Commits for markd

v465_base to v466_preview (2024-05-13 to 2024-05-20) v466

8541001ae3a49443eea4234a2f4a32e274dd9b44 Mon May 13 12:00:41 2024 -0700

• import of final release of gencode V46
  • src/hg/makeDb/doc/hg38/gencode.txt - lines changed 38, 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/trackDb/human/hg38/wgEncodeGencodeSuper.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV46.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV46.ra - lines changed 2, context: html, text, full: html, text

5f18ea51c37c998166e6ec19d62fde6537323d75 Mon May 13 14:09:04 2024 -0700

• updated test results due to chain changes
  • src/hg/makeDb/outside/gencode/tests/expected/buildGencodeToUcscLiftHs38Test.chain - lines changed 1995, context: html, text, full: html, text

f42f0a335bac6371c989f6251acd34a82ce20cec Mon May 13 14:21:11 2024 -0700

• added option to drop certain transcript to support filter lift back problem clases
  • src/hg/makeDb/outside/gencode/bin/buildGencodeToUcscLift - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/bin/gencodeBackMapMetadataIds - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/bin/gencodeExonSupportToTable - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/bin/gencodeGxfToAttrs - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/bin/gencodeGxfToGenePred - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/bin/gencodeMakeAttrs - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/bin/gencodeMakeTracks - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/bin/gencodePolyaGxfToGenePred - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/lib/gencode/__init__.py - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/lib/gencode/gencodeGenes.py - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/lib/gencode/gencodeProcess.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/tests/expected/specialCases1Test.gp - lines changed 74, context: html, text, full: html, text

70fde199fda0e697d5c0e5e01470ff433fa00dc1 Tue May 14 00:06:40 2024 -0700

• Import of GENCODE V46lift37, including add an option to import code to drop specific transcripts. This deals incorrectly included PAR transcript.
  • src/hg/makeDb/doc/hg19.gencode.txt - lines changed 46, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/bin/gencodeGxfToGenePred - lines changed 1, 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 89, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV46lift37.html - lines changed 32, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV46lift37.ra - lines changed 210, context: html, text, full: html, text

132eda4ef5ec2d89a572ab1732672a345a5a1cef Tue May 14 00:33:51 2024 -0700

• import of GENCODE VM35
  • src/hg/makeDb/outside/gencode/gencodeLoad.mk - lines changed 2, 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/wgEncodeGencodeVM35.html - lines changed 1, context: html, text, full: html, text

c616cb4971fb62f396957d38fe123e3b689744d2 Tue May 14 00:34:06 2024 -0700

• import of GENCODE VM35
  • src/hg/makeDb/doc/mm39/gencode.txt - lines changed 37, context: html, text, full: html, text

c6cc8633fc898187cefc3d3a8969c3381be9fa0f Tue May 14 00:35:32 2024 -0700

• add V46lift37 to trackDb
  • src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra - lines changed 1, context: html, text, full: html, text

62c5cbd5c584c147c2d11904a4b23d666ff07f95 Tue May 14 01:27:38 2024 -0700

• update gencode expected results due to order difference merge on MT mappings
  • src/hg/makeDb/outside/gencode/tests/expected/specialCases1Test.gp - lines changed 74, context: html, text, full: html, text

