All File Changes

v310_preview2 to v310_base (2014-12-15 to 2015-01-05) v310

• src/hg/encode/encodeExp/encodeExp.c
  • lines changed 15, context: html, text, full: html, text
    Extend ENCODE experiment table tools for more flexibility. Most ENCODE metadata of general interest can be obtained from experiment (without requiring metaDb)
• src/hg/hgBeacon/README.txt
  • lines changed 1, context: html, text, full: html, text
    changes after code review, refs #14545
  • lines changed 1, context: html, text, full: html, text
    changes after code review, refs #14545
• src/hg/hgBeacon/hgBeacon
  • lines changed 89, context: html, text, full: html, text
    making hgBeacon source slightly better
  • lines changed 4, context: html, text, full: html, text
    changes after code review, refs #14545
• src/hg/hgBeacon/makefile
  • lines changed 15, context: html, text, full: html, text
    changes after code review, refs #14545
  • lines changed 5, context: html, text, full: html, text
    fixing bug in hgBeacon makefile
  • lines changed 3, context: html, text, full: html, text
    Suppressing 'no config file' warning from pylint, refs #14393
• src/hg/hgBeacon/pylint.rc
  • lines changed 249, context: html, text, full: html, text
    Suppressing 'no config file' warning from pylint, refs #14393
• src/hg/hgBlat/hgBlat.c
  • lines changed 54, context: html, text, full: html, text
    blat support on assembly hubs
  • lines changed 2, context: html, text, full: html, text
    strip off the name in a few places in hgBlat
• src/hg/hgTables/hal.c
  • lines changed 12, context: html, text, full: html, text
    upgrade to new version of HAL.
• src/hg/hgTracks/bedTrack.c
  • lines changed 3, context: html, text, full: html, text
    tweak to get labelOnFeature to work correctly in pack mode (don't addspace for label)
    
  • lines changed 17, context: html, text, full: html, text
    changes after code review, refs #14545
• src/hg/hgTracks/hgTracks.c
  • lines changed 11, context: html, text, full: html, text
    adding a measuretiming for the bottleneck, refs #14539
• src/hg/hgTracks/retroGene.c
  • lines changed 7, context: html, text, full: html, text
    added support for transmap V3 which includes source databases in mapped alignment idenitifier
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    oops.. broke density graph mode when I made changes in response to codereview.
    
  • lines changed 2, context: html, text, full: html, text
    sheez... another mistake I made in making changes for code review.ALWAYS TEST!
    
  • lines changed 7, context: html, text, full: html, text
    tweak to get labelOnFeature to work correctly in pack mode (don't addspace for label)
    
  • lines changed 21, context: html, text, full: html, text
    changes after code review, refs #14545
• src/hg/hgTracks/snakeTrack.c
  • lines changed 6, context: html, text, full: html, text
    upgrade to new version of HAL.
• src/hg/hgTracks/transMapTracks.c
  • lines changed 2, context: html, text, full: html, text
    added support for transmap V3 which includes source databases in mapped alignment idenitifier
• src/hg/hgc/transMapClick.c
  • lines changed 3, context: html, text, full: html, text
    added support for transmap V3 which includes source databases in mapped alignment idenitifier
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 7, context: html, text, full: html, text
    Added block requirements for BED format
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 3, context: html, text, full: html, text
    adding bosTau8 release info
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 1, context: html, text, full: html, text
    adding bosTau8 release info
  • lines changed 1, context: html, text, full: html, text
    made minor correction to date for bostau8
  • lines changed 8, context: html, text, full: html, text
    moved bosTau8 credits to UMD section
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 5, context: html, text, full: html, text
    Adding warning that without a specified number, bigBeds default to 3 field display
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 3, context: html, text, full: html, text
    adding linkIdInName trackDb statement doc, refs #14534
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html
  • lines changed 3, context: html, text, full: html, text
    adding linkIdInName trackDb statement doc, refs #14534
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 21, context: html, text, full: html, text
    adding linkIdInName trackDb statement doc, refs #14534
  • lines changed 1, context: html, text, full: html, text
