Commits for markd

v421_preview2 to v421_base (2021-09-20 to 2021-09-27) v421

dc98c2a3d02cea597839f3be202b7262e62d54ed Tue Sep 21 08:47:36 2021 -0700

• disable compiling findMotif on Apple M1 CPUs (arm64) due to using SSE instructions
  • src/utils/makefile - lines changed 6, context: html, text, full: html, text

5601f85204f7a4d863c54dd0217c3e7704c4ef73 Sat Sep 25 13:42:42 2021 -0700

• up gencode mapping to use assembly reports rather than ensemblToUcsc, due to problems with the ensemblToUcsc process and weird ensembl reverse-complemented sequences
  • src/hg/makeDb/outside/gencode/bin/ensToUcscMkLift - lines changed 99, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/bin/gencodeGenerateTrackDbsOldSchema - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/bin/gencodeGxfToAttrs - lines changed 1, 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/outside/gencode/tests/expected/ensToUcscMkLiftHs37Test.chain - lines changed 742, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/ensToUcscMkLiftHs38Test.chain - lines changed 1976, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/ensToUcscMkLiftMm38Test.chain - lines changed 471, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/exonSupport1Test.exons - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/specialCases1Test.gp - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/specialCases1Test.unmapped.gp - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/input/GCF_000001405.25_GRCh37.p13_assembly_report.txt - lines changed 333, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/input/GCF_000001405.39_GRCh38.p13_assembly_report.txt - lines changed 703, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/input/GCF_000001635.26_GRCm38.p6_assembly_report.txt - lines changed 282, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/makefile - lines changed 12, context: html, text, full: html, text

f8e605d52fb7a05d5c5b19d3d6a14e7e554c0a0a Sat Sep 25 13:59:34 2021 -0700

• change ensembl to ucsc names (programs, files, variables) to be gencode to ucsc, as gencode does not actually use ensembl names, it use ENCODE, which uses UCSC for primary assembly and GenBank access or other sequences
  • src/hg/makeDb/outside/gencode/bin/buildGencodeToUcscLift - lines changed 153, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/bin/ensToUcscMkLift - lines changed 153, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/bin/gencodeExonSupportToTable - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/bin/gencodeGxfToGenePred - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/gencodeHgGeneLoad.mk - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/gencodeLoad.mk - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/buildGencodeToUcscLiftHs37Test.chain - lines changed 612, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/buildGencodeToUcscLiftHs38Test.chain - lines changed 1280, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/buildGencodeToUcscLiftMm38Test.chain - lines changed 478, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/ensToUcscMkLiftHs37Test.chain - lines changed 612, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/ensToUcscMkLiftHs38Test.chain - lines changed 1280, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/ensToUcscMkLiftMm38Test.chain - lines changed 478, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/makefile - lines changed 28, context: html, text, full: html, text

352d3ef1b538bbebc21acf30fad247d49af09c02 Sat Sep 25 16:29:13 2021 -0700

• removed code for failed gencode/hgGene redo
  • src/hg/makeDb/outside/gencode/bin/gencodeGenerateTrackDbs - lines changed 178, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/bin/gencodeGenerateTrackDbsOldSchema - lines changed 707, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/gencodeHgGeneLoad.mk - lines changed 421, context: html, text, full: html, text

bd0945ac583598387ea83c8b3c20593bd934b06a Sat Sep 25 16:29:23 2021 -0700

• reload V38 with new changes
  • src/hg/makeDb/doc/hg38/gencode.txt - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/gencodeLoad.mk - lines changed 12, context: html, text, full: html, text