b31907d700c1fe956e4e4c20e64d91de027d7c84 Tue May 14 02:03:33 2024 -0700

• merge blatHuge implementation
  • .gitignore - lines changed 2, context: html, text, full: html, text
  • src/blat/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/blat/hCrea.geno - lines changed 100, context: html, text, full: html, text
  • src/blat/hCrea.mrna - lines changed 23, context: html, text, full: html, text
  • src/blat/hCrea.pep - lines changed 7, context: html, text, full: html, text
  • src/blat/mCrea.geno - lines changed 114, context: html, text, full: html, text
  • src/blat/mCrea.mrna - lines changed 24, context: html, text, full: html, text
  • src/blat/mCrea.pep - lines changed 7, context: html, text, full: html, text
  • src/blat/makefile - lines changed 44, context: html, text, full: html, text
  • src/blat/refFine.psl - lines changed 6, context: html, text, full: html, text
  • src/blat/refProt.psl - lines changed 7, context: html, text, full: html, text
  • src/blat/refProtX.psl - lines changed 6, context: html, text, full: html, text
  • src/blat/refRna.psl - lines changed 6, context: html, text, full: html, text
  • src/blat/refRnaX.psl - lines changed 6, context: html, text, full: html, text
  • src/blat/test/basic/hCrea.geno - lines changed 100, context: html, text, full: html, text
  • src/blat/test/basic/hCrea.mrna - lines changed 23, context: html, text, full: html, text
  • src/blat/test/basic/hCrea.pep - lines changed 7, context: html, text, full: html, text
  • src/blat/test/basic/mCrea.geno - lines changed 114, context: html, text, full: html, text
  • src/blat/test/basic/mCrea.mrna - lines changed 24, context: html, text, full: html, text
  • src/blat/test/basic/mCrea.pep - lines changed 7, context: html, text, full: html, text
  • src/blat/test/basic/refFine.psl - lines changed 6, context: html, text, full: html, text
  • src/blat/test/basic/refProt.psl - lines changed 7, context: html, text, full: html, text
  • src/blat/test/basic/refProtX.psl - lines changed 6, context: html, text, full: html, text
  • src/blat/test/basic/refRna.psl - lines changed 6, context: html, text, full: html, text
  • src/blat/test/basic/refRnaX.psl - lines changed 6, context: html, text, full: html, text
  • src/blat/test/hugeProt/lungfish.prot.psl - lines changed 18, context: html, text, full: html, text
  • src/blat/test/hugeTrans/lungfish.rna.psl - lines changed 885, context: html, text, full: html, text
  • src/blat/test/hugeUntrans/lungfish.rna.psl - lines changed 275, context: html, text, full: html, text
  • src/blat/test/intron50k/expected/test1.psl - lines changed 6, context: html, text, full: html, text
  • src/blat/test/intron50k/expected/test2.psl - lines changed 7, context: html, text, full: html, text
  • src/blat/test/intron50k/expected/test3.psl - lines changed 8, context: html, text, full: html, text
  • src/blat/test/intron50k/test1.psl - lines changed 6, context: html, text, full: html, text
  • src/blat/test/intron50k/test2.psl - lines changed 7, context: html, text, full: html, text
  • src/blat/test/intron50k/test3.psl - lines changed 8, context: html, text, full: html, text
  • src/blat/test/makefile - lines changed 70, context: html, text, full: html, text
  • src/blat/test/throwback/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/blat/test/throwback/test.psl - lines changed 8, context: html, text, full: html, text
  • src/blat/test/v29skips/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/blat/test/v29skips/ex1.psl - lines changed 6, context: html, text, full: html, text
  • src/blat/test/v29skips/ex1_reference.psl - lines changed 6, context: html, text, full: html, text
  • src/blat/test/v29skips/ex2.psl - lines changed 6, context: html, text, full: html, text
  • src/blat/test/v29skips/ex2_reference.psl - lines changed 6, context: html, text, full: html, text
  • src/blat/version.doc - lines changed 4, context: html, text, full: html, text
  • src/gfClient/AB000095.fa - lines changed 49, context: html, text, full: html, text
  • src/gfClient/AB000220.fa - lines changed 39, context: html, text, full: html, text
  • src/gfClient/makefile - lines changed 12, context: html, text, full: html, text
  • src/gfClient/repeat.fa - lines changed 7, context: html, text, full: html, text
  • src/gfClient/test1.fa - lines changed 11, context: html, text, full: html, text
  • src/gfClient/test2.fa - lines changed 7, context: html, text, full: html, text
  • src/gfClient/test3.fa - lines changed 9, context: html, text, full: html, text
  • src/gfClient/tests/expected/AB000095.psl - lines changed 1, context: html, text, full: html, text
  • src/gfClient/tests/expected/AB000220.psl - lines changed 1, context: html, text, full: html, text
  • src/gfClient/tests/expected/repeat.psl - lines changed 89, context: html, text, full: html, text
  • src/gfClient/tests/expected/test1.psl - lines changed 1, context: html, text, full: html, text
  • src/gfClient/tests/expected/test2.psl - lines changed 1, context: html, text, full: html, text
  • src/gfClient/tests/expected/test3.psl - lines changed 74, context: html, text, full: html, text
  • src/gfClient/tests/input/AB000095.fa - lines changed 49, context: html, text, full: html, text
  • src/gfClient/tests/input/AB000220.fa - lines changed 39, context: html, text, full: html, text
  • src/gfClient/tests/input/repeat.fa - lines changed 7, context: html, text, full: html, text
  • src/gfClient/tests/input/test1.fa - lines changed 11, context: html, text, full: html, text