    fixing typo, refs #14534
  • lines changed 9, context: html, text, full: html, text
    Adding trackDbLibrary note about visibility for composite subtracks refs #10015
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 17, context: html, text, full: html, text
    staging announcement for release of YouTube channel. refs #14408
  • lines changed 30, context: html, text, full: html, text
    added news item for bosTau8
• src/hg/htdocs/images/phylo/hg38_17way.png
  • lines changed 0, context: html, text, full: html, text
    hg38 phylo tree for primate alignment refs #14560
• src/hg/htdocs/images/phylo/tarSyr2_17way.png
  • lines changed 0, context: html, text, full: html, text
    tarSyr2 phylo tree for primate alignment refs #14560
• src/hg/htdocs/images/training/titleInformatics.jpg
  • lines changed 0, context: html, text, full: html, text
    Adding bob's new logo image and new body background class to css sheet for use in training docs. refs #14408
• src/hg/htdocs/indexNews.html
  • lines changed 14, context: html, text, full: html, text
    staging announcement for release of YouTube channel. refs #14408
  • lines changed 0, context: html, text, full: html, text
    staging announcement for release of YouTube channel. refs #14408
  • lines changed 75, context: html, text, full: html, text
    adding news announcement for bosTau8
  • lines changed 15, context: html, text, full: html, text
    fixed formatting issue
  • lines changed 2, context: html, text, full: html, text
    fixed spacing issue
  • lines changed 0, context: html, text, full: html, text
    fixed spacing issue
• src/hg/htdocs/staff.html
  • lines changed 1, context: html, text, full: html, text
    Jim is no longer the co-PI of the UCSC GB, so changing the wording so that he is the sole PI
  • lines changed 31, context: html, text, full: html, text
    additional updates to the staff: simplifying Jim's role, adding Co-PI to Bob, changing Pauline to Outreach, moving Max from postdoc to staff section
• src/hg/htdocs/style/HGStyle.css
  • lines changed 4, context: html, text, full: html, text
    Adding bob's new logo image and new body background class to css sheet for use in training docs. refs #14408
• src/hg/htdocs/training/ashg2014/index.html
  • lines changed 10, context: html, text, full: html, text
    added some text to clarify the content on the ashg2014 pages, per code review. thanks jonathan. refs #14541
• src/hg/htdocs/training/index.html
  • lines changed 11, context: html, text, full: html, text
    adding page for videos and links to it
  • lines changed 1, context: html, text, full: html, text
    added space before YouTube link
  • lines changed 2, context: html, text, full: html, text
    added some text to clarify the content on the ashg2014 pages, per code review. thanks jonathan. refs #14541
  • lines changed 1, context: html, text, full: html, text
    Adding link to youtube channel. refs #14525
• src/hg/htdocs/training/vids/index.html
  • lines changed 198, context: html, text, full: html, text
    adding page for videos and links to it
• src/hg/inc/encode/encodeExp.h
  • lines changed 10, context: html, text, full: html, text
    Extend ENCODE experiment table tools for more flexibility. Most ENCODE metadata of general interest can be obtained from experiment (without requiring metaDb)
• src/hg/inc/trackHub.h
  • lines changed 3, context: html, text, full: html, text
    blat support on assembly hubs
• src/hg/inc/transMapStuff.h
  • lines changed 11, context: html, text, full: html, text
    added support for transmap V3 which includes source databases in mapped alignment idenitifier
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v310
• src/hg/lib/encode/encodeExp.c
  • lines changed 35, context: html, text, full: html, text
    Extend ENCODE experiment table tools for more flexibility. Most ENCODE metadata of general interest can be obtained from experiment (without requiring metaDb)
• src/hg/lib/hdb.c
  • lines changed 1, context: html, text, full: html, text
    blat support on assembly hubs
• src/hg/lib/hui.c
  • lines changed 42, context: html, text, full: html, text
    adding a bit of javascript to the wiggle drawing options that grey outthe min/max fields if auto-scaling is "on". Also move the auto-scaling
    dropdown box up one line, so it's easier to see that a part below is
    greyed out. refs #14561
    
• src/hg/lib/trackHub.c
  • lines changed 18, context: html, text, full: html, text
    blat support on assembly hubs
• src/hg/lib/trackHubCheck.c
  • lines changed 6, context: html, text, full: html, text
    upgrade to new version of HAL.
