File Changes for markd

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

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src/hg/hgTracks/gencodeTracks.c
- lines changed 35, 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
- lines changed 4, 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/hgc/gencodeClick.c
- lines changed 17, 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
- lines changed 121, 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/inc/gencodeTracksCommon.h
- lines changed 20, 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/lib/encode/wgEncodeGencodeAttrs.as
- lines changed 1, context: html, text, full: html, text
  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.c
- lines changed 2, context: html, text, full: html, text
  ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
  import of GENCODE V42 final release with addition of transcript rankings
src/hg/lib/gencodeTracksCommon.c
- lines changed 33, 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/lib/hui.c
- lines changed 15, context: html, text, full: html, text
  6bd333f69401150f11cfa8d592165ad9b655f80f Wed Nov 2 23:01:02 2022 -0700
  added track hub control to set max transcripts
- lines changed 9, 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/makefile
- lines changed 2, 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
- lines changed 3, context: html, text, full: html, text
  28a32014fae85f167f805fe51e3eee91df731732 Fri Nov 4 14:48:45 2022 -0700
  Merge branch 'master' into all-gencode-ranks
src/hg/makeDb/doc/hg19.gencode.txt
- lines changed 60, context: html, text, full: html, text
  1fe89284953dd069f7155892bdcb8306adea13ef Thu Nov 3 21:31:54 2022 -0700
  import of v42lift37
src/hg/makeDb/doc/hg38/gencode.txt
- lines changed 36, context: html, text, full: html, text
  ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
  import of GENCODE V42 final release with addition of transcript rankings
- lines changed 2, context: html, text, full: html, text
  622669affcb25b3fe27c6f3ec188a01ec35b6f58 Thu Nov 3 11:07:28 2022 -0700
  got Ensembl version wrong
src/hg/makeDb/doc/mm39/gencode.txt
- lines changed 34, context: html, text, full: html, text
  f1a6509a2f33b00f4908de15d47f6625118b6a93 Thu Nov 3 12:46:19 2022 -0700
  import of All GENCODE VM31
src/hg/makeDb/outside/gencode/bin/buildGencodeToUcscLift
- lines changed 4, context: html, text, full: html, text
  ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
  import of GENCODE V42 final release with addition of transcript rankings
src/hg/makeDb/outside/gencode/bin/gencodeGenerateTrackDbs
- lines changed 17, 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
- lines changed 4, 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'
- lines changed 36, 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
- lines changed 1, 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/gencodeGxfToAttrs
- lines changed 36, context: html, text, full: html, text
  ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
  import of GENCODE V42 final release with addition of transcript rankings
src/hg/makeDb/outside/gencode/gencodeLoad.mk
- lines changed 5, context: html, text, full: html, text
  ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
  import of GENCODE V42 final release with addition of transcript rankings
- lines changed 5, context: html, text, full: html, text
  f1a6509a2f33b00f4908de15d47f6625118b6a93 Thu Nov 3 12:46:19 2022 -0700
  import of All GENCODE VM31
- lines changed 10, context: html, text, full: html, text
  1fe89284953dd069f7155892bdcb8306adea13ef Thu Nov 3 21:31:54 2022 -0700
  import of v42lift37
- lines changed 13, 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/lib/gencode/biotypes.py
- lines changed 2, context: html, text, full: html, text
  ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
  import of GENCODE V42 final release with addition of transcript rankings
src/hg/makeDb/outside/gencode/lib/gencode/gencodeGenes.py
- lines changed 1, context: html, text, full: html, text
  ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
  import of GENCODE V42 final release with addition of transcript rankings
src/hg/makeDb/outside/gencode/lib/gencode/gencodeTags.py
- lines changed 1, context: html, text, full: html, text
  ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
  import of GENCODE V42 final release with addition of transcript rankings
