Commits for braney

v426_preview2 to v426_base (2022-01-24 to 2022-01-31) v426

0564395ec363631f2ff8d295da6f6b50f873fda4 Mon Jan 24 17:01:53 2022 -0800

• more chromAlias work: some name changes and support for the new genark chromAlias format
  • src/hg/hgTables/bigBed.c - lines changed 7, context: html, text, full: html, text
  • src/hg/hgTables/bigWig.c - lines changed 4, context: html, text, full: html, text
  • src/hg/hgTracks/bigBedTrack.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTracks/bigWigTrack.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTracks/chainTrack.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c - lines changed 2, context: html, text, full: html, text
  • src/hg/hgTracks/vcfTrack.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTracks/wigMafTrack.c - lines changed 3, context: html, text, full: html, text
  • src/hg/hgc/barChartClick.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgc/bigBedClick.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgc/bigDbSnpClick.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgc/bigRmskClick.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgc/clinvarSubLolly.c - lines changed 2, context: html, text, full: html, text
  • src/hg/hgc/encodeClick.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgc/hgc.c - lines changed 6, context: html, text, full: html, text
  • src/hg/hgc/lrgClick.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgc/mafClick.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgc/transMapClick.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgc/wiggleClick.c - lines changed 1, context: html, text, full: html, text
  • src/hg/inc/chromAlias.h - lines changed 4, context: html, text, full: html, text
  • src/hg/inc/trackHub.h - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/chainNetDbLoad.c - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/chromAlias.c - lines changed 126, context: html, text, full: html, text
  • src/hg/lib/customFactory.c - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/hdb.c - lines changed 41, context: html, text, full: html, text
  • src/hg/lib/hgHgvs.c - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/trackHub.c - lines changed 81, context: html, text, full: html, text
  • src/inc/fieldedTable.h - lines changed 5, context: html, text, full: html, text
  • src/lib/fieldedTable.c - lines changed 27, context: html, text, full: html, text

9d2c9bfd7841afe2fe70852f9f462238c36c64f2 Wed Jan 26 11:53:21 2022 -0800

• call chromAliasSetup at start up in hgCustom
  • src/hg/hgCustom/hgCustom.c - lines changed 2, context: html, text, full: html, text

7f2f65b61d5546d8a875fc00df6a6d43a9267e25 Wed Jan 26 11:59:53 2022 -0800

• do a null check for database in chromAlias setup
  • src/hg/lib/chromAlias.c - lines changed 3, context: html, text, full: html, text

5f032f4769aca06fedde822c0ccff089321369a4 Thu Jan 27 15:46:04 2022 -0800

• stop passing in NULL for database in getChromAlias()
  • src/hg/hgc/hgc.c - lines changed 1, context: html, text, full: html, text
  • src/hg/inc/chainNetDbLoad.h - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/chainNetDbLoad.c - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/customFactory.c - lines changed 4, context: html, text, full: html, text

1173f00de45632d6ad1e8c7f458259c1f3a61049 Thu Jan 27 16:07:33 2022 -0800

• add knownGeneVM28 to mm39
  • src/hg/makeDb/trackDb/mouse/mm39/knownGene.alpha.ra - lines changed 40, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/knownGeneVM28.html - lines changed 142, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra - lines changed 3, context: html, text, full: html, text

8c1556b22eefbda707f88e2b5011992ad96c47d2 Thu Jan 27 16:29:02 2022 -0800

• add mm39 knownGene archive supertrack
  • src/hg/makeDb/trackDb/mouse/mm39/knownGeneArchive.ra - lines changed 34, context: html, text, full: html, text

815bce4cc505b607c7178d06d45f52d864aa0584 Fri Jan 28 09:00:34 2022 -0800

• fix memory access problem in custom maf support
  • src/hg/lib/customFactory.c - lines changed 2, context: html, text, full: html, text

70f5ad4d3afb51df8cd4c1b40dd75a6a0d0ee915 Sat Jan 29 08:13:53 2022 -0800

• require that chromAliasSetup be called at init time to avoid potential thread race conditions
  • src/hg/lib/chromAlias.c - lines changed 9, context: html, text, full: html, text
  • src/hg/lib/tests/customTrackTester.c - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/tests/hgvsTester.c - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/hgvsToVcf/hgvsToVcf.c - lines changed 2, context: html, text, full: html, text

cce51ca0744763b5d358c73cf6190d7a6ea29399 Sun Jan 30 07:38:58 2022 -0800

• oops ... added an errant lineFileClose on the last checkin
  • src/hg/lib/chromAlias.c - lines changed 3, context: html, text, full: html, text
  • src/lib/fieldedTable.c - lines changed 9, context: html, text, full: html, text