• src/hg/lib/transMapStuff.c
  • lines changed 23, context: html, text, full: html, text
    added support for transmap V3 which includes source databases in mapped alignment idenitifier
• src/hg/makeDb/doc/ailMel1.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/allMis1.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/amaVit1.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/anoCar2.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/bosTau8.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/calJac3.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/canFam3.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/cavPor3.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/cerSim1.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/chiLan1.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/choHof1.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/criGri1.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/danRer7.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/dasNov3.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/dipOrd1.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/echTel2.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/encode3/hg38_encode2_dnase1.txt
  • lines changed 166, context: html, text, full: html, text
    Add scores to peaks and hotspots. refs #14353
• src/hg/makeDb/doc/encodeRegHg19.txt
  • lines changed 3, context: html, text, full: html, text
    Minor corrections
• src/hg/makeDb/doc/equCab2.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/eriEur2.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/falPer1.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/felCat5.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/fr3.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/gadMor1.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/galGal4.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/gasAcu1.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/geoFor1.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/gorGor3.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/hetGla2.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/hg19.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 46, context: html, text, full: html, text
    First cut UW DNase tracks for hg38. refs #14353
  • lines changed 47, context: html, text, full: html, text
    Add scores to peaks and hotspots. refs #14353
• src/hg/makeDb/doc/hg38/lastzRuns.txt
  • lines changed 863, context: html, text, full: html, text
    almost done with all primates refs #14560
  • lines changed 4, context: html, text, full: html, text
    16 primates alignments done refs #14560
  • lines changed 79, context: html, text, full: html, text
    ready for downloads and pushQ refs #13560
• src/hg/makeDb/doc/hg38/multiz17way.txt
  • lines changed 1603, context: html, text, full: html, text
    ready for downloads and pushQ refs #13560
  • lines changed 18, context: html, text, full: html, text
    done with 17-way downloads refs #14560
• src/hg/makeDb/doc/hg38/reg.txt
  • lines changed 264, context: html, text, full: html, text
    Add scores to peaks and hotspots. refs #14353
  • lines changed 62, context: html, text, full: html, text
    DNase Clusters track from UW/ENCODE data mapped to hg38. refs #14353
  • lines changed 329, context: html, text, full: html, text
    Resolve merge conflict
• src/hg/makeDb/doc/latCha1.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/loxAfr3.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/macEug2.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/melGal1.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/melUnd1.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/micMur1.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/mm10.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/mm9.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/monDom5.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/musFur1.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/myoLuc2.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/nomLeu3.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/ochPri3.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/oreNil2.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/ornAna1.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/oryCun2.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/oryLat2.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/otoGar3.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/oviAri3.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
  • lines changed 21, context: html, text, full: html, text
    liftOver to oviAri1 refs #14582
• src/hg/makeDb/doc/panPan1.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/panTro4.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/papAnu2.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/petMar2.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/ponAbe2.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/proCap1.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/pteVam1.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/rn5.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/saiBol1.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/sarHar1.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/sorAra2.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/speTri2.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/susScr3.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/taeGut2.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/tarSyr1.txt
