All File Changes

v314_base to v315_preview (2015-03-30 to 2015-04-08) v315

• src/hg/hgTables/bigBed.c
  • lines changed 1, context: html, text, full: html, text
    hgTables fixes to support bigBed and VCF tracks that have no mysql table,
    only a bigDataUrl setting that may point to a local file.
    refs #15059
    
• src/hg/hgTables/filterFields.c
  • lines changed 10, context: html, text, full: html, text
    hgTables fixes to support bigBed and VCF tracks that have no mysql table,
    only a bigDataUrl setting that may point to a local file.
    refs #15059
    
• src/hg/hgTables/hgTables.c
  • lines changed 25, context: html, text, full: html, text
    hgTables fixes to support bigBed and VCF tracks that have no mysql table,
    only a bigDataUrl setting that may point to a local file.
    refs #15059
    
• src/hg/hgTables/hgTables.h
  • lines changed 4, context: html, text, full: html, text
    hgTables fixes to support bigBed and VCF tracks that have no mysql table,
    only a bigDataUrl setting that may point to a local file.
    refs #15059
    
• src/hg/hgTables/vcf.c
  • lines changed 20, context: html, text, full: html, text
    hgTables fixes to support bigBed and VCF tracks that have no mysql table,
    only a bigDataUrl setting that may point to a local file.
    refs #15059
    
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 8, context: html, text, full: html, text
    first cut at knownGene based on Gencode
    
• src/hg/hgTracks/gencodeTracks.c
  • lines changed 13, context: html, text, full: html, text
    import of GENCODE V22
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 39, context: html, text, full: html, text
    first cut at knownGene based on Gencode
    
• src/hg/hgc/gencodeClick.c
  • lines changed 49, context: html, text, full: html, text
    import of GENCODE V22
    
• src/hg/hgc/hgc.c
  • lines changed 4, context: html, text, full: html, text
    Wrap hgc's track description html in a div with limited width, so if the
    page is extremely wide due to long details, the description text will
    wrap and you won't have to scroll back and forth to read it.
    
• src/hg/hgc/hgc.h
  • lines changed 3, context: html, text, full: html, text
    import of GENCODE V22
    
• src/hg/hgc/vcfClick.c
  • lines changed 110, context: html, text, full: html, text
    When VCF ##INFO description and data seem to have the same number of
    |-separated columns (and at least 3 apparent columns), display them
    as separate tables below the big table of INFO tags and settings
    because they can be quite large; for example, VEP annotations may
    have >40 |-separated columns for each alt allele & transcript.
    refs #14379
    
  • lines changed 1, context: html, text, full: html, text
    Use class stdTbl instead of making up new class.
    
• src/hg/htdocs/ENCODE/releaseLog.html
  • lines changed 1895, context: html, text, full: html, text
    Having these in the repo still means that these old out-of-date versions can end up getting rsynced to hgwdev and hgwbeta.
    
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 1, context: html, text, full: html, text
    fixed a few typos, refs #14376
    
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 2, context: html, text, full: html, text
    Updated docs for danRer10 release; refs #14017
    
  • lines changed 2, context: html, text, full: html, text
    Standard release edits for tarSyr2, refs #14410
    
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 3, context: html, text, full: html, text
    Updated docs for danRer10 release; refs #14017
    
  • lines changed 5, context: html, text, full: html, text
    Standard release edits for tarSyr2, refs #14410
    
• src/hg/htdocs/goldenPath/help/bigGenePred.html
  • lines changed 16, context: html, text, full: html, text
    fixed a few typos, refs #14376
    
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 2, context: html, text, full: html, text
    Adding small changes to gbib.html code review feedback refs #15088
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 38, context: html, text, full: html, text
    Updated docs for danRer10 release; refs #14017
    
  • lines changed 10, context: html, text, full: html, text
    Adding announcement for new training video. refs#13969
    
  • lines changed 28, context: html, text, full: html, text
    Standard release edits for tarSyr2, refs #14410
    
  • lines changed 1, context: html, text, full: html, text
    Fixing minor typo in tarsier announcement
    
• src/hg/htdocs/goldenPath/releaseLog.html
  • lines changed 14866, context: html, text, full: html, text
    Having these in the repo still means that these old out-of-date versions can end up getting rsynced to hgwdev and hgwbeta.
    
