All File Changes

v326_base to v327_preview (2015-12-07 to 2015-12-14) v327

• src/hg/cirm/cdw/lib/cdwDataset.h
  • lines changed 67, context: html, text, full: html, text
    the h file for cdwDataset
    
• src/hg/hgConvert/hgConvert.c
  • lines changed 4, context: html, text, full: html, text
    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/hg/hgGene/hgGene.c
  • lines changed 1, context: html, text, full: html, text
    adding malacards section to hgGene, refs #14417
    
• src/hg/hgGene/hgGene.h
  • lines changed 4, context: html, text, full: html, text
    adding malacards section to hgGene, refs #14417
    
• src/hg/hgGene/hgGeneData/section.ra
  • lines changed 5, context: html, text, full: html, text
    adding malacards section to hgGene, refs #14417
    
• src/hg/hgGene/makefile
  • lines changed 1, context: html, text, full: html, text
    adding malacards section to hgGene, refs #14417
    
• src/hg/hgGene/malacards.c
  • lines changed 84, context: html, text, full: html, text
    adding malacards section to hgGene, refs #14417
    
  • lines changed 1, context: html, text, full: html, text
    fixing malacards after update, refs #14417
    
• src/hg/hgIntegrator/hgIntegrator.c
  • lines changed 5, context: html, text, full: html, text
    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/hg/hgTables/hgTables.c
  • lines changed 4, context: html, text, full: html, text
    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/hg/hgTracks/bedTrack.c
  • lines changed 24, context: html, text, full: html, text
    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/hg/hgTracks/cds.c
  • lines changed 79, context: html, text, full: html, text
    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/hg/hgTracks/config.c
  • lines changed 237, context: html, text, full: html, text
    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
  • lines changed 1, context: html, text, full: html, text
    oops fix spelling of chromosome
    
• src/hg/hgTracks/cytoBandTrack.c
  • lines changed 14, context: html, text, full: html, text
    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/hg/hgTracks/expRatioTracks.c
  • lines changed 4, context: html, text, full: html, text
    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/hg/hgTracks/extTools.c
  • lines changed 5, context: html, text, full: html, text
    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/hg/hgTracks/extTools.ra
  • lines changed 2, context: html, text, full: html, text
    small fixed to two external tools, refs #16308
    
• src/hg/hgTracks/factorSource.c
  • lines changed 2, context: html, text, full: html, text
    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/hg/hgTracks/gtexTracks.c
  • lines changed 112, context: html, text, full: html, text
    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 4237, context: html, text, full: html, text
    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
  • lines changed 1, context: html, text, full: html, text
    needs limits.h
    
  • lines changed 3, context: html, text, full: html, text
    oops fix spelling of chromosome
    
  • lines changed 32, context: html, text, full: html, text
    cleanup
    
  • lines changed 7, context: html, text, full: html, text
    fixing 12242 comment 92 part 2. If guidelines are turned off, the 'Highlighting alternating regions' doesn't work ( reported by kate )
    
• src/hg/hgTracks/hgTracks.h
  • lines changed 190, context: html, text, full: html, text
    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/hg/hgTracks/imageV2.c
  • lines changed 46, context: html, text, full: html, text
    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/hg/hgTracks/imageV2.h
  • lines changed 18, context: html, text, full: html, text
    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
  • lines changed 4, context: html, text, full: html, text
    remove obsolete commented out variables, no longer usable refs #1612
    
• src/hg/hgTracks/menu.c
  • lines changed 4, context: html, text, full: html, text
    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/hg/hgTracks/rmskJoinedTrack.c
  • lines changed 113, context: html, text, full: html, text
    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/hg/hgTracks/rmskTrack.c
  • lines changed 6, context: html, text, full: html, text
    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1308, context: html, text, full: html, text
    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
  • lines changed 3, context: html, text, full: html, text
    oops fix spelling of chromosome
    