src/hg/makeDb/outside/gencode/makefile
- lines changed 1, context: html, text, full: html, text
  ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
  import of GENCODE V42 final release with addition of transcript rankings
src/hg/makeDb/outside/gencode/tests/expected/attrsPseudoGff3Tests.tsv
- lines changed 2, context: html, text, full: html, text
  ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
  import of GENCODE V42 final release with addition of transcript rankings
src/hg/makeDb/outside/gencode/tests/expected/attrsRankTest.tsv
- lines changed 96, context: html, text, full: html, text
  ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
  import of GENCODE V42 final release with addition of transcript rankings
src/hg/makeDb/outside/gencode/tests/expected/attrsSet1GtfTest.tsv
- lines changed 82, context: html, text, full: html, text
  ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
  import of GENCODE V42 final release with addition of transcript rankings
src/hg/makeDb/outside/gencode/tests/expected/attrsTagGff3Tests.tsv
- lines changed 16, context: html, text, full: html, text
  ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
  import of GENCODE V42 final release with addition of transcript rankings
src/hg/makeDb/outside/gencode/tests/expected/attrsTagGtfTests.tsv
- lines changed 16, context: html, text, full: html, text
  ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
  import of GENCODE V42 final release with addition of transcript rankings
src/hg/makeDb/outside/gencode/tests/expected/attrsV19GtfTest.tsv
- lines changed 5, context: html, text, full: html, text
  ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
  import of GENCODE V42 final release with addition of transcript rankings
src/hg/makeDb/outside/gencode/tests/expected/attrsV21Gff3Test.tsv
- lines changed 117, context: html, text, full: html, text
  ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
  import of GENCODE V42 final release with addition of transcript rankings
src/hg/makeDb/outside/gencode/tests/expected/attrsV21GtfTest.tsv
- lines changed 117, context: html, text, full: html, text
  ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
  import of GENCODE V42 final release with addition of transcript rankings
src/hg/makeDb/outside/gencode/tests/expected/attrsV27ParGff3Test.tsv
- lines changed 15, context: html, text, full: html, text
  ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
  import of GENCODE V42 final release with addition of transcript rankings
src/hg/makeDb/outside/gencode/tests/expected/attrsV27ParGtfTest.tsv
- lines changed 15, context: html, text, full: html, text
  ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
  import of GENCODE V42 final release with addition of transcript rankings
src/hg/makeDb/outside/gencode/tests/expected/buildGencodeToUcscLiftHs38Test.chain
- lines changed 2277, context: html, text, full: html, text
  ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
  import of GENCODE V42 final release with addition of transcript rankings
src/hg/makeDb/outside/gencode/tests/expected/makeAttrsTest.attrs.tab
- lines changed 82, context: html, text, full: html, text
  ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
  import of GENCODE V42 final release with addition of transcript rankings
src/hg/makeDb/outside/gencode/tests/expected/set1.attrs.tsv
- lines changed 83, 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/makeDb/outside/gencode/tests/input/v42.gff3
- lines changed 2334, context: html, text, full: html, text
  ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
  import of GENCODE V42 final release with addition of transcript rankings
src/hg/makeDb/outside/gencode/tests/input/v42.transcript_rankings.txt
- lines changed 95, context: html, text, full: html, text
  ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
  import of GENCODE V42 final release with addition of transcript rankings
src/hg/makeDb/outside/gencode/tests/makefile
- lines changed 7, context: html, text, full: html, text
  ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
  import of GENCODE V42 final release with addition of transcript rankings
src/hg/makeDb/schema/all.joiner
- lines changed 95, context: html, text, full: html, text
  f1a6509a2f33b00f4908de15d47f6625118b6a93 Thu Nov 3 12:46:19 2022 -0700
  import of All GENCODE VM31
- lines changed 90, context: html, text, full: html, text