• src/hg/htdocs/index.html
  • lines changed 3, context: html, text, full: html, text
    Removed link to Ebola portal from left-hand menu.
    
• src/hg/htdocs/indexNews.html
  • lines changed 68, context: html, text, full: html, text
    Updated docs for danRer10 release; refs #14017
    
  • lines changed 40, context: html, text, full: html, text
    Adding announcement for new training video. refs#13969
    
  • lines changed 44, context: html, text, full: html, text
    Standard release edits for tarSyr2, refs #14410
    
  • lines changed 1, context: html, text, full: html, text
    Fixing minor typo in tarsier announcement
    
• src/hg/htdocs/style/HGStyle.css
  • lines changed 5, context: html, text, full: html, text
    Wrap hgc's track description html in a div with limited width, so if the
    page is extremely wide due to long details, the description text will
    wrap and you won't have to scroll back and forth to read it.
    
  • lines changed 5, context: html, text, full: html, text
    When VCF ##INFO description and data seem to have the same number of
    |-separated columns (and at least 3 apparent columns), display them
    as separate tables below the big table of INFO tags and settings
    because they can be quite large; for example, VEP annotations may
    have >40 |-separated columns for each alt allele & transcript.
    refs #14379
    
  • lines changed 5, context: html, text, full: html, text
    Use class stdTbl instead of making up new class.
    
• src/hg/htdocs/training/index.html
  • lines changed 1, context: html, text, full: html, text
    Updating training pages in prep for release of new training video. refs #13969
    
  • lines changed 5, context: html, text, full: html, text
    Fixing casing to have a minor edit to allow erich to repush file.
    
  • lines changed 29, context: html, text, full: html, text
    adding list of scheduled workshops
    
  • lines changed 10, context: html, text, full: html, text
    Adding info for upcoming workshops. refs #15011
    
  • lines changed 14, context: html, text, full: html, text
    added JAX lab training. refs #15011
    
• src/hg/htdocs/training/vids/index.html
  • lines changed 4, context: html, text, full: html, text
    Updating training pages in prep for release of new training video. refs #13969
    
• src/hg/inc/annoStreamDbKnownGene.h
  • lines changed 21, context: html, text, full: html, text
    Added a special annoStreamer for knownGene, to tack on kgXref.geneSymbol
    at the end. Now in hgVai, the geneSymbol is shown instead of the protein ID.
    The new column is also available in hgIntegrator. Now users can get the
    gene symbol that goes with their items, without changing gene track.
    refs #11752 #14579
    
• src/hg/js/model/hgIntegrator/hgIntegratorModel.js
  • lines changed 4, context: html, text, full: html, text
    Remove track groups from incoming groupedTrackDb if they have no tracks.
    Currently this removes 'All Tracks' and 'All Tables'; if there is demand
    for those, they could be constructed at this stage.
    refs #14579
    
• src/hg/lib/annoFormatVep.c
  • lines changed 4, context: html, text, full: html, text
    Added a special annoStreamer for knownGene, to tack on kgXref.geneSymbol
    at the end. Now in hgVai, the geneSymbol is shown instead of the protein ID.
    The new column is also available in hgIntegrator. Now users can get the
    gene symbol that goes with their items, without changing gene track.
    refs #11752 #14579
    
• src/hg/lib/annoStreamDbKnownGene.c
  • lines changed 178, context: html, text, full: html, text
    Added a special annoStreamer for knownGene, to tack on kgXref.geneSymbol
    at the end. Now in hgVai, the geneSymbol is shown instead of the protein ID.
    The new column is also available in hgIntegrator. Now users can get the
    gene symbol that goes with their items, without changing gene track.
    refs #11752 #14579
    
• src/hg/lib/customFactory.c
  • lines changed 9, context: html, text, full: html, text
    changes to UDC that allow to
    1. load bigDataUrls from a specific local directory, configured in hg.conf.
    this is useful in GBIB and mirrors where lots of time and space is wasted on
    loading local files via the http protocol.
    2. deactivate the udc cache. This is useful on OSX which
    doesn't support sparse files and so quickly fills any harddisk with
    hundreds of gigabytes of files full with zeros.
    