• src/hg/hgTracks/snakeTrack.c
  • lines changed 7, context: html, text, full: html, text
    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/hg/hgTracks/variation.c
  • lines changed 23, context: html, text, full: html, text
    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/hg/hgVai/hgVai.c
  • lines changed 4, context: html, text, full: html, text
    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
  • lines changed 366, context: html, text, full: html, text
    Add dbNSFP v3.1a (including VEST scores) to hg38 for hgVai.
    Add hgVai options for adding in transcript status info: GENCODE tags
    when applicable, knownCanonical for knownGene, refSeqStatus for refGene.
    refs #16502, #16503
    
  • lines changed 39, context: html, text, full: html, text
    Corrected the description of knownCanonical for hg38 as suggested by Matt
    and fixed missing-geneSymbol bug found by Matt -- thanks!
    refs #16502
    
  • lines changed 3, context: html, text, full: html, text
    Make "add pgSnp or VCF custom track" button go to the 'add custom tracks' page
    instead of the 'manage custom tracks' page -- but the "manage custom tracks" button
    still goes to the 'manage custom tracks' page.
    
  • lines changed 22, context: html, text, full: html, text
    Add 'add track hub' button next to 'add pgSnp or VCF custom track' button as
    suggested by Matt. Update dbNSFP v3 reference per Matt. Thanks!
    refs #16503, #16504
    
• src/hg/hgc/hgc.c
  • lines changed 31, context: html, text, full: html, text
    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 1, context: html, text, full: html, text
    Updating genePredExtended format description to include score not id, refs #16482
    
• src/hg/htdocs/FAQ/index.html
  • lines changed 51, context: html, text, full: html, text
    Changed top Help menu to FAQs & Search. Added help doc & gateway search to FAQ page. refs #16461
    
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 27, context: html, text, full: html, text
    Making some changes to correct small typos (Chromsome/higlight) and indent lines for new optParams section of customTrackText.html refs #16106
    
  • lines changed 11, context: html, text, full: html, text
    Making links relative for customTrackText.html refs #16106
    
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 1, context: html, text, full: html, text
    Fixing typo as per code review, refs #16492
    
• src/hg/htdocs/goldenPath/help/multiRegionHelp.html
  • lines changed 309, context: html, text, full: html, text
    Starting work on multi-region help doc
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 33, context: html, text, full: html, text
    Adding announcement for 1000 Genomes Phase 3 track release, refs #14325
    
• src/hg/htdocs/images/Oxytricha_trifallax.jpg
  • lines changed 0, context: html, text, full: html, text
    photo from NHGRI 79122 public rights refs no redmine
    
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 1, context: html, text, full: html, text
    Changed top Help menu to FAQs & Search. Added help doc & gateway search to FAQ page. refs #16461
    
• src/hg/htdocs/indexNews.html
  • lines changed 61, context: html, text, full: html, text
    Adding announcement for 1000 Genomes Phase 3 track release, refs #14325
    
  • lines changed 7, context: html, text, full: html, text
    holiday greetings. thanks Brian Lee!
    
• src/hg/htdocs/training/index.html
  • lines changed 22, context: html, text, full: html, text
    dropping completed Davis workshop, adding February Korea workshop
    
• src/hg/inc/annoFormatVep.h
  • lines changed 4, context: html, text, full: html, text
    Add dbNSFP v3.1a (including VEST scores) to hg38 for hgVai.
    Add hgVai options for adding in transcript status info: GENCODE tags
    when applicable, knownCanonical for knownGene, refSeqStatus for refGene.
    refs #16502, #16503
    
• src/hg/inc/annoStreamDb.h
  • lines changed 5, context: html, text, full: html, text
    Add dbNSFP v3.1a (including VEST scores) to hg38 for hgVai.
    Add hgVai options for adding in transcript status info: GENCODE tags
    when applicable, knownCanonical for knownGene, refSeqStatus for refGene.
    refs #16502, #16503
    
