Commits for markd

v422_preview2 to v422_base (2021-10-11 to 2021-10-18) v422

8268f8067b6ad8a5e0b0f426bedc16e567ae116a Sun Oct 3 13:38:16 2021 -0700

• fixed typo in make variable names that keeps it from being used as a environment variable
  • src/hg/hgTracks/makefile - lines changed 1, context: html, text, full: html, text
  • src/inc/cgi_build_rules.mk - lines changed 5, context: html, text, full: html, text

b275bed5b8219c6f88a98602a5e82d1655166415 Sun Oct 3 13:42:11 2021 -0700

• fixed rule that copies phyloPng to a BINDIR to take from the correct CGI dir
  • src/hg/phyloPng/makefile - lines changed 2, context: html, text, full: html, text

a705056fed4ed3269b4dcbca18194b4f166a36c0 Fri Oct 15 17:11:33 2021 -0700

• import of gencode V39 pre-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 11, context: html, text, full: html, text
  • src/hg/makeDb/schema/all.joiner - lines changed 95, 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/wgEncodeGencodeV39.html - lines changed 47, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV39.ra - lines changed 286, context: html, text, full: html, text

4e0ba60ac25fa6a44e6446852ce5c2aeda68d757 Fri Oct 15 17:18:43 2021 -0700

• fixed gencode release date
  • src/hg/makeDb/doc/hg38/gencode.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV39.html - lines changed 1, context: html, text, full: html, text

676d7fc25a5c8533edd747f23ef7a526f45468d0 Sat Oct 16 16:52:45 2021 -0700

• switch to using chromAlias table for getting mappings (thanks Hiram)
  • src/hg/makeDb/outside/gencode/bin/buildGencodeToUcscLift - lines changed 103, context: html, text, full: html, text

e1b0f07ffbe7508b97259a9d3c28956152bacfa9 Sat Oct 16 16:55:27 2021 -0700

• import of All gencode VM28
  • src/hg/makeDb/doc/mm39/gencode.txt - lines changed 37, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/gencodeLoad.mk - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/schema/all.joiner - lines changed 95, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM28.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM28.ra - lines changed 286, context: html, text, full: html, text

6606cc2195a5299cf1cea8e2de7661e57c7ac67f Sat Oct 16 17:30:05 2021 -0700

• don't restrict chromAlias entries, as some ensembl ones are omitted to to strand swap
  • src/hg/makeDb/outside/gencode/bin/buildGencodeToUcscLift - lines changed 3, context: html, text, full: html, text

32ff80a3c1fba843c93106505abb1dcf0ad7f91c Sat Oct 16 17:31:11 2021 -0700

• forgot to include new ra file
  • src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra - lines changed 1, context: html, text, full: html, text

e949d9121dea4c10ccce47ff7a781df9b0f01813 Sat Oct 16 18:51:58 2021 -0700

• ignore contamination unplaced chromsome in GRCh38
  • src/hg/makeDb/outside/gencode/bin/buildGencodeToUcscLift - lines changed 5, context: html, text, full: html, text

ec73df8e4499d2aecb76ead6e14cadff3f390de9 Sun Oct 17 09:46:15 2021 -0700

• import of all gencode v39lift37
  • src/hg/makeDb/doc/hg19.gencode.txt - lines changed 46, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/bin/buildGencodeToUcscLift - lines changed 3, 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/schema/all.joiner - lines changed 90, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV39lift37.html - lines changed 32, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV39lift37.ra - lines changed 224, context: html, text, full: html, text

ec9318204bf7a42acd791c03d0a6f93393843bd7 Sun Oct 17 10:12:22 2021 -0700

• fixed typo in build doc
  • src/hg/makeDb/doc/hg19.gencode.txt - lines changed 1, context: html, text, full: html, text

5b19f269d7e89acb83b34ad0ffeb1f6451a8210b Sun Oct 17 19:32:25 2021 -0700

• added option to bigBedToBed to write autoSql style column header
  • src/utils/bigBedToBed/bigBedToBed.c - lines changed 25, context: html, text, full: html, text