Commits for markd

v439_base to v440_preview (2022-10-31 to 2022-11-07) v440

ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700

• import of GENCODE V42 final release with addition of transcript rankings
  • src/hg/lib/encode/wgEncodeGencodeAttrs.as - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/encode/wgEncodeGencodeAttrs.c - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/gencode.txt - lines changed 36, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/bin/buildGencodeToUcscLift - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/bin/gencodeGxfToAttrs - lines changed 36, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/gencodeLoad.mk - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/lib/gencode/biotypes.py - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/lib/gencode/gencodeGenes.py - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/lib/gencode/gencodeTags.py - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsPseudoGff3Tests.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsRankTest.tsv - lines changed 96, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsSet1GtfTest.tsv - lines changed 82, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsTagGff3Tests.tsv - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsTagGtfTests.tsv - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsV19GtfTest.tsv - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsV21Gff3Test.tsv - lines changed 117, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsV21GtfTest.tsv - lines changed 117, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsV27ParGff3Test.tsv - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/attrsV27ParGtfTest.tsv - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/buildGencodeToUcscLiftHs38Test.chain - lines changed 2277, 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/input/v42.gff3 - lines changed 2334, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/input/v42.transcript_rankings.txt - lines changed 95, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/makefile - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeSuper.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV42.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV42.ra - lines changed 6, context: html, text, full: html, text

feeb6019339b80b90124476e6303e8dffb0f5f0b Sat Oct 29 14:59:04 2022 -0700

• Compute versione table names rather then get them from trackDb. I have no idea why I did it this way, but it causes problems because a table was missing
  • src/hg/hgc/gencodeClick.c - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/bin/gencodeGenerateTrackDbs - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV42.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM30.ra - lines changed 15, context: html, text, full: html, text

6175649026c35358cc0871c3f2cdf39328736885 Sun Oct 30 20:44:31 2022 -0700

• initial implementation of all gencode transcript rank filters, not GUI yet
  • src/hg/hgTracks/gencodeTracks.c - lines changed 35, context: html, text, full: html, text
  • src/hg/hgc/gencodeClick.c - lines changed 121, context: html, text, full: html, text
  • src/hg/inc/gencodeTracksCommon.h - lines changed 20, context: html, text, full: html, text
  • src/hg/lib/gencodeTracksCommon.c - lines changed 33, context: html, text, full: html, text
  • src/hg/lib/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/set1.attrs.tsv - lines changed 83, context: html, text, full: html, text

6bd333f69401150f11cfa8d592165ad9b655f80f Wed Nov 2 23:01:02 2022 -0700

• added track hub control to set max transcripts
  • src/hg/hgTracks/gencodeTracks.c - lines changed 4, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 15, context: html, text, full: html, text

622669affcb25b3fe27c6f3ec188a01ec35b6f58 Thu Nov 3 11:07:28 2022 -0700

• got Ensembl version wrong
  • src/hg/makeDb/doc/hg38/gencode.txt - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV42.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV42.ra - lines changed 6, context: html, text, full: html, text

f1a6509a2f33b00f4908de15d47f6625118b6a93 Thu Nov 3 12:46:19 2022 -0700

• import of All GENCODE VM31
  • src/hg/makeDb/doc/mm39/gencode.txt - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/gencodeLoad.mk - lines changed 5, 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/trackDb.gencode.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeSuper.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM31.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM31.ra - lines changed 271, context: html, text, full: html, text

1fe89284953dd069f7155892bdcb8306adea13ef Thu Nov 3 21:31:54 2022 -0700

• import of v42lift37
  • src/hg/makeDb/doc/hg19.gencode.txt - lines changed 60, 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/schema/all.joiner - lines changed 90, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV42lift37.html - lines changed 32, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV42lift37.ra - lines changed 210, context: html, text, full: html, text

cbc16c6d771f324f8e752f41578648e4d11f9510 Fri Nov 4 10:39:34 2022 -0700

• enable All GENCODE maxTrans checking explictly in trackDb, so lift37 will not have it, since we don't have transcriptRanks for them, but want to keep the column in the attrs table'
  • src/hg/lib/hui.c - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/bin/gencodeGenerateTrackDbs - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV42.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM31.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text

cef070ed6c72e0247012855fa88e3e82144a7a9b Fri Nov 4 13:45:47 2022 -0700

• added all gencode transcript ranks to the track descriptions
  • src/hg/makeDb/trackDb/wgEncodeGencodeDisplay1.shared.html - lines changed 43, context: html, text, full: html, text

e863249eae18325e041c2948722b98cb5a5643e4 Fri Nov 4 14:47:29 2022 -0700

• Dropped GENCODE 2-way pseudogenes from latest releases. These should have never been included
  • src/hg/makeDb/outside/gencode/bin/gencodeGenerateTrackDbs - lines changed 36, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/gencodeLoad.mk - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/schema/all.joiner - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV42lift37.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV42.ra - lines changed 27, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM31.ra - lines changed 27, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/wgEncodeGencodeDisplay1.shared.html - lines changed 17, context: html, text, full: html, text

28a32014fae85f167f805fe51e3eee91df731732 Fri Nov 4 14:48:45 2022 -0700

• Merge branch 'master' into all-gencode-ranks
  • src/hg/lib/makefile - lines changed 3, context: html, text, full: html, text

7e2ceb55c803eaeaf15b61d3b2d1b12792a0d127 Sat Nov 5 10:18:27 2022 -0700

• fixed GENCODE view reference
  • src/hg/makeDb/outside/gencode/bin/gencodeGenerateTrackDbs - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV42.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM31.ra - lines changed 1, context: html, text, full: html, text

5021f89a5ebb829503b4b900280862429c09bf92 Sat Nov 5 13:21:42 2022 -0700

• change GENCODE credits to link directly to GENCODE page
  • src/hg/makeDb/trackDb/wgEncodeGencodeCredits1.shared.html - lines changed 98, context: html, text, full: html, text