  • lines changed 15, context: html, text, full: html, text
    liftOver to tarSyr2 computed in 8 days refs #14410
• src/hg/makeDb/doc/tarSyr2/initialBuild.txt
  • lines changed 260, context: html, text, full: html, text
    ready for downloads and pushQ refs #13560
  • lines changed 22, context: html, text, full: html, text
    tarSyr2 browser in the pushQ refs #14410
• src/hg/makeDb/doc/tarSyr2/lastzRuns.txt
  • lines changed 1427, context: html, text, full: html, text
    almost done with all primates refs #14560
  • lines changed 12, context: html, text, full: html, text
    16 primates alignments done refs #14560
• src/hg/makeDb/doc/tarSyr2/multiz17way.txt
  • lines changed 1606, context: html, text, full: html, text
    ready for downloads and pushQ refs #13560
• src/hg/makeDb/doc/tetNig2.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/transMapTracks.txt
  • lines changed 60, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/triMan1.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/tupBel1.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/turTru2.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/vicPac2.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/doc/xenTro7.txt
  • lines changed 3, context: html, text, full: html, text
    transmap V3 build
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 1, context: html, text, full: html, text
    turning on genbank updates for bosTau8
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 1, context: html, text, full: html, text
    turning on genbank updates for bosTau8
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    removing iedbPred tables from all.joiner checks, refs #14467
  • lines changed 4, context: html, text, full: html, text
    Moving around spAnnot and spStruct tablesIgnored entries, refs #13688
  • lines changed 148, context: html, text, full: html, text
    added support for transmap V3 which includes source databases in mapped alignment idenitifier
  • lines changed 7, context: html, text, full: html, text
    adding tarSyr2 refs #14560
  • lines changed 7, context: html, text, full: html, text
    clean up tarSyr2 refs #14560
• src/hg/makeDb/trackDb/anopheles/anoGam1/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    Adding release alpha tags to snoGam1, droPer1, droSec1, droSim1 dm3 chain/net tracks
• src/hg/makeDb/trackDb/drosophila/droPer1/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    Adding release alpha tags to snoGam1, droPer1, droSec1, droSim1 dm3 chain/net tracks
• src/hg/makeDb/trackDb/drosophila/droSec1/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    Adding release alpha tags to snoGam1, droPer1, droSec1, droSim1 dm3 chain/net tracks
• src/hg/makeDb/trackDb/drosophila/droSim1/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    Adding release alpha tags to snoGam1, droPer1, droSec1, droSim1 dm3 chain/net tracks
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.iedbPred.ra
  • lines changed 1, context: html, text, full: html, text
    Removing score filtering option for IEDB Pred tracks, refs #14467
  • lines changed 7, context: html, text, full: html, text
    shortening titles and removing score filters, refs #14467
  • lines changed 1, context: html, text, full: html, text
    fixing mistake in last commit
• src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Removing release tag for iedPred tracks, refs #14467
  • lines changed 3, context: html, text, full: html, text
    Changes to UniProt composite track, removing unnecessary lines from Ebola trackDb. refs #13688
• src/hg/makeDb/trackDb/gwipsRiboseq.html
  • lines changed 69, context: html, text, full: html, text
    Adding initial trackDb.ra entry and description page for GWIPS Ribo-seq track; refs #14066
  • lines changed 69, context: html, text, full: html, text
    Changed everything from GWIPS to GWIPS-viz; refs #14066
• src/hg/makeDb/trackDb/gwipsvizRiboseq.html
  • lines changed 204, context: html, text, full: html, text
    Changed everything from GWIPS to GWIPS-viz; refs #14066
  • lines changed 30, context: html, text, full: html, text
    Made final edits to description page; refs #14066
• src/hg/makeDb/trackDb/human/chainNetOtoGar1.ra
  • lines changed 2, context: html, text, full: html, text
    continue adding and fixing up primate chain net ordering refs #14543 #14560
• src/hg/makeDb/trackDb/human/chainNetOtoGar3.ra
  • lines changed 2, context: html, text, full: html, text
    continue adding and fixing up primate chain net ordering refs #14543 #14560
• src/hg/makeDb/trackDb/human/chainNetPrimate.ra
  • lines changed 102, context: html, text, full: html, text
    continue adding and fixing up primate chain net ordering refs #14543 #14560
• src/hg/makeDb/trackDb/human/chainNetRBestOtoGar1.ra
  • lines changed 2, context: html, text, full: html, text
    continue adding and fixing up primate chain net ordering refs #14543 #14560
• src/hg/makeDb/trackDb/human/chainNetRBestOtoGar3.ra
  • lines changed 2, context: html, text, full: html, text
    continue adding and fixing up primate chain net ordering refs #14543 #14560
