Commits for braney

v400_preview2 to v400_base (2020-06-15 to 2020-06-22) v400

95efc27edf24bba8d0c7e53d2ef4aead59982826 Mon Jun 15 18:29:39 2020 -0700

• Merging in our gencode merge code to master branch
  • src/hg/hgGene2/assoc.c - lines changed 77, context: html, text, full: html, text
  • src/hg/hgGene2/assoc.h - lines changed 17, context: html, text, full: html, text
  • src/hg/hgGene2/hgGene2.c - lines changed 104, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c - lines changed 9, context: html, text, full: html, text
  • src/hg/inc/gencodeAnnotationRemark.h - lines changed 64, context: html, text, full: html, text
  • src/hg/inc/gencodeAttrs.h - lines changed 72, context: html, text, full: html, text
  • src/hg/inc/gencodeExonSupport.h - lines changed 69, context: html, text, full: html, text
  • src/hg/inc/gencodeGeneSource.h - lines changed 64, context: html, text, full: html, text
  • src/hg/inc/gencodeTag.h - lines changed 64, context: html, text, full: html, text
  • src/hg/inc/gencodeToEntrezGene.h - lines changed 64, context: html, text, full: html, text
  • src/hg/inc/gencodeToGeneSymbol.h - lines changed 65, context: html, text, full: html, text
  • src/hg/inc/gencodeToPdb.h - lines changed 64, context: html, text, full: html, text
  • src/hg/inc/gencodeToPubMed.h - lines changed 64, context: html, text, full: html, text
  • src/hg/inc/gencodeToRefSeq.h - lines changed 65, context: html, text, full: html, text
  • src/hg/inc/gencodeToUniProt.h - lines changed 71, context: html, text, full: html, text
  • src/hg/inc/gencodeTranscriptSource.h - lines changed 64, context: html, text, full: html, text
  • src/hg/inc/gencodeTranscriptSupport.h - lines changed 65, context: html, text, full: html, text
  • src/hg/inc/gencodeTranscriptionSupportLevel.h - lines changed 64, context: html, text, full: html, text
  • src/hg/lib/gencodeAnnotationRemark.as - lines changed 6, context: html, text, full: html, text
  • src/hg/lib/gencodeAnnotationRemark.c - lines changed 126, context: html, text, full: html, text
  • src/hg/lib/gencodeAnnotationRemark.sql - lines changed 12, context: html, text, full: html, text
  • src/hg/lib/gencodeAttrs.as - lines changed 14, context: html, text, full: html, text
  • src/hg/lib/gencodeAttrs.c - lines changed 187, context: html, text, full: html, text
  • src/hg/lib/gencodeAttrs.sql - lines changed 24, context: html, text, full: html, text
  • src/hg/lib/gencodeExonSupport.as - lines changed 11, context: html, text, full: html, text
  • src/hg/lib/gencodeExonSupport.c - lines changed 160, context: html, text, full: html, text
  • src/hg/lib/gencodeExonSupport.sql - lines changed 17, context: html, text, full: html, text
  • src/hg/lib/gencodeGeneSource.as - lines changed 6, context: html, text, full: html, text
  • src/hg/lib/gencodeGeneSource.c - lines changed 126, context: html, text, full: html, text
  • src/hg/lib/gencodeGeneSource.sql - lines changed 12, context: html, text, full: html, text
  • src/hg/lib/gencodeTag.as - lines changed 6, context: html, text, full: html, text
  • src/hg/lib/gencodeTag.c - lines changed 126, context: html, text, full: html, text
  • src/hg/lib/gencodeTag.sql - lines changed 13, context: html, text, full: html, text
  • src/hg/lib/gencodeToEntrezGene.as - lines changed 6, context: html, text, full: html, text
  • src/hg/lib/gencodeToEntrezGene.c - lines changed 123, context: html, text, full: html, text
  • src/hg/lib/gencodeToEntrezGene.sql - lines changed 12, context: html, text, full: html, text
  • src/hg/lib/gencodeToGeneSymbol.as - lines changed 7, context: html, text, full: html, text
  • src/hg/lib/gencodeToGeneSymbol.c - lines changed 134, context: html, text, full: html, text
  • src/hg/lib/gencodeToGeneSymbol.sql - lines changed 13, context: html, text, full: html, text
  • src/hg/lib/gencodeToPdb.as - lines changed 6, context: html, text, full: html, text
  • src/hg/lib/gencodeToPdb.c - lines changed 126, context: html, text, full: html, text
  • src/hg/lib/gencodeToPdb.sql - lines changed 13, context: html, text, full: html, text
  • src/hg/lib/gencodeToPubMed.as - lines changed 6, context: html, text, full: html, text
  • src/hg/lib/gencodeToPubMed.c - lines changed 123, context: html, text, full: html, text
  • src/hg/lib/gencodeToPubMed.sql - lines changed 12, context: html, text, full: html, text
  • src/hg/lib/gencodeToRefSeq.as - lines changed 7, context: html, text, full: html, text
  • src/hg/lib/gencodeToRefSeq.c - lines changed 134, context: html, text, full: html, text
  • src/hg/lib/gencodeToRefSeq.sql - lines changed 13, context: html, text, full: html, text
  • src/hg/lib/gencodeToUniProt.as - lines changed 8, context: html, text, full: html, text
  • src/hg/lib/gencodeToUniProt.c - lines changed 145, context: html, text, full: html, text
  • src/hg/lib/gencodeToUniProt.sql - lines changed 14, context: html, text, full: html, text
  • src/hg/lib/gencodeTranscriptSource.as - lines changed 6, context: html, text, full: html, text
  • src/hg/lib/gencodeTranscriptSource.c - lines changed 126, context: html, text, full: html, text
  • src/hg/lib/gencodeTranscriptSource.sql - lines changed 12, context: html, text, full: html, text
  • src/hg/lib/gencodeTranscriptSupport.as - lines changed 7, context: html, text, full: html, text
  • src/hg/lib/gencodeTranscriptSupport.c - lines changed 134, context: html, text, full: html, text
  • src/hg/lib/gencodeTranscriptSupport.sql - lines changed 13, context: html, text, full: html, text
  • src/hg/lib/gencodeTranscriptionSupportLevel.as - lines changed 6, context: html, text, full: html, text
  • src/hg/lib/gencodeTranscriptionSupportLevel.c - lines changed 126, context: html, text, full: html, text
  • src/hg/lib/gencodeTranscriptionSupportLevel.sql - lines changed 12, context: html, text, full: html, text
  • src/hg/lib/htmlTables.as - lines changed 6, context: html, text, full: html, text
  • src/hg/lib/makefile - lines changed 7, context: html, text, full: html, text
  • src/hg/lib/mergedBGP.as - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/doc/ucscGenes/hg38.mergeGene.sh - lines changed 94, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/bin/ensToUcscMkLift - lines changed 112, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/bin/gencodeBackMapMetadataIds - lines changed 81, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/bin/gencodeExonSupportToTable - lines changed 56, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/bin/gencodeGenerateTrackDbs - lines changed 703, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/bin/gencodeGxfToAttrs - lines changed 185, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/bin/gencodeGxfToGenePred - lines changed 92, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/gencodeGenerateTrackDbs - lines changed 703, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/gencodeHgGene2Load.mk - lines changed 420, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/lib/gencode/__init__.py - lines changed 20, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/lib/gencode/biotypes.py - lines changed 186, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/lib/gencode/gencodeGff3Parser.py - lines changed 76, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/lib/gencode/gencodeGtfParser.py - lines changed 78, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/lib/gencode/gencodeGxfParser.py - lines changed 65, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/lib/gencode/gencodeGxfRec.py - lines changed 53, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/lib/gencode/gencodeProcess.py - lines changed 75, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/setup.cfg - lines changed 5, 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 55, 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/ensToUcscMkLiftHs37Test.chain - lines changed 250, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/ensToUcscMkLiftHs38Test.chain - lines changed 960, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/ensToUcscMkLiftMm38Test.chain - lines changed 176, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/exonSupport1Test.exons - lines changed 20, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/set1AnnotTest.gp - lines changed 54, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/specialCases1Test.gp - lines changed 81, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/specialCases1Test.unmapped.gp - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/expected/ummappingWarnHs38Test.gp - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • 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 12, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/input/examples1.Exon_supporting_feature - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/input/mappingErrorsHs38.gtf - lines changed 73, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/input/set1.gtf - lines changed 597, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/input/specialCases1.gtf - lines changed 231, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/input/tags.gff3 - lines changed 235, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/input/tags.gtf - lines changed 233, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/input/v19.gtf - lines changed 54, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/input/v21.gff3 - lines changed 584, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/input/v21.gtf - lines changed 585, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/input/v27.par.gff3 - lines changed 192, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/input/v27.par.gtf - lines changed 191, context: html, text, full: html, text
  • src/hg/makeDb/outside/gencode/tests/makefile - lines changed 164, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/mergedBGP.ra - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makefile - lines changed 1, context: html, text, full: html, text