• src/hg/lib/hAnno.c
  • lines changed 16, context: html, text, full: html, text
    Added a special annoStreamer for knownGene, to tack on kgXref.geneSymbol
    at the end. Now in hgVai, the geneSymbol is shown instead of the protein ID.
    The new column is also available in hgIntegrator. Now users can get the
    gene symbol that goes with their items, without changing gene track.
    refs #11752 #14579
    
• src/hg/lib/hui.c
  • lines changed 3, context: html, text, full: html, text
    changes to UDC that allow to
    1. load bigDataUrls from a specific local directory, configured in hg.conf.
    this is useful in GBIB and mirrors where lots of time and space is wasted on
    loading local files via the http protocol.
    2. deactivate the udc cache. This is useful on OSX which
    doesn't support sparse files and so quickly fills any harddisk with
    hundreds of gigabytes of files full with zeros.
    
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Added a special annoStreamer for knownGene, to tack on kgXref.geneSymbol
    at the end. Now in hgVai, the geneSymbol is shown instead of the protein ID.
    The new column is also available in hgIntegrator. Now users can get the
    gene symbol that goes with their items, without changing gene track.
    refs #11752 #14579
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 45, context: html, text, full: html, text
    Updated ExAC to release 0.3 and added subtrack with calling regions.
    refs #14379
    
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 48, context: html, text, full: html, text
    import of GENCODE V22
    
• src/hg/makeDb/doc/hg38/multiz20way.txt
  • lines changed 1674, context: html, text, full: html, text
    running up a 20-way conservation to get outgroups in the 17-way refs #14970
    
• src/hg/makeDb/doc/hg38/splitRegions.pl
  • lines changed 73, context: html, text, full: html, text
    running up a 20-way conservation to get outgroups in the 17-way refs #14970
    
• src/hg/makeDb/doc/makeEnsembl.txt
  • lines changed 50, context: html, text, full: html, text
    v79 ensGene done refs #15005
    
• src/hg/makeDb/doc/papAnu2.txt
  • lines changed 41, context: html, text, full: html, text
    add ucscToEnsembl table refs #15005
    
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes16.csh
  • lines changed 737, context: html, text, full: html, text
    first cut at knownGene based on Gencode
    
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes16.sh
  • lines changed 789, context: html, text, full: html, text
    first cut at knownGene based on Gencode
    
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 19, context: html, text, full: html, text
    adding ornAna2 refs #15098
    
  • lines changed 26, context: html, text, full: html, text
    add braNey38 to genbank
    
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 2, context: html, text, full: html, text
    Adding tarSyr2 to beta GenBank updates, refs #14410
    
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 2, context: html, text, full: html, text
    Added danRer10 to rr.dbs; refs #14017
    
  • lines changed 2, context: html, text, full: html, text
    Turning on RR genbank updates for tarSyr2, refs #14410
    
• src/hg/makeDb/makeGencodeKnownGene/makeGencodeKnownGene.c
  • lines changed 496, context: html, text, full: html, text
    first cut at knownGene based on Gencode
    
• src/hg/makeDb/makeGencodeKnownGene/makefile
  • lines changed 3, context: html, text, full: html, text
    first cut at knownGene based on Gencode
    
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 9, context: html, text, full: html, text
    import of GENCODE V22
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 10, context: html, text, full: html, text
    adding aquChr2 rules refs #15096
    
