CVS changes by file

review to branch (2010-01-12 to 2010-01-19) v223

• src/hg/encode/DAFs/UMass5C.DAF
  • 1.4 lines changed: 43, context: html, text, full: html, text
    2nd cut of Dekker lab files
• src/hg/encode/DAFs/UMass5C.DDF
  • 1.2 lines changed: 11, context: html, text, full: html, text
    2nd cut of Dekker lab files
• src/hg/encode/DAFs/UwDnaseValid.daf
  • 1.1 lines changed: 0, context: html, text, full: html, text
    First cut DNAse validatation metadata files for UW
• src/hg/encode/DAFs/UwDnaseValid.ddf
  • 1.1 lines changed: 0, context: html, text, full: html, text
    First cut DNAse validatation metadata files for UW
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.197 lines changed: 9, context: html, text, full: html, text
    BRF2 is no longer provisional
  • 1.196 lines changed: 12, context: html, text, full: html, text
    provisionally added BRF2 for Yale
  • 1.195 lines changed: 10, context: html, text, full: html, text
    add 1x25 readType and bow10 mapping method
  • 1.194 lines changed: 8, context: html, text, full: html, text
    Added TFIIIC antibody for Struhl
  • 1.193 lines changed: 32, context: html, text, full: html, text
    Added antibody, fixed antibody tags and spelled insulin correctly
  • 1.192 lines changed: 6, context: html, text, full: html, text
    add insertLength of 400
  • 1.191 lines changed: 7, context: html, text, full: html, text
    Finally got the proper description for Nrf1 antibody
  • 1.190 lines changed: 10, context: html, text, full: html, text
    Added insolin and forskolin treatments for Snyder
  • 1.189 lines changed: 13, context: html, text, full: html, text
    Fixed a number of problems with cut and pasted special chars (alpha,gamma,etc.)
  • 1.188 lines changed: 28, context: html, text, full: html, text
    Added 2 new cell lines for HudsonAlpha
  • 1.187 lines changed: 12, context: html, text, full: html, text
    Six cell lines from provisional to approved for Stam lab
  • 1.186 lines changed: 60, context: html, text, full: html, text
    Added 6 new antibodies for Snyder
  • 1.185 lines changed: 1, context: html, text, full: html, text
    How many changes is this going to take until it is correct?
  • 1.184 lines changed: 5, context: html, text, full: html, text
    add 1x75D
  • 1.183 lines changed: 1, context: html, text, full: html, text
    Nrf1 didn't have a type
  • 1.182 lines changed: 9, context: html, text, full: html, text
    Added Nrf1 as a provisional antibody so that Mike Wilson can get his data in before the freeze
• src/hg/encode/encodeValidate/config/pi.ra
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Restore hyphen for now, for reporting use
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Fix hyphen problem
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Fix hyphen problem
  • 1.7 lines changed: 2, context: html, text, full: html, text
    Adjust Dekker lab entry
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.214 lines changed: 1, context: html, text, full: html, text
    Added support for the phase variable
• src/hg/encode/hgEncodeSubmit/app/controllers/pipeline_controller.rb
  • 1.96 lines changed: 1, context: html, text, full: html, text
    removing status superseded
• src/hg/encode/hgEncodeSubmit/app/views/pipeline/new.rhtml
  • 1.13 lines changed: 1, context: html, text, full: html, text
    more deadline stuff - do not block out admins
  • 1.12 lines changed: 16, context: html, text, full: html, text
    temporary workaround for deadline handling - later do something more complete with freeze-date in yml file and handle security better in controller. we were limited by changes that did not require restarting the server
• src/hg/encode/hgEncodeSubmit/app/views/pipeline/show.rhtml
  • 1.51 lines changed: 8, context: html, text, full: html, text
    temporary workaround for deadline handling - later do something more complete with freeze-date in yml file and handle security better in controller. we were limited by changes that did not require restarting the server
  • 1.50 lines changed: 14, context: html, text, full: html, text
    fixing status to handle more post-"loaded" status values, i.e. to treat them as non-active
  • 1.49 lines changed: 23, context: html, text, full: html, text
    somebody wants showd_af and show_ddf even for loaded status
• src/hg/hgCustom/hgCustom.c
  • 1.136 lines changed: 2, context: html, text, full: html, text
    Added link to BAM format (thanks Ann).
• src/hg/hgTracks/bamTrack.c
  • 1.24 lines changed: 18, context: html, text, full: html, text
    Moving cartOrTdbClosest to library as cartOrTdbString. Making bigBed pay attention to scoreFilter in case where not using linked features.
• src/hg/hgTracks/bedTrack.c
  • 1.23 lines changed: 8, context: html, text, full: html, text
    Making bigBed code in dense mode bypass the fast summary based method if a score filter is on.
  • 1.22 lines changed: 5, context: html, text, full: html, text
    Moving cartOrTdbClosest to library as cartOrTdbString. Making bigBed pay attention to scoreFilter in case where not using linked features.
• src/hg/hgTracks/bigBedTrack.c
  • 1.2 lines changed: 11, context: html, text, full: html, text
    Making bigBed code in dense mode bypass the fast summary based method if a score filter is on.
• src/hg/hgTracks/hgTracks.h
  • 1.197 lines changed: 5, context: html, text, full: html, text
    Making bigBed code in dense mode bypass the fast summary based method if a score filter is on.
• src/hg/hgTracks/simpleTracks.c
  • 1.121 lines changed: 3, context: html, text, full: html, text
    Making bigBed code in dense mode bypass the fast summary based method if a score filter is on.
  • 1.120 lines changed: 2, context: html, text, full: html, text
    Moving cartOrTdbClosest to library as cartOrTdbString. Making bigBed pay attention to scoreFilter in case where not using linked features.
• src/hg/hgc/hgc.c
  • 1.1588 lines changed: 54, context: html, text, full: html, text
    adding vega gene version identifier to those gene clicks
  • 1.1587 lines changed: 4, context: html, text, full: html, text
    Updated doTrnaGenesGb() per Lowe Lab input.
• src/hg/hgc/lowelab.c
  • 1.42 lines changed: 3, context: html, text, full: html, text
    add chrom to select tRNA
• src/hg/inc/cart.h
  • 1.47 lines changed: 10, context: html, text, full: html, text
    Adding cartOrTdbString and related functions.
• src/hg/inc/versionInfo.h
  • 1.164 lines changed: 1, context: html, text, full: html, text
    "New version number v223"
• src/hg/instinct/bioInt2/makeClusterFiles.c
  • 1.6 lines changed: 9, context: html, text, full: html, text
    Added some stuff dealing with pathways with no values, which was causing a seg fault
• src/hg/instinct/extractData/README
  • 1.1 lines changed: 0, context: html, text, full: html, text
    updated
• src/hg/instinct/extractData/example.py
  • 1.1 lines changed: 0, context: html, text, full: html, text
    added python code
• src/hg/instinct/extractData/extractData.c
  • 1.7 lines changed: 8, context: html, text, full: html, text
    added python code
  • 1.6 lines changed: 12, context: html, text, full: html, text
    updated
  • 1.5 lines changed: 188, context: html, text, full: html, text
    updated
  • 1.4 lines changed: 15, context: html, text, full: html, text
    updated
  • 1.3 lines changed: 21, context: html, text, full: html, text
    updated
  • 1.2 lines changed: 36, context: html, text, full: html, text
    updated
  • 1.1 lines changed: 169, context: html, text, full: html, text
    initial commit
• src/hg/instinct/extractData/makefile
  • 1.2 lines changed: 4, context: html, text, full: html, text
    updated
  • 1.1 lines changed: 4, context: html, text, full: html, text
    initial commit
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.TCGAControlAnalysis.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    add TCGA analysis track ra
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.TCGAPublicBrowser.ra
  • 1.8 lines changed: 73, context: html, text, full: html, text
    