• src/hg/inc/cart.h
  • lines changed 11, context: html, text, full: html, text
    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/hg/inc/jksql.h
  • lines changed 2, context: html, text, full: html, text
    Add dbNSFP v3.1a (including VEST scores) to hg38 for hgVai.
    Add hgVai options for adding in transcript status info: GENCODE tags
    when applicable, knownCanonical for knownGene, refSeqStatus for refGene.
    refs #16502, #16503
    
• src/hg/js/autocomplete.js
  • lines changed 9, context: html, text, full: html, text
    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/hg/js/hgGateway.js
  • lines changed 5, context: html, text, full: html, text
    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/hg/js/hgTracks.js
  • lines changed 713, context: html, text, full: html, text
    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/hg/js/hgVarAnnogrator.js
  • lines changed 23, context: html, text, full: html, text
    Add dbNSFP v3.1a (including VEST scores) to hg38 for hgVai.
    Add hgVai options for adding in transcript status info: GENCODE tags
    when applicable, knownCanonical for knownGene, refSeqStatus for refGene.
    refs #16502, #16503
    
  • lines changed 8, context: html, text, full: html, text
    Make "add pgSnp or VCF custom track" button go to the 'add custom tracks' page
    instead of the 'manage custom tracks' page -- but the "manage custom tracks" button
    still goes to the 'manage custom tracks' page.
    
• src/hg/js/model/hgIntegrator/hgIntegratorModel.js
  • lines changed 2, context: html, text, full: html, text
    Add dbNSFP v3.1a (including VEST scores) to hg38 for hgVai.
    Add hgVai options for adding in transcript status info: GENCODE tags
    when applicable, knownCanonical for knownGene, refSeqStatus for refGene.
    refs #16502, #16503
    
• src/hg/js/utils.js
  • lines changed 43, context: html, text, full: html, text
    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/hg/lib/annoFormatVep.c
  • lines changed 101, context: html, text, full: html, text
    Add dbNSFP v3.1a (including VEST scores) to hg38 for hgVai.
    Add hgVai options for adding in transcript status info: GENCODE tags
    when applicable, knownCanonical for knownGene, refSeqStatus for refGene.
    refs #16502, #16503
    
• src/hg/lib/annoStreamDb.c
  • lines changed 39, context: html, text, full: html, text
    Add dbNSFP v3.1a (including VEST scores) to hg38 for hgVai.
    Add hgVai options for adding in transcript status info: GENCODE tags
    when applicable, knownCanonical for knownGene, refSeqStatus for refGene.
    refs #16502, #16503
    
• src/hg/lib/cart.c
  • lines changed 53, context: html, text, full: html, text
    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/hg/lib/dbNsfpMutationTaster.as
  • lines changed 3, context: html, text, full: html, text
    Add dbNSFP v3.1a (including VEST scores) to hg38 for hgVai.
    Add hgVai options for adding in transcript status info: GENCODE tags
    when applicable, knownCanonical for knownGene, refSeqStatus for refGene.
    refs #16502, #16503
    
• src/hg/lib/dbNsfpSift.as
  • lines changed 3, context: html, text, full: html, text
    Add dbNSFP v3.1a (including VEST scores) to hg38 for hgVai.
    Add hgVai options for adding in transcript status info: GENCODE tags
    when applicable, knownCanonical for knownGene, refSeqStatus for refGene.
    refs #16502, #16503
    
• src/hg/lib/dbNsfpVest.as
  • lines changed 19, context: html, text, full: html, text
    Add dbNSFP v3.1a (including VEST scores) to hg38 for hgVai.
    Add hgVai options for adding in transcript status info: GENCODE tags
    when applicable, knownCanonical for knownGene, refSeqStatus for refGene.
    refs #16502, #16503
    
• src/hg/lib/hdb.c
  • lines changed 30, context: html, text, full: html, text
    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/hg/lib/soTerm.c
  • lines changed 1, context: html, text, full: html, text
    Sequence Ontology name change: non_coding_exon_variant --> non_coding_transcript_exon_variant.
    
