Commits for braney

v433_preview2 to v433_base (2022-06-20 to 2022-06-27) v433

e37c8b2581aa25f3deb43db2f54642cfc53abeff Thu Jun 23 13:29:46 2022 -0700

• create hs1 hub
  • src/hg/makeDb/doc/hs1/initial.txt - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.assembly.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.augustus.html - lines changed 106, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.catLiftOffGenesV1.html - lines changed 104, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.censat.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.chainNet.html - lines changed 183, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.clinVar20220313.html - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.cpgIslands.html - lines changed 78, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.dbSNP155.html - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.description.html - lines changed 131, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.encode.html - lines changed 41, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.gc5Base.html - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.gwasSNPs2022-03-08.html - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.hgCactus.html - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.hgLiftOver.html - lines changed 245, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.hgUnique.html - lines changed 45, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.liftJkAll.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.microsatellites.html - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.proseq.html - lines changed 57, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.rdnaModel.html - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.refSeqComposite.html - lines changed 186, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.repeatMasker.html - lines changed 149, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.rnaseq.html - lines changed 68, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.sedefSegDups.html - lines changed 43, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.sgdpCopyNumber.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.simpleRepeat.html - lines changed 48, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.t2tRepeatMasker.html - lines changed 153, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.tanDups.html - lines changed 101, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.windowMasker.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.xenoRefGene.html - lines changed 88, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/trackDb.ra - lines changed 6132, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text

eb977447c35d01a2aa61f7ff47a1de0ed477b6cf Fri Jun 24 09:51:46 2022 -0700

• check to make sure database exists before accessing it
  • src/hg/makeDb/trackDb/maybeBuildHub - lines changed 15, context: html, text, full: html, text

e32ecd59b34531455b424a6f0249353fe5ec4262 Fri Jun 24 10:54:16 2022 -0700

• fix problem with geneType in knownGene bigGenePred file
  • src/hg/makeDb/trackDb/human/hs1/liftJkAll.ra - lines changed 54, context: html, text, full: html, text
  • src/hg/utils/genePredToBigGenePred/genePredToBigGenePred.c - lines changed 9, context: html, text, full: html, text
  • src/hg/utils/otto/knownGene/buildCore.sh - lines changed 2, context: html, text, full: html, text

52269827f6e4219781da466967850ca0011d1445 Fri Jun 24 10:55:37 2022 -0700

• oops... add jkLiftAll
  • src/hg/makeDb/trackDb/human/hs1/trackDb.ra - lines changed 52, context: html, text, full: html, text

b7f5213aa30a1a6f58773601b5c7f0885e909264 Fri Jun 24 13:08:18 2022 -0700

• explicating the function of this code in response to code review
  • src/hg/ratStuff/mafCounts/mafCounts.c - lines changed 23, context: html, text, full: html, text

45a43477fb72105c168c76e551407e7a68eeabdd Sat Jun 25 11:46:46 2022 -0700

• change commas in source table entries to underbars to prevent confustion in comma-separated list
  • src/hg/txGraph/txgToAgx/txgToAgx.c - lines changed 1, context: html, text, full: html, text