  • src/gfClient/tests/input/test2.fa - lines changed 7, context: html, text, full: html, text
  • src/gfClient/tests/input/test3.fa - lines changed 9, context: html, text, full: html, text
  • src/gfClient/tests/makefile - lines changed 17, context: html, text, full: html, text
  • src/gfServer/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/gfServer/gfServer.c - lines changed 18, context: html, text, full: html, text
  • src/gfServer/makefile - lines changed 46, context: html, text, full: html, text
  • src/gfServer/tests/bin/runHugeTest - lines changed 46, context: html, text, full: html, text
  • src/gfServer/tests/bin/testDynServer - lines changed 22, context: html, text, full: html, text
  • src/gfServer/tests/bin/testDynServerPcr - lines changed 22, context: html, text, full: html, text
  • src/gfServer/tests/bin/testDynServerPerSeqMax - lines changed 24, context: html, text, full: html, text
  • src/gfServer/tests/bin/testDynServerTrans - lines changed 22, context: html, text, full: html, text
  • src/gfServer/tests/bin/testDynServerWithDir - lines changed 22, context: html, text, full: html, text
  • src/gfServer/tests/bin/testIndexFile - lines changed 22, context: html, text, full: html, text
  • src/gfServer/tests/bin/testIndexFileTrans - lines changed 22, context: html, text, full: html, text
  • src/gfServer/tests/bin/testPcr - lines changed 13, context: html, text, full: html, text
  • src/gfServer/tests/bin/testProtNib - lines changed 15, context: html, text, full: html, text
  • src/gfServer/tests/bin/testProtTwoBit - lines changed 15, context: html, text, full: html, text
  • src/gfServer/tests/bin/testTransNib - lines changed 15, context: html, text, full: html, text
  • src/gfServer/tests/bin/testTransTwoBit - lines changed 15, context: html, text, full: html, text
  • src/gfServer/tests/dynTester - lines changed 7, context: html, text, full: html, text
  • src/gfServer/tests/expected/directNibTest.out - lines changed 24, context: html, text, full: html, text
  • src/gfServer/tests/expected/directTwoBitTest.out - lines changed 21, context: html, text, full: html, text
  • src/gfServer/tests/expected/testHugeProt.out - lines changed 60, context: html, text, full: html, text
  • src/gfServer/tests/expected/testHugeProt.psl - lines changed 11, context: html, text, full: html, text
  • src/gfServer/tests/expected/testHugeTrans.out - lines changed 2680, context: html, text, full: html, text
  • src/gfServer/tests/expected/testHugeTrans.psl - lines changed 933, context: html, text, full: html, text
  • src/gfServer/tests/expected/testHugeUntrans.out - lines changed 102, context: html, text, full: html, text
  • src/gfServer/tests/expected/testHugeUntrans.psl - lines changed 142, context: html, text, full: html, text
  • src/gfServer/tests/expected/testIndexFile - lines changed 20, context: html, text, full: html, text
  • src/gfServer/tests/expected/testIndexFileTrans - lines changed 94, context: html, text, full: html, text
  • src/gfServer/tests/expected/testNib.out - lines changed 24, context: html, text, full: html, text
  • src/gfServer/tests/expected/testTwoBit.out - lines changed 21, context: html, text, full: html, text
  • src/gfServer/tests/input/lungfish.prot.fa - lines changed 47, context: html, text, full: html, text
  • src/gfServer/tests/input/lungfish.rna.fa - lines changed 206, context: html, text, full: html, text
  • src/gfServer/tests/makefile - lines changed 113, context: html, text, full: html, text
  • src/gfServer/tests/testDynServer - lines changed 17, context: html, text, full: html, text
  • src/gfServer/tests/testDynServerPcr - lines changed 17, context: html, text, full: html, text
  • src/gfServer/tests/testDynServerPerSeqMax - lines changed 19, context: html, text, full: html, text
  • src/gfServer/tests/testDynServerTrans - lines changed 17, context: html, text, full: html, text
  • src/gfServer/tests/testDynServerWithDir - lines changed 17, context: html, text, full: html, text
  • src/gfServer/tests/testIndexFile - lines changed 14, context: html, text, full: html, text
  • src/gfServer/tests/testIndexFileTrans - lines changed 14, context: html, text, full: html, text
  • src/gfServer/tests/testPcr - lines changed 5, context: html, text, full: html, text
  • src/gfServer/tests/testProtNib - lines changed 6, context: html, text, full: html, text
  • src/gfServer/tests/testProtTwoBit - lines changed 6, context: html, text, full: html, text
  • src/gfServer/tests/testTransNib - lines changed 6, context: html, text, full: html, text
  • src/gfServer/tests/testTransTwoBit - lines changed 6, context: html, text, full: html, text
  • src/hg/mouseStuff/regionPicker/regionPicker.c - lines changed 1, context: html, text, full: html, text
  • src/inc/bits.h - lines changed 26, context: html, text, full: html, text
  • src/inc/common.h - lines changed 1, context: html, text, full: html, text
  • src/inc/genoFind.h - lines changed 48, context: html, text, full: html, text
  • src/inc/gfPcrLib.h - lines changed 1, context: html, text, full: html, text
  • src/inc/userApp.mk - lines changed 1, context: html, text, full: html, text
  • src/jkOwnLib/genoFind.c - lines changed 228, context: html, text, full: html, text
  • src/jkOwnLib/makefile - lines changed 13, context: html, text, full: html, text
  • src/jkOwnLib/patSpace.c - lines changed 1, context: html, text, full: html, text
  • src/lib/bits.c - lines changed 73, context: html, text, full: html, text
  • src/lib/memalloc.c - lines changed 3, context: html, text, full: html, text