  • lines changed 8, context: html, text, full: html, text
    adding ornAna2 rules refs #15098
    
  • lines changed 85, context: html, text, full: html, text
    import of GENCODE V22
    
• src/hg/makeDb/trackDb/birds/geoFor1/cons7way.html
  • lines changed 1, context: html, text, full: html, text
    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/cat/felCat3/multiz4way.html
  • lines changed 1, context: html, text, full: html, text
    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/cat/felCat4/cons6way.html
  • lines changed 1, context: html, text, full: html, text
    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/chicken/galGal2/multiz7way.html
  • lines changed 1, context: html, text, full: html, text
    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/chicken/galGal3/multiz7way.html
  • lines changed 1, context: html, text, full: html, text
    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/chimp/panTro3/cons12way.html
  • lines changed 1, context: html, text, full: html, text
    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/cow/bosTau4/multiz5way.html
  • lines changed 1, context: html, text, full: html, text
    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/dog/canFam1/mzHg17Mm5_phast.html
  • lines changed 1, context: html, text, full: html, text
    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/dog/canFam2/multiz4way.html
  • lines changed 1, context: html, text, full: html, text
    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/drosophila/dm2/multiz12way.html
  • lines changed 1, context: html, text, full: html, text
    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/drosophila/dm2/multiz15way.html
  • lines changed 1, context: html, text, full: html, text
    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/drosophila/dm2/multiz8way.html
  • lines changed 1, context: html, text, full: html, text
    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/drosophila/dm2/multiz9way.html
  • lines changed 1, context: html, text, full: html, text
    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/drosophila/dm3/multiz15way.html
  • lines changed 1, context: html, text, full: html, text
    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/drosophila/dm6/cons27way.html
  • lines changed 1, context: html, text, full: html, text
    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/drosophila/mzDy1Dp2Ag1_phast.html
  • lines changed 1, context: html, text, full: html, text
    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/ebola/eboVir3/cons160way.html
  • lines changed 1, context: html, text, full: html, text
    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/fugu/fr2/multiz5way.html
  • lines changed 1, context: html, text, full: html, text
    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/fugu/fr3/cons8way.html
  • lines changed 1, context: html, text, full: html, text
    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/gorilla/gorGor3/cons11way.html
  • lines changed 1, context: html, text, full: html, text
    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/horse/equCab2/multiz6way.html
  • lines changed 1, context: html, text, full: html, text
    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/hg17/encodeTbaElements.html
  • lines changed 1, context: html, text, full: html, text
    Typo corrections based on code review, #15086
    
• src/hg/makeDb/trackDb/human/hg17/multiz17way.html
  • lines changed 1, context: html, text, full: html, text
    Typo corrections based on code review, #15086
    
• src/hg/makeDb/trackDb/human/hg18/multiz28way.html
  • lines changed 1, context: html, text, full: html, text
    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/hg18/multizPrimate.html
  • lines changed 1, context: html, text, full: html, text
    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/hg19/cons100way.html
  • lines changed 1, context: html, text, full: html, text
    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/hg19/cons46way.html
  • lines changed 1, context: html, text, full: html, text
    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/hg19/exac.html
  • lines changed 41, context: html, text, full: html, text
    Updated ExAC to release 0.3 and added subtrack with calling regions.
    refs #14379
    
  • lines changed 11, context: html, text, full: html, text
    A couple tweaks to ExAC description/metadata.
    refs #14379
    
• src/hg/makeDb/trackDb/human/hg19/exacVariants.html
  • lines changed 39, context: html, text, full: html, text
    Updated ExAC to release 0.3 and added subtrack with calling regions.
    refs #14379
    
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 18, context: html, text, full: html, text
    Updated ExAC to release 0.3 and added subtrack with calling regions.
    refs #14379
    
  • lines changed 1, context: html, text, full: html, text
    A couple tweaks to ExAC description/metadata.
    refs #14379
    