• src/hg/lib/tests/annoGratorTester.c
  • lines changed 1, context: html, text, full: html, text
    Add dbNSFP v3.1a (including VEST scores) to hg38 for hgVai.
    Add hgVai options for adding in transcript status info: GENCODE tags
    when applicable, knownCanonical for knownGene, refSeqStatus for refGene.
    refs #16502, #16503
    
• src/hg/lib/tests/expected/annoGrator/gpFx.txt
  • lines changed 1, context: html, text, full: html, text
    Sequence Ontology name change: non_coding_exon_variant --> non_coding_transcript_exon_variant.
    
• src/hg/lib/tests/expected/annoGrator/vepOut.txt
  • lines changed 2, context: html, text, full: html, text
    Sequence Ontology name change: non_coding_exon_variant --> non_coding_transcript_exon_variant.
    
• src/hg/lib/tests/expected/annoGrator/vepOutIndelTrim.txt
  • lines changed 4, context: html, text, full: html, text
    Sequence Ontology name change: non_coding_exon_variant --> non_coding_transcript_exon_variant.
    
• src/hg/lib/web.c
  • lines changed 7, context: html, text, full: html, text
    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/hg/makeDb/doc/aptMan1/initialBuild.txt
  • lines changed 477, context: html, text, full: html, text
    About halfway through the aptMan build, here is the doc, refs #16029
    
• src/hg/makeDb/doc/hg17.txt
  • lines changed 2, context: html, text, full: html, text
    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/hg/makeDb/doc/hg18.txt
  • lines changed 3, context: html, text, full: html, text
    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 24, context: html, text, full: html, text
    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 46, context: html, text, full: html, text
    import of GENCODE V24 (not being pushed)
    
• src/hg/makeDb/doc/hg38/variation.txt
  • lines changed 64, context: html, text, full: html, text
    Add dbNSFP v3.1a (including VEST scores) to hg38 for hgVai.
    Add hgVai options for adding in transcript status info: GENCODE tags
    when applicable, knownCanonical for knownGene, refSeqStatus for refGene.
    refs #16502, #16503
    
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes14.csh
  • lines changed 4, context: html, text, full: html, text
    adding makedoc for malacards refs #14417
    
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes16.sh
  • lines changed 12, context: html, text, full: html, text
    adding makedoc for malacards refs #14417
    
  • lines changed 5, context: html, text, full: html, text
    updating malacards makedoc refs #14417
    
• src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes15.csh
  • lines changed 9, context: html, text, full: html, text
    add ucscGenePfam track to mm10 (no redmine)
    
• src/hg/makeDb/doc/ucscGenes/mm9.ucscGenes12.csh
  • lines changed 10, context: html, text, full: html, text
    add ucscGenePfam from mm9 #16465
    
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added oxyTri2 - Oxytricha trifallax refs no redmine
    
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 16, context: html, text, full: html, text
    Added oxyTri2 Oxytricha trifallax refs no redmine
    
  • lines changed 1, context: html, text, full: html, text
    missing oxyTri2.refseq.mrna.native.pslCDnaFilter refs no redmine
    
  • lines changed 17, context: html, text, full: html, text
    added aptMan brown kiwi refs #16029
    
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added oxyTri2 - Oxytricha trifallax refs no redmine
    
• src/hg/makeDb/genbank/src/extFileUpdate/raInfoTbl.c
  • lines changed 3, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/makeDb/genbank/src/gbSanity/chkMetaDataTbls.c
  • lines changed 4, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 2, context: html, text, full: html, text
    Added oxyTri2 Oxytricha trifallax refs no redmine
    
  • lines changed 2, context: html, text, full: html, text
    added aptMan brown kiwi refs #16029
    
• src/hg/makeDb/genbank/src/repair/refPepRepair.c
  • lines changed 3, context: html, text, full: html, text
    fixup gcc warnings for -Wunused-but-set-variable refs #16121
    
• src/hg/makeDb/hgLoadSeq/hgLoadSeq.c
  • lines changed 1, context: html, text, full: html, text
    Fixed bug with previous commit which generate an error when -drop is used (RM #16034)
    
