Commits for markd

v429_base to v430_preview (2022-04-04 to 2022-04-11) v430

8ee357c0d328758d1bbbbc692981f4c2e8eddc38 Wed Apr 6 18:51:44 2022 -0700

• added catLiftOffGenes GTF/GFF3
  • src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/build.txt - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/makefile - lines changed 13, context: html, text, full: html, text

d053fa86c4f6a51cd351b468eaad73f6c894f25d Sat Apr 9 14:42:55 2022 -0700

• update CHM13 liftover due to missing chrM
  • src/hg/makeDb/doc/hg19.txt - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/chm13LiftOver.txt - lines changed 6, context: html, text, full: html, text

2e33343a4408ecab24f88bebae9cf2f994a8599d Sat Apr 9 14:42:02 2022 -0700

• Updates for genome name changes, update hgLiftover
  • src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/build.txt - lines changed 286, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/doc/chm13v2.0_CytoBandMapping.readme.txt - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/doc/chm13v2.0_CytoBandMapping.tsv - lines changed 863, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/html/catLiftOffGenesV1.html - lines changed 104, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/html/censat.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/html/clinVar20220313.html - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/html/dbSNP155.html - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/html/gwasSNPs2022-03-08.html - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/html/hgCactus.html - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/html/hgLiftOver.html - lines changed 92, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/html/hgUnique.html - lines changed 45, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/html/proseq.html - lines changed 57, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/html/rdnaModel.html - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/html/rnaseq.html - lines changed 68, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/html/sedefSegDups.html - lines changed 43, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/makefile - lines changed 79, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/schema/cenSat.as - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/schema/sedefSegDups.as - lines changed 48, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/trackDb/catLiftOffGenesV1.trackDb.txt - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/trackDb/censat.trackDb.txt - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/trackDb/clinVar20220313.trackDb.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/trackDb/cytoBandMapped.trackDb.txt - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/trackDb/dbSNP155.trackDb.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/trackDb/gwasSNPs2022-03-08.trackDb.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/trackDb/hgCactus.trackDb.txt - lines changed 46, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/trackDb/hgLiftOver.trackDb.txt - lines changed 32, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/trackDb/hgUnique.trackDb.txt - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/trackDb/proseq.trackDb.txt - lines changed 80, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/trackDb/rdnaModel.trackDb.txt - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/trackDb/rnaseq.trackDb.txt - lines changed 46, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_CHM13_T2T_v2.0/trackDb/sedefSegDups.trackDb.txt - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/build.txt - lines changed 326, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/doc/chm13v2.0_CytoBandMapping.readme.txt - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/doc/chm13v2.0_CytoBandMapping.tsv - lines changed 863, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/html/catLiftOffGenesV1.html - lines changed 104, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/html/censat.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/html/clinVar20220313.html - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/html/dbSNP155.html - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/html/gwasSNPs2022-03-08.html - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/html/hgCactus.html - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/html/hgLiftOver.html - lines changed 92, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/html/hgUnique.html - lines changed 45, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/html/proseq.html - lines changed 57, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/html/rdnaModel.html - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/html/rnaseq.html - lines changed 68, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/html/sedefSegDups.html - lines changed 43, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/makefile - lines changed 80, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/schema/cenSat.as - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/schema/sedefSegDups.as - lines changed 48, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/trackDb/catLiftOffGenesV1.trackDb.txt - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/trackDb/censat.trackDb.txt - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/trackDb/clinVar20220313.trackDb.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/trackDb/cytoBandMapped.trackDb.txt - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/trackDb/dbSNP155.trackDb.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/trackDb/gwasSNPs2022-03-08.trackDb.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/trackDb/hgCactus.trackDb.txt - lines changed 46, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/trackDb/hgLiftOver.trackDb.txt - lines changed 32, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/trackDb/hgUnique.trackDb.txt - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/trackDb/proseq.trackDb.txt - lines changed 80, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/trackDb/rdnaModel.trackDb.txt - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/trackDb/rnaseq.trackDb.txt - lines changed 46, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/trackDb/sedefSegDups.trackDb.txt - lines changed 11, context: html, text, full: html, text

eb8d108a0120f22ef926740fba982fc5d595f0d8 Sun Apr 10 16:29:30 2022 -0700

• renamed chm13v2.0 T2T supplied data documentation directory to something sane
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/build.txt - lines changed 326, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/doc/chm13v2.0_CytoBandMapping.readme.txt - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/doc/chm13v2.0_CytoBandMapping.tsv - lines changed 863, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/html/catLiftOffGenesV1.html - lines changed 104, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/html/censat.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/html/clinVar20220313.html - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/html/dbSNP155.html - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/html/gwasSNPs2022-03-08.html - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/html/hgCactus.html - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/html/hgLiftOver.html - lines changed 92, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/html/hgUnique.html - lines changed 45, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/html/proseq.html - lines changed 57, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/html/rdnaModel.html - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/html/rnaseq.html - lines changed 68, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/html/sedefSegDups.html - lines changed 43, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/makefile - lines changed 80, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/schema/cenSat.as - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/schema/sedefSegDups.as - lines changed 48, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/trackDb/catLiftOffGenesV1.trackDb.txt - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/trackDb/censat.trackDb.txt - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/trackDb/clinVar20220313.trackDb.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/trackDb/cytoBandMapped.trackDb.txt - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/trackDb/dbSNP155.trackDb.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/trackDb/gwasSNPs2022-03-08.trackDb.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/trackDb/hgCactus.trackDb.txt - lines changed 46, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/trackDb/hgLiftOver.trackDb.txt - lines changed 32, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/trackDb/hgUnique.trackDb.txt - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/trackDb/proseq.trackDb.txt - lines changed 80, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/trackDb/rdnaModel.trackDb.txt - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/trackDb/rnaseq.trackDb.txt - lines changed 46, context: html, text, full: html, text
  • src/hg/makeDb/doc/GCA_009914755.4_T2T-CHM13v2.0/trackDb/sedefSegDups.trackDb.txt - lines changed 11, context: html, text, full: html, text