dbf814664e8400296fb98c1b7d30c7f09e685809 Tue Jun 16 06:53:09 2020 -0700

• temp fix to merge genes
  • src/hg/makeDb/trackDb/human/hg38/mergedBGP.ra - lines changed 1, context: html, text, full: html, text

a073bb760b58adfe68dc9bf28efdfef778baedb3 Tue Jun 16 08:29:49 2020 -0700

• remove hgGene2 from makefile
  • src/hg/makefile - lines changed 1, context: html, text, full: html, text

c97db9f0a5f3c6d03d63042130e5919ec3542226 Tue Jun 16 09:42:48 2020 -0700

• oops.. a couple of other things the world isn't ready for yet
  • src/hg/makeDb/trackDb/human/hg38/mergedBGP.ra - lines changed 2, context: html, text, full: html, text

138c9fcee4159430e9652c28e2e9b0390e412454 Tue Jun 16 13:13:50 2020 -0700

• remove dependency on kgXref if using a bigGenePred file for UCSC genes
  • src/hg/hgTracks/simpleTracks.c - lines changed 1, context: html, text, full: html, text

9c20ec91f0ecd76e8fad18fa0e381c8be894236b Thu Jun 18 12:35:00 2020 -0700

• if the trackDb table has changed in the last five minutes, avoid caching because the table may not be done changing. Updates are not atomic.
  • src/hg/lib/hdb.c - lines changed 9, context: html, text, full: html, text

ba9760c85ff89f15590a5c5f26d6e08f40b46636 Mon Jun 22 09:51:48 2020 -0700

• v400 final build
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 3, context: html, text, full: html, text

e24be750c2eaaeb78ed10b81b44471b19476c6c1 Mon Jun 22 09:58:57 2020 -0700

• New version number v400
  • src/hg/inc/versionInfo.h - lines changed 1, context: html, text, full: html, text
  • src/inc/srcVersion.h - lines changed 1, context: html, text, full: html, text