, full: html, text

032903d6adc6d0c49cbedf17c51f4319052cb8ef Thu Apr 16 12:43:59 2026 -0700

• improved variable naming fixup problems process in work refs #31811
  • src/hg/utils/automation/kegAlignLastz.sh - lines changed 42, context: html, text, full: html, text

fd4b9f71e184d33ced4948ba1ba8618faed8d576 Thu Apr 16 13:42:54 2026 -0700

• make it possible to run either the galaxy kegAlign or the classic UCSC process, function up the bigBed creation and featureBits calculations, make everything in the kegAlign process reentrant so the script can be run repeatedly to fix broken issues refs #31811
  • src/hg/utils/automation/kegAlignLastz.sh - lines changed 152, context: html, text, full: html, text

bc8249599cb2e1365b24e7e331f5b61a2e6c73ff Fri Apr 17 08:57:06 2026 -0700

• rais ram limit during chain run to 64g to prevent out of memory crashes
  • src/hg/utils/automation/doBlastzChainNet.pl - lines changed 2, context: html, text, full: html, text

cd2eb699ee42cfe22aa6d1587ed3ac444953d8e9 Fri Apr 17 13:00:43 2026 -0700

• fixup to get geneName2 column correctly populated refs #14450
  • src/hg/utils/automation/doXenoRefGene.pl - lines changed 7, context: html, text, full: html, text

87eb4afb1cb9d39eb4d175462a467c23306f091c Fri Apr 17 14:59:00 2026 -0700

• logs should accumulate only, never overwrite
  • src/hg/utils/automation/pairLastz.sh - lines changed 8, context: html, text, full: html, text

96adb44e8265446fccbaac39dd13bae7217d4825 Fri Apr 17 15:13:38 2026 -0700

• verify given GenArk assemblies actually exist in GenArk before proceeding refs #37380
  • src/hg/utils/automation/pairLastz.sh - lines changed 40, context: html, text, full: html, text

c6b00020d3775552377ee3fda1a77d9cb39c453d Fri Apr 17 15:16:44 2026 -0700

• correct specification for the linearGap and scoreMatrix inputs refs #31811
  • src/hg/utils/automation/kegAlignLastz.sh - lines changed 26, context: html, text, full: html, text

7edafbf8e253dec09305b4c540ebff3cd9557837 Fri Apr 17 16:30:08 2026 -0700

• add the genark verification check and fixup errors in the scripting refs #31811
  • src/hg/utils/automation/kegAlignLastz.sh - lines changed 58, context: html, text, full: html, text

fda87ad3679538899bf2adecc27a6e9c0bc678c8 Sun Apr 19 10:37:42 2026 -0700

• correctly naming the liftOver and liftOverSwap file outputs refs #31811
  • src/hg/utils/automation/kegAlign.json.ga - lines changed 18, context: html, text, full: html, text

c078aaab1bcbfbc23b26931b850430af6f352c3f Sun Apr 19 10:41:30 2026 -0700

• correctly naming the liftOver and liftOverSwap file outputs refs #31811
  • src/hg/utils/automation/kegAlignLastz.sh - lines changed 12, context: html, text, full: html, text