Commits for markd

v426_preview2 to v426_base (2022-01-24 to 2022-01-31) v426

7f3a7738bd88d2762069a28e9ee35039fa915f48 Wed Jan 26 07:28:30 2022 -0800

• import of GENCODE V40 pre-release
  • src/hg/makeDb/doc/hg38/gencode.txt - lines changed 35, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/gencodeLoad.mk - lines changed 9, 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/wgEncodeGencodeV40.html - lines changed 47, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV40.ra - lines changed 286, context: html, text, full: html, text

07942970a19230fee2cbb6bf8ae1c15427533c66 Wed Jan 26 08:53:49 2022 -0800

• loaded GENCODE VM29 pre-release
  • src/hg/makeDb/doc/mm39/gencode.txt - lines changed 33, 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 95, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM29.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM29.ra - lines changed 286, context: html, text, full: html, text

3e26e9f7be9e99c947ab28385336feef14ee348b Wed Jan 26 08:55:33 2022 -0800

• loaded GENCODE VM29 pre-release
  • src/hg/makeDb/doc/mm39/gencode.txt - lines changed 2, context: html, text, full: html, text

7b9d4ae382ad4ef6f30ea743d518543b25da87a7 Thu Jan 27 17:21:32 2022 -0800

• Update gencode import to finish remove of use of older code in a different tree. This is the first step towards simplifying the build process
  • src/hg/makeDb/outside/gencode/bin/buildGencodeToUcscLift - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/bin/gencodeBackMapMetadataIds - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/bin/gencodeGenerateTrackDbs - lines changed 37, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/bin/gencodeGxfToAttrs - lines changed 62, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/bin/gencodeGxfToGenePred - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/bin/gencodeMakeAttrs - lines changed 87, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/bin/gencodeMakeTracks - lines changed 67, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/bin/gencodePolyaGxfToGenePred - lines changed 54, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/gencodeLoad.mk - lines changed 23, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/lib/gencode/biotypes.py - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/lib/gencode/gencodeGenes.py - lines changed 607, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/lib/gencode/gencodeProcess.py - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/lib/gencode/gencodeTags.py - lines changed 88, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsPseudoGff3Tests.attrs - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsPseudoGff3Tests.tags - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsPseudoGff3Tests.tsl - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsPseudoGff3Tests.tsv - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsSet1GtfTest.attrs - lines changed 54, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsSet1GtfTest.tags - lines changed 40, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsSet1GtfTest.tsl - lines changed 54, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsSet1GtfTest.tsv - lines changed 83, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsTagGff3Tests.attrs - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsTagGff3Tests.tags - lines changed 58, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsTagGff3Tests.tsl - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsTagGff3Tests.tsv - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsTagGtfTests.attrs - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsTagGtfTests.tags - lines changed 58, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsTagGtfTests.tsl - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsTagGtfTests.tsv - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsV19GtfTest.attrs - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsV19GtfTest.tags - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsV19GtfTest.tsl - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsV19GtfTest.tsv - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsV21Gff3Test.attrs - lines changed 117, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsV21Gff3Test.tags - lines changed 123, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsV21Gff3Test.tsl - lines changed 117, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsV21Gff3Test.tsv - lines changed 118, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsV21GtfTest.attrs - lines changed 117, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsV21GtfTest.tags - lines changed 123, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsV21GtfTest.tsl - lines changed 117, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsV21GtfTest.tsv - lines changed 118, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsV27ParGff3Test.attrs - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsV27ParGff3Test.tags - lines changed 54, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsV27ParGff3Test.tsl - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsV27ParGff3Test.tsv - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsV27ParGtfTest.attrs - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsV27ParGtfTest.tags - lines changed 54, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsV27ParGtfTest.tsl - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsV27ParGtfTest.tsv - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/badMappedErrorsHs38Test.out - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/buildGencodeToUcscLiftHs37Test.chain - lines changed 1959, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/buildGencodeToUcscLiftHs38Test.chain - lines changed 4659, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/buildGencodeToUcscLiftMm38Test.chain - lines changed 1552, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/makeAttrsTest.attrs.tab - lines changed 82, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/makeAttrsTest.tags.tab - lines changed 191, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/makeAttrsTest.tsl.tab - lines changed 82, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/makeTracksBasicTest.gp - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/makeTracksCompTest.gp - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/makeTracksPseudoTest.gp - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/ployAGpTest.gp - lines changed 43, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/set1AnnotTest.gp - lines changed 120, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/ummappingWarnHs38Test.out - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/ummappingWarnHs38Test.unmapped.gp - lines changed 6, 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/input/mappingErrorsHs38.gtf - lines changed 36, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/input/missingSeqsHs38.gtf - lines changed 36, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/input/polyA.gff3 - lines changed 50, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/input/set1.gff3 - lines changed 931, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/input/set1.gtf - lines changed 1524, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/makefile - lines changed 106, context: html, text, full: html, text

e0dcc4f87e4051aa6094860e0f2a9536e90c97c9 Thu Jan 27 18:02:39 2022 -0800

• import of GENCODE V40lift37 pre-release
  • src/hg/makeDb/doc/hg19.gencode.txt - lines changed 27, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/bin/gencodeBackMapMetadataIds - lines changed 36, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/gencodeLoad.mk - lines changed 3, 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/wgEncodeGencodeV40lift37.html - lines changed 32, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV40lift37.ra - lines changed 224, context: html, text, full: html, text

458a5bb9b8a7f91f4a85a9a65432627bc7dfcf6c Thu Jan 27 18:08:54 2022 -0800

• fixed confusing usage message per user complaint
  • src/hg/utils/overlapSelect/usage.txt - lines changed 7, context: html, text, full: html, text