• src/hg/makeDb/trackDb/human/chainNetStray.ra
  • lines changed 33, context: html, text, full: html, text
    no longer stray chain nets, now in composites refs #14560
• src/hg/makeDb/trackDb/human/chainNetTarSyr1.ra
  • lines changed 2, context: html, text, full: html, text
    continue adding and fixing up primate chain net ordering refs #14543 #14560
• src/hg/makeDb/trackDb/human/chainNetTarSyr2.ra
  • lines changed 2, context: html, text, full: html, text
    continue adding and fixing up primate chain net ordering refs #14543 #14560
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    oops, setting pathway track to hide again
• src/hg/makeDb/trackDb/human/hg38/trackDb.17way.ra
  • lines changed 105, context: html, text, full: html, text
    adding 17-way trackDb refs #14560
  • lines changed 1, context: html, text, full: html, text
    continue adding and fixing up primate chain net ordering refs #14543 #14560
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    First cut UW DNase tracks for hg38. refs #14353
  • lines changed 1, context: html, text, full: html, text
    adding 17-way trackDb refs #14560
• src/hg/makeDb/trackDb/human/hg38/uwDnase.html
  • lines changed 52, context: html, text, full: html, text
    Add track draft track descriptions and tweak configs. refs #14353
• src/hg/makeDb/trackDb/human/hg38/uwDnase.ra
  • lines changed 2819, context: html, text, full: html, text
    Add scores to peaks and hotspots. refs #14353
  • lines changed 17, context: html, text, full: html, text
    DNase Clusters track from UW/ENCODE data mapped to hg38. refs #14353
  • lines changed 16, context: html, text, full: html, text
    Add track draft track descriptions and tweak configs. refs #14353
  • lines changed 1, context: html, text, full: html, text
    Tweak vis
  • lines changed 96, context: html, text, full: html, text
    More track config tweaks.
  • lines changed 8, context: html, text, full: html, text
    Fix treatment tag flagged by tdbQuery. Retire pValue filters for now (they don't work with bigBed, but we may want them later). refs #14353
• src/hg/makeDb/trackDb/human/hg38/uwDnaseClusters.html
  • lines changed 37, context: html, text, full: html, text
    Add track draft track descriptions and tweak configs. refs #14353
• src/hg/makeDb/trackDb/human/hg38/uwDnaseSignal.html
  • lines changed 46, context: html, text, full: html, text
    Add track draft track descriptions and tweak configs. refs #14353
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    Adding initial trackDb.ra entry and description page for GWIPS Ribo-seq track; refs #14066
  • lines changed 4, context: html, text, full: html, text
    Changed everything from GWIPS to GWIPS-viz; refs #14066
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 2, context: html, text, full: html, text
    First cut UW DNase tracks for hg38. refs #14353
  • lines changed 1, context: html, text, full: html, text
    Add scores to peaks and hotspots. refs #14353
  • lines changed 2, context: html, text, full: html, text
    temporarily fixing a trackDb error, but final resolution left to Kate
  • lines changed 10, context: html, text, full: html, text
    Remove unnecessary/wrong pValueFilter and qValueFilter settings that override the *Filter wildcard setting. Note that xxFilter will not be flagged if it's missing from tagTypes. It will inherit settings from *Filter.
• src/hg/makeDb/trackDb/tarsier/tarSyr2/cons17way.html
  • lines changed 446, context: html, text, full: html, text
    initial contents description page 17-way refs #14560
  • lines changed 4, context: html, text, full: html, text
    update gene annotation note refs #14560
• src/hg/makeDb/trackDb/tarsier/tarSyr2/trackDb.17way.ra
  • lines changed 105, context: html, text, full: html, text
    17-way on tarSyr2 reference refs #14560
  • lines changed 1, context: html, text, full: html, text
    turning on frames annotations refs #14560
• src/hg/makeDb/trackDb/tarsier/tarSyr2/trackDb.chainNet.ra
  • lines changed 107, context: html, text, full: html, text
    correct ordering for chain net tracks refs #14560
• src/hg/makeDb/trackDb/tarsier/tarSyr2/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    17-way on tarSyr2 reference refs #14560
  • lines changed 1, context: html, text, full: html, text
    correct ordering for chain net tracks refs #14560
• src/hg/makeDb/trackDb/trackDb.chainNet.primates.ra
  • lines changed 121, context: html, text, full: html, text
    adding nasLar1 and rhiRox1 refs #14560
  • lines changed 30, context: html, text, full: html, text
    release tags and overrides confuse tdbQuery remove release alpha refs #14560
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    shortening shortLabel, refs #13688
  • lines changed 2, context: html, text, full: html, text
    removing score filters, refs #13688
  • lines changed 13, context: html, text, full: html, text
    Changes to UniProt composite track, removing unnecessary lines from Ebola trackDb. refs #13688
• src/hg/makefile
  • lines changed 1, context: html, text, full: html, text
    changes after code review, refs #14545
• src/hg/pslCDnaGenomeMatch/pslCDnaGenomeMatch.c
  • lines changed 59, context: html, text, full: html, text
    Changed code to use only 2bit files instead of nib files.