  1fe89284953dd069f7155892bdcb8306adea13ef Thu Nov 3 21:31:54 2022 -0700
  import of v42lift37
- lines changed 3, 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/trackDb/human/hg19/trackDb.gencode.ra
- lines changed 1, context: html, text, full: html, text
  1fe89284953dd069f7155892bdcb8306adea13ef Thu Nov 3 21:31:54 2022 -0700
  import of v42lift37
src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
- lines changed 4, context: html, text, full: html, text
  1fe89284953dd069f7155892bdcb8306adea13ef Thu Nov 3 21:31:54 2022 -0700
  import of v42lift37
src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV42lift37.html
- lines changed 32, context: html, text, full: html, text
  1fe89284953dd069f7155892bdcb8306adea13ef Thu Nov 3 21:31:54 2022 -0700
  import of v42lift37
src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV42lift37.ra
- lines changed 210, context: html, text, full: html, text
  1fe89284953dd069f7155892bdcb8306adea13ef Thu Nov 3 21:31:54 2022 -0700
  import of v42lift37
- lines changed 2, 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/trackDb/human/hg38/wgEncodeGencodeSuper.html
- lines changed 4, context: html, text, full: html, text
  ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
  import of GENCODE V42 final release with addition of transcript rankings
src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV42.html
- lines changed 2, context: html, text, full: html, text
  ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
  import of GENCODE V42 final release with addition of transcript rankings
- lines changed 1, context: html, text, full: html, text
  622669affcb25b3fe27c6f3ec188a01ec35b6f58 Thu Nov 3 11:07:28 2022 -0700
  got Ensembl version wrong
src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV42.ra
- lines changed 6, context: html, text, full: html, text
  ca39d76b0c4deafcb785e8bea631d316b3bb59ed Fri Oct 28 21:28:51 2022 -0700
  import of GENCODE V42 final release with addition of transcript rankings
- lines changed 15, 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
- lines changed 6, context: html, text, full: html, text
  622669affcb25b3fe27c6f3ec188a01ec35b6f58 Thu Nov 3 11:07:28 2022 -0700
  got Ensembl version wrong
- lines changed 1, 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'
- lines changed 27, 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
- lines changed 1, context: html, text, full: html, text
  7e2ceb55c803eaeaf15b61d3b2d1b12792a0d127 Sat Nov 5 10:18:27 2022 -0700
  fixed GENCODE view reference
src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra
- lines changed 1, context: html, text, full: html, text
  f1a6509a2f33b00f4908de15d47f6625118b6a93 Thu Nov 3 12:46:19 2022 -0700
  import of All GENCODE VM31
src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeSuper.html
- lines changed 4, context: html, text, full: html, text
  f1a6509a2f33b00f4908de15d47f6625118b6a93 Thu Nov 3 12:46:19 2022 -0700
  import of All GENCODE VM31
src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM30.ra
- lines changed 15, 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/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM31.html
- lines changed 30, context: html, text, full: html, text
  f1a6509a2f33b00f4908de15d47f6625118b6a93 Thu Nov 3 12:46:19 2022 -0700
  import of All GENCODE VM31
src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM31.ra
- lines changed 271, context: html, text, full: html, text
  f1a6509a2f33b00f4908de15d47f6625118b6a93 Thu Nov 3 12:46:19 2022 -0700
  import of All GENCODE VM31
- lines changed 1, 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'
- lines changed 27, 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
- lines changed 1, context: html, text, full: html, text
  7e2ceb55c803eaeaf15b61d3b2d1b12792a0d127 Sat Nov 5 10:18:27 2022 -0700
  fixed GENCODE view reference
src/hg/makeDb/trackDb/tagTypes.tab
- lines changed 1, 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/makeDb/trackDb/wgEncodeGencodeCredits1.shared.html
- lines changed 98, 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/wgEncodeGencodeDisplay1.shared.html
- lines changed 43, context: html, text, full: html, text
  cef070ed6c72e0247012855fa88e3e82144a7a9b Fri Nov 4 13:45:47 2022 -0700
  added all gencode transcript ranks to the track descriptions
- lines changed 17, 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

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