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 12, context: html, text, full: html, text
    import of GENCODE V24 (not being pushed)
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 36, context: html, text, full: html, text
    Fixing the bugs with the tRNA track, overriding for hg19 and hg38, refs #15107 and #11694
    
  • lines changed 105, context: html, text, full: html, text
    Add dbNSFP v3.1a (including VEST scores) to hg38 for hgVai.
    Add hgVai options for adding in transcript status info: GENCODE tags
    when applicable, knownCanonical for knownGene, refSeqStatus for refGene.
    refs #16502, #16503
    
  • lines changed 9, context: html, text, full: html, text
    adding oxyTri2 refs no redmine
    
  • lines changed 9, context: html, text, full: html, text
    changing the all.joiner for the brown kiwi, aptMan1, refs #16029
    
• src/hg/makeDb/trackDb/altLocations.html
  • lines changed 6, context: html, text, full: html, text
    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/hg/makeDb/trackDb/birds/aptMan1/description.html
  • lines changed 63, context: html, text, full: html, text
    adding the aptMan1 files created by makeDb.pl, refs #16029
    
• src/hg/makeDb/trackDb/birds/aptMan1/gap.html
  • lines changed 30, context: html, text, full: html, text
    adding the aptMan1 files created by makeDb.pl, refs #16029
    
• src/hg/makeDb/trackDb/birds/aptMan1/gold.html
  • lines changed 34, context: html, text, full: html, text
    adding the aptMan1 files created by makeDb.pl, refs #16029
    
• src/hg/makeDb/trackDb/birds/aptMan1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    adding the aptMan1 files created by makeDb.pl, refs #16029
    
• src/hg/makeDb/trackDb/cat/trackDb.chainNet.ra
  • lines changed 2, context: html, text, full: html, text
    Updating chainNet desc page with updated matrix, refs #14412
    
• src/hg/makeDb/trackDb/ciliate/oxyTri2/description.html
  • lines changed 63, context: html, text, full: html, text
    adding oxyTri2 to the build refs no redmine
    
  • lines changed 48, context: html, text, full: html, text
    updated with references to papers and explination of chrom constructon refs no redmine
    
• src/hg/makeDb/trackDb/ciliate/oxyTri2/gap.html
  • lines changed 30, context: html, text, full: html, text
    adding oxyTri2 to the build refs no redmine
    
• src/hg/makeDb/trackDb/ciliate/oxyTri2/gold.html
  • lines changed 34, context: html, text, full: html, text
    adding oxyTri2 to the build refs no redmine
    
• src/hg/makeDb/trackDb/ciliate/oxyTri2/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    adding oxyTri2 to the build refs no redmine
    
  • lines changed 6, context: html, text, full: html, text
    overrides for default visibilities refs no redmine
    
  • lines changed 3, context: html, text, full: html, text
    default vis full for rmsk refs no redmine
    
  • lines changed 11, context: html, text, full: html, text
    adding chainSelf refs no redmine
    
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 4, context: html, text, full: html, text
    Updating sciencell links, refs #16472
    
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    Making cv.ra change to metaData for Gingeras SkMC cells per Encode3 portal to have description say Skeletal muscleyosatellite cells
    
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    Correcting link pre code review refs #16488
    
• src/hg/makeDb/trackDb/cv/beta/cv.ra
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    Updating sciencell links, refs #16472
    
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    Making cv.ra change to metaData for Gingeras SkMC cells per Encode3 portal to have description say Skeletal muscleyosatellite cells
    
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    Correcting link pre code review refs #16488
    
• src/hg/makeDb/trackDb/cv/public/cv.ra
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    Updating sciencell links, refs #16472
    
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    Making cv.ra change to metaData for Gingeras SkMC cells per Encode3 portal to have description say Skeletal muscleyosatellite cells
    
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    Correcting link pre code review refs #16488
    
• src/hg/makeDb/trackDb/drosophila/dm6/refGene.html
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    Adding link to RefSeq for corrections on other refGene pages refs #15961
    
• src/hg/makeDb/trackDb/drosophila/refGene.html
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    Adding link to RefSeq for corrections on other refGene pages refs #15961
    
• src/hg/makeDb/trackDb/fugu/fr2/description.html
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    Replaced 307 error url (no RM tix).
    