• src/hg/regulate/regClusterMakeTableOfTables/regClusterMakeTableOfTables.c
  • lines changed 25, context: html, text, full: html, text
    Extend normalization tool for cluster racks to handle DNase from ENCODE EAP (for hg38). refs #14353
• src/hg/utils/automation/doBlastzChainNet.pl
  • lines changed 10, context: html, text, full: html, text
    construct downloads for synNet refs #14560
• src/hg/utils/phyloTrees/183way.commonNames.nh
  • lines changed 183, context: html, text, full: html, text
    adding nasLar1 rhiRox1 refs #14560
  • lines changed 1, context: html, text, full: html, text
    update tarSyr1 to tarSyr2 refs #14560
• src/hg/utils/phyloTrees/183way.nh
  • lines changed 183, context: html, text, full: html, text
    adding nasLar1 rhiRox1 refs #14560
  • lines changed 1, context: html, text, full: html, text
    update tarSyr1 to tarSyr2 refs #14560
• src/hg/utils/phyloTrees/183way.scientificNames.nh
  • lines changed 183, context: html, text, full: html, text
    adding nasLar1 rhiRox1 refs #14560
• src/hg/utils/phyloTrees/asciiTree.pl
  • lines changed 41, context: html, text, full: html, text
    adding nasLar1 rhiRox1 refs #14560
• src/hg/utils/phyloTrees/commonNames.sh
  • lines changed 4, context: html, text, full: html, text
    adding nasLar1 rhiRox1 refs #14560
  • lines changed 1, context: html, text, full: html, text
    update tarSyr1 to tarSyr2 refs #14560
• src/hg/utils/phyloTrees/makefile
  • lines changed 7, context: html, text, full: html, text
    adding nasLar1 rhiRox1 refs #14560
• src/hg/utils/phyloTrees/scientificNames.sh
  • lines changed 2, context: html, text, full: html, text
    adding nasLar1 rhiRox1 refs #14560
• src/hg/utils/pslMap/pslMap.c
  • lines changed 14, context: html, text, full: html, text
    speed up loading a very number of overlapping chains by pslMap
  • lines changed 9, context: html, text, full: html, text
    fixed bug in previous change to optimize list merge
• src/inc/common.h
  • lines changed 3, context: html, text, full: html, text
    changes after code review, refs #14545
• src/inc/common.mk
  • lines changed 3, context: html, text, full: html, text
    add a wee bit of release control to the hal libraries
• src/lib/common.c
  • lines changed 11, context: html, text, full: html, text
    changes after code review, refs #14545
• src/makefile
  • lines changed 8, context: html, text, full: html, text
    changes after code review, refs #14545
• src/utils/bigBedInfo/makefile
  • lines changed 29, context: html, text, full: html, text
    adding bigBedInfo to the beacon binaries, refs #14393
• src/utils/bigBedToBed/makefile
  • lines changed 29, context: html, text, full: html, text
    changes after code review, refs #14545
• src/utils/makefile
  • lines changed 10, context: html, text, full: html, text
    adding bigBedInfo to the beacon binaries, refs #14393
  • lines changed 6, context: html, text, full: html, text
    trying to fix a makefile problem
  • lines changed 2, context: html, text, full: html, text
    adding comment, refs #14393
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v310 preview2 refs #14506
  • lines changed 3, context: html, text, full: html, text
    v310 final build refs #14494

• lines changed: 13874
• files changed: 238