Commits for markd

v434_preview2 to v434_base (2022-07-11 to 2022-07-18) v434

2ac71d8e46cf67f4532b49ca144a4aa913400b23 Tue Jul 12 11:01:16 2022 -0700

• import of final GENCODE V41 release
  • src/hg/makeDb/doc/hg38/gencode.txt - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/gencodeLoad.mk - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/lib/gencode/biotypes.py - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/lib/gencode/gencodeTags.py - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeSuper.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV41.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV41.ra - lines changed 2, context: html, text, full: html, text

b9b3c73197da510f27595dcf63646cabeb3ebe8c Tue Jul 12 11:53:41 2022 -0700

• add All GENCODE VM30
  • src/hg/makeDb/doc/mm39/gencode.txt - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/gencodeLoad.mk - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeSuper.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM30.html - lines changed 1, context: html, text, full: html, text

fd376287654bd9695e0f8c2da1cb611519ac29ba Tue Jul 12 11:54:23 2022 -0700

• add All GENCODE VM30
  • src/hg/makeDb/doc/mm39/gencode.txt - lines changed 1, context: html, text, full: html, text

b610fbd43a68ff6fc49fcce3c638274831ca60ba Tue Jul 12 13:04:52 2022 -0700

• added All GENCODE V41lift37
  • src/hg/makeDb/doc/hg19.gencode.txt - lines changed 27, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/gencodeLoad.mk - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/schema/all.joiner - lines changed 90, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV41lift37.html - lines changed 32, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV41lift37.ra - lines changed 224, context: html, text, full: html, text

18b8815d717cb178232321e32c31dba40fd5e72d Wed Jul 13 17:12:25 2022 -0700

• integrate bigRmsk track updates from Robert Hubley
  • src/hg/hgTracks/bigRmskTrack.c - lines changed 275, context: html, text, full: html, text
  • src/hg/hgc/bigRmskClick.c - lines changed 127, context: html, text, full: html, text

c200ff2fb784fbbb87ef547abde79d805217d3b5 Fri Jul 15 20:32:22 2022 -0700

• re-did the quick and dirty import of the GenArk T2T-supplied tracks so it will be possible to add pending tracks
  • src/hg/htdocs/images/rmskExample1.svg - lines changed 51, context: html, text, full: html, text
  • src/hg/htdocs/images/rmskExample2.svg - lines changed 67, context: html, text, full: html, text
  • src/hg/htdocs/images/rmskExample3.svg - lines changed 77, context: html, text, full: html, text
  • src/hg/htdocs/images/rmskExample4.svg - lines changed 69, context: html, text, full: html, text
  • src/hg/makeDb/doc/hs1/initial.txt - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/doc/hs1/t2t-supplied.txt - lines changed 381, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/catLiftOffGenesV1.trackDb.ra - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/censat.trackDb.ra - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/clinVar20220313.trackDb.ra - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/cytoBandMapped.trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/dbSNP155.trackDb.ra - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/encode.trackDb.ra - lines changed 1599, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/gwasSNPs2022-03-08.trackDb.ra - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/hgCactus.trackDb.ra - lines changed 46, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/hgLiftOver.trackDb.ra - lines changed 70, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/hgUnique.trackDb.ra - lines changed 32, 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.clinVar20220313.html - lines changed 14, 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.encode.html - lines changed 41, 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.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.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.t2tRepeatMasker.html - lines changed 153, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/catLiftOffGenesV1.html - lines changed 104, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/censat.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/clinVar20220313.html - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/dbSNP155.html - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/encode.html - lines changed 41, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/gwasSNPs2022-03-08.html - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/hgCactus.html - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/hgLiftOver.html - lines changed 251, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/hgUnique.html - lines changed 45, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/microsatellites.html - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/proseq.html - lines changed 57, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/rdnaModel.html - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/rnaseq.html - lines changed 68, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/sedefSegDups.html - lines changed 43, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/sgdpCopyNumber.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/html/t2tRepeatMasker.html - lines changed 236, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/microsatellites.trackDb.ra - lines changed 48, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/proseq.trackDb.ra - lines changed 80, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/rdnaModel.trackDb.ra - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/rnaseq.trackDb.ra - lines changed 46, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/schema/cenSat.as - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/schema/sedefSegDups.as - lines changed 48, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/sedefSegDups.trackDb.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/sgdpCopyNumber.trackDb.ra - lines changed 3498, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/t2t-supplied.trackDb.ra - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/t2tRepeatMasker.trackDb.ra - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/trackDb.ra - lines changed 5481, context: html, text, full: html, text