File Changes for markd

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

• src/hg/makeDb/doc/hg38/gencode.txt
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    bd0945ac583598387ea83c8b3c20593bd934b06a Sat Sep 25 16:29:23 2021 -0700
    reload V38 with new changes
• src/hg/makeDb/outside/gencode/bin/buildGencodeToUcscLift
  • lines changed 153, 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/ensToUcscMkLift
  • lines changed 99, 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
  • lines changed 153, 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/gencodeExonSupportToTable
  • lines changed 4, 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/gencodeGenerateTrackDbs
  • lines changed 178, 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/gencodeGenerateTrackDbsOldSchema
  • lines changed 2, 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
  • lines changed 707, 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/gencodeGxfToAttrs
  • lines changed 1, 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/gencodeGxfToGenePred
  • lines changed 4, 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/gencodeHgGeneLoad.mk
  • lines changed 8, 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
  • lines changed 421, 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/gencodeLoad.mk
  • lines changed 2, 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
  • lines changed 10, 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
  • lines changed 12, context: html, text, full: html, text
    bd0945ac583598387ea83c8b3c20593bd934b06a Sat Sep 25 16:29:23 2021 -0700
    reload V38 with new changes
• src/hg/makeDb/outside/gencode/tests/expected/buildGencodeToUcscLiftHs37Test.chain
  • lines changed 612, 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/tests/expected/buildGencodeToUcscLiftHs38Test.chain
  • lines changed 1280, 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/tests/expected/buildGencodeToUcscLiftMm38Test.chain
  • lines changed 478, 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/tests/expected/ensToUcscMkLiftHs37Test.chain
  • lines changed 742, 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
  • lines changed 612, 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/tests/expected/ensToUcscMkLiftHs38Test.chain
  • lines changed 1976, 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
  • lines changed 1280, 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/tests/expected/ensToUcscMkLiftMm38Test.chain
  • lines changed 471, 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
  • lines changed 478, 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/tests/expected/exonSupport1Test.exons
  • lines changed 10, 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/tests/expected/specialCases1Test.gp
  • lines changed 5, 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/tests/expected/specialCases1Test.unmapped.gp
  • lines changed 10, 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/tests/input/GCF_000001405.25_GRCh37.p13_assembly_report.txt
  • lines changed 333, 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/tests/input/GCF_000001405.39_GRCh38.p13_assembly_report.txt
  • lines changed 703, 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/tests/input/GCF_000001635.26_GRCm38.p6_assembly_report.txt
  • lines changed 282, 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/tests/makefile
  • lines changed 12, 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
  • lines changed 28, 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/utils/makefile
  • lines changed 6, context: html, text, full: html, text
    dc98c2a3d02cea597839f3be202b7262e62d54ed Tue Sep 21 08:47:36 2021 -0700
    disable compiling findMotif on Apple M1 CPUs (arm64) due to using SSE instructions