  • lines changed 1, context: html, text, full: html, text
    Adding exonNumbers off to a couple of tracks
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV10.ra
  • lines changed 5, context: html, text, full: html, text
    Modify older gencode trackDb entries to use tranckHandler. This will allow for getting rid of per-release track registration. Most of these are no longer in sue
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV11.ra
  • lines changed 5, context: html, text, full: html, text
    Modify older gencode trackDb entries to use tranckHandler. This will allow for getting rid of per-release track registration. Most of these are no longer in sue
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV12.ra
  • lines changed 5, context: html, text, full: html, text
    Modify older gencode trackDb entries to use tranckHandler. This will allow for getting rid of per-release track registration. Most of these are no longer in sue
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV13.ra
  • lines changed 5, context: html, text, full: html, text
    Modify older gencode trackDb entries to use tranckHandler. This will allow for getting rid of per-release track registration. Most of these are no longer in sue
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV14.ra
  • lines changed 5, context: html, text, full: html, text
    Modify older gencode trackDb entries to use tranckHandler. This will allow for getting rid of per-release track registration. Most of these are no longer in sue
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV15.ra
  • lines changed 5, context: html, text, full: html, text
    Modify older gencode trackDb entries to use tranckHandler. This will allow for getting rid of per-release track registration. Most of these are no longer in sue
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV16.ra
  • lines changed 5, context: html, text, full: html, text
    Modify older gencode trackDb entries to use tranckHandler. This will allow for getting rid of per-release track registration. Most of these are no longer in sue
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV17.ra
  • lines changed 5, context: html, text, full: html, text
    Modify older gencode trackDb entries to use tranckHandler. This will allow for getting rid of per-release track registration. Most of these are no longer in sue
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV18.ra
  • lines changed 5, context: html, text, full: html, text
    Modify older gencode trackDb entries to use tranckHandler. This will allow for getting rid of per-release track registration. Most of these are no longer in sue
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV19.ra
  • lines changed 5, context: html, text, full: html, text
    Modify older gencode trackDb entries to use tranckHandler. This will allow for getting rid of per-release track registration. Most of these are no longer in sue
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV3.ra
  • lines changed 3, context: html, text, full: html, text
    Modify older gencode trackDb entries to use tranckHandler. This will allow for getting rid of per-release track registration. Most of these are no longer in sue
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV4.ra
  • lines changed 4, context: html, text, full: html, text
    Modify older gencode trackDb entries to use tranckHandler. This will allow for getting rid of per-release track registration. Most of these are no longer in sue
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV7.ra
  • lines changed 5, context: html, text, full: html, text
    Modify older gencode trackDb entries to use tranckHandler. This will allow for getting rid of per-release track registration. Most of these are no longer in sue
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV9.ra
  • lines changed 5, context: html, text, full: html, text
    Modify older gencode trackDb entries to use tranckHandler. This will allow for getting rid of per-release track registration. Most of these are no longer in sue
    
• src/hg/makeDb/trackDb/human/hg38/cons17way.html
  • lines changed 1, context: html, text, full: html, text
    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/hg38/cons7way.html
  • lines changed 1, context: html, text, full: html, text
    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    import of GENCODE V22
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV19.ra
  • lines changed 6, context: html, text, full: html, text
    Modify older gencode trackDb entries to use tranckHandler. This will allow for getting rid of per-release track registration. Most of these are no longer in sue
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV20.ra
  • lines changed 5, context: html, text, full: html, text
    Modify older gencode trackDb entries to use tranckHandler. This will allow for getting rid of per-release track registration. Most of these are no longer in sue
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV21.ra
  • lines changed 6, context: html, text, full: html, text
    Modify older gencode trackDb entries to use tranckHandler. This will allow for getting rid of per-release track registration. Most of these are no longer in sue
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV22.html
  • lines changed 334, context: html, text, full: html, text
    import of GENCODE V22
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV22.ra
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    import of GENCODE V22
    
• src/hg/makeDb/trackDb/human/trackDb.ra
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    Turning off exon numbers for DGV, as b0b requested.
    refs #7474
    