f4aa15bef8c781b695f09979a28a9beb68c90963 Wed May 15 00:09:39 2024 -0700

• change workaround for gencode gene symbol file with short rows
  • src/hg/makeDb/doc/hg19.gencode.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/gencodeLoad.mk - lines changed 2, context: html, text, full: html, text

3f6eb7eb31edcf73fc79707baeda85cf70e52992 Wed May 15 08:12:10 2024 -0700

• re-import fixed version of GENCODE V46lift37 gene symbol table from EBI
  • src/hg/makeDb/doc/hg19.gencode.txt - lines changed 6, context: html, text, full: html, text

c631d4d20178d19ed60da27cd7e34d63872d4a90 Thu May 16 10:34:45 2024 -0700

• added pslSpliceJunctions to gather information in splice junctions to use in comprative mapping analysis
  • src/utils/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/pslSpliceJunctions/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/pslSpliceJunctions/pslSpliceJunctions.c - lines changed 144, context: html, text, full: html, text
  • src/utils/pslSpliceJunctions/tests/expected/rnahg38Test.tsv - lines changed 64, context: html, text, full: html, text
  • src/utils/pslSpliceJunctions/tests/input/rna-hg38.psl - lines changed 3, context: html, text, full: html, text
  • src/utils/pslSpliceJunctions/tests/makefile - lines changed 21, context: html, text, full: html, text

25367be1ea1cf374e19f3773f276cc6a0faa651d Thu May 16 10:43:16 2024 -0700

• change "Reset filters" label to "Clear filters", as that is really what the button does RM 33727
  • src/hg/lib/hui.c - lines changed 2, context: html, text, full: html, text

48cc0aa29826d6f6e99357a12eda728d76a7d132 Fri May 17 02:31:33 2024 -0700

• fixed error in pslSpliceJunctions TSV header
  • src/utils/pslSpliceJunctions/pslSpliceJunctions.c - lines changed 1, context: html, text, full: html, text
  • src/utils/pslSpliceJunctions/tests/expected/rnahg38Test.tsv - lines changed 1, context: html, text, full: html, text