• src/hg/makeDb/trackDb/human/chainNetVertebrate.ra
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    xenTro should be before latCha refs #9868
    
• src/hg/makeDb/trackDb/human/chainNetXenTro3.ra
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    xenTro should be before latCha refs #9868
    
• src/hg/makeDb/trackDb/human/chainNetXenTro7.ra
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    xenTro should be before latCha refs #9868
    
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    Removing release tags for 1000 Genomes Phase 3 tracks, refs #14325
    
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    Fixing the bugs with the tRNA track, overriding for hg19 and hg38, refs #15107 and #11694
    
• src/hg/makeDb/trackDb/human/hg38/altLocations.html
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    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/hg/makeDb/trackDb/human/hg38/nonCodingRNAs.ra
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    Changing the short label for lincRNA Transcripts to lincRNA TUCP, refs #11694
    
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    fixingi the short label lengths, refs #11694
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    Fixing the bugs with the tRNA track, overriding for hg19 and hg38, refs #15107 and #11694
    
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    Removing the override for tRNAs from trackDb, it is in nonCodingRNAs.ra, refs #11694
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.wgEncode.ra
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    import of GENCODE V24 (not being pushed)
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV24.html
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    import of GENCODE V24 (not being pushed)
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV24.ra
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    import of GENCODE V24 (not being pushed)
    
• src/hg/makeDb/trackDb/human/wgRna.html
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    Updating miRBase link on desc page, refs #11694
    
• src/hg/makeDb/trackDb/makefile
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    swapped lines because it should be the other order.
    
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    Added a warning about running multiple instances
    
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    adding oxyTri2 to the build refs no redmine
    
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    Updating the trackDb makefile to have aptMan1 in it, refs #16029
    
• src/hg/makeDb/trackDb/refGene.html
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    Adding link to RefSeq for corrections on other refGene pages refs #15961
    
• src/hg/makeDb/trackDb/squirt/refGene.html
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    Adding link to RefSeq for corrections on other refGene pages refs #15961
    
• src/hg/makeDb/trackDb/tRNAs.html
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    Fixing the bugs with the tRNA track, overriding for hg19 and hg38, refs #15107 and #11694
    
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    Escaping html chars in tRNAs desc page, refs #15107
    
• src/hg/makeDb/trackDb/trackDb.ra
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    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
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    Fixing the bugs with the tRNA track, overriding for hg19 and hg38, refs #15107 and #11694
    
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    fixing a bug Brian Lee caught immediatly, oops, refs #11694
    
• src/hg/makeDb/trackDb/worm/refGene.html
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    Adding link to RefSeq for corrections on other refGene pages refs #15961
    
• src/hg/utils/cpAndLinkToResourceFiles.pl
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    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/hg/utils/dbNsfpToBed.pl
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    Add dbNSFP v3.1a (including VEST scores) to hg38 for hgVai.
    Add hgVai options for adding in transcript status info: GENCODE tags
    when applicable, knownCanonical for knownGene, refSeqStatus for refGene.
    refs #16502, #16503
    
• src/hg/utils/otto/lovd/checkAndLoad.sh
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    hacking around a problem with LOVD otto that they will not fix.
    
• src/hg/utils/otto/lovd/makefile
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    hacking around a problem with LOVD otto that they will not fix.
    
• src/inc/common.mk
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    start using htslib for BAM, CRAM, and vcf/tabix support #14717
    
• src/inc/spaceSaver.h
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    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/inc/udc.h
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    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/lib/jsonParse.c
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    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/lib/spaceSaver.c
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    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/lib/udc.c
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    Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.
    
• src/utils/newPythonProg/newPythonProg.c
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    fixing an issue with the common.py path, refs #16156
    
• src/utils/qa/weeklybld/buildEnv.csh
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    v327 preview1 refs #16419
    

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