• src/hg/makeDb/trackDb/lamprey/petMar1/multiz6way.html
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    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/lamprey/petMar2/cons7way.html
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    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/lancelet/braFlo1/multiz5way.html
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    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/lizard/anoCar2/cons7way.html
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    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/marmoset/calJac1/multiz9way.html
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    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/marmoset/calJac3/cons13way.html
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    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/medaka/oryLat2/multiz5way.html
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    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/mouse/mm10/cons60way.html
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    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/mouse/mm7/multiz17way.html
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    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/mouse/mm8/multiz17way.html
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    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/mouse/mm9/cons30way.html
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    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/mouse/mm9/multiz30way.html
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    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/opossum/monDom4/multiz7way.html
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    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/opossum/monDom5/multiz9way.html
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    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/opossum/multiz5way.html
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    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/orangutan/ponAbe2/multiz8way.html
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    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/platypus/ornAna1/multiz6way.html
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    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/rat/rn4/multiz9way.html
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    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/rat/rn5/cons13way.html
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    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/sacCer/multizYeast.html
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    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/sacCer/sacCer2/multiz7way.html
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    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/sacCer/sacCer3/multiz7way.html
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    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/stickleback/gasAcu1/multiz8way.html
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    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/tagTypes.tab
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    Updated ExAC to release 0.3 and added subtrack with calling regions.
    refs #14379
    
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    import of GENCODE V22
    
• src/hg/makeDb/trackDb/tarsier/tarSyr2/cons17way.html
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    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/trackDb.ra
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    Adding exonNumbers off to a couple of tracks
    
• src/hg/makeDb/trackDb/worm/ce10/cons7way.html
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    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/worm/ce10/cons9way.html
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    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/worm/ce2/c_briggsae_pwMaf.html
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    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/worm/ce4/multiz5way.html
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    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/worm/ce6/multiz6way.html
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    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/xenTro/xenTro2/multiz7way.html
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    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/xenTro/xenTro3/cons9way.html
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    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/zebrafish/danRer3/multiz5way.html
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    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/zebrafish/danRer4/multiz7way.html
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    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/zebrafish/danRer6/multiz6way.html
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    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/zebrafish/danRer7/cons8way.html
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    Finish updating link to Adam Siepels site at CSHL, refs #15050
    
• src/hg/oneShot/testSimpleD3/testSimpleD3.c
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    Testing some D3 pie graphs in the CIRM database browser
    
  • lines changed 33, context: html, text, full: html, text
    Added some bells and whistles, users can put in a title and subtitle
    
• src/lib/udc.c
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    changes to UDC that allow to
    1. load bigDataUrls from a specific local directory, configured in hg.conf.
    this is useful in GBIB and mirrors where lots of time and space is wasted on
    loading local files via the http protocol.
    2. deactivate the udc cache. This is useful on OSX which
    doesn't support sparse files and so quickly fills any harddisk with
    hundreds of gigabytes of files full with zeros.
    
• src/product/ex.hg.conf
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    documenting two new hg.conf options for udc
    
• src/utils/bedClip/bedClip.c
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    Updating usage message in utils that now accept a URL for chrom.sizes.
    resolves #14857
    
• src/utils/bedGraphToBigWig/bedGraphToBigWig.c
  • lines changed 6, context: html, text, full: html, text
    Updating usage message in utils that now accept a URL for chrom.sizes.
    resolves #14857
    
• src/utils/bedToBigBed/bedToBigBed.c
  • lines changed 6, context: html, text, full: html, text
    Updating usage message in utils that now accept a URL for chrom.sizes.
    resolves #14857
    
• src/utils/qa/weeklybld/buildEnv.csh
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    v315 preview1
    
• src/utils/wigToBigWig/wigToBigWig.c
  • lines changed 6, context: html, text, full: html, text
    Updating usage message in utils that now accept a URL for chrom.sizes.
    resolves #14857
    

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• files changed: 170