  • 1.7 lines changed: 3, context: html, text, full: html, text
    
  • 1.6 lines changed: 3, context: html, text, full: html, text
    
  • 1.5 lines changed: 1, context: html, text, full: html, text
    
  • 1.4 lines changed: 20, context: html, text, full: html, text
    
  • 1.3 lines changed: 1, context: html, text, full: html, text
    
  • 1.2 lines changed: 21, context: html, text, full: html, text
    
• src/hg/instinct/hgHeatmap2/hgHeatmapFrontend/index.html
  • 1.36 lines changed: 1, context: html, text, full: html, text
    Updated position box to accept return, also allow caps CHR and single chrom for jumping to the GB
• src/hg/instinct/hgHeatmap2/hgHeatmapFrontend/js/hgHeatmap.js
  • 1.77 lines changed: 19, context: html, text, full: html, text
    Updated position box to accept return, also allow caps CHR and single chrom for jumping to the GB
• src/hg/instinct/webUserAdmin/webUserAdmin.c
  • 1.12 lines changed: 11, context: html, text, full: html, text
    Added an error msg when the hg.conf variables aren't defined, also removed hard references to fan and instead pull from adminEmail
• src/hg/lib/cart.c
  • 1.116 lines changed: 29, context: html, text, full: html, text
    Adding cartOrTdbString and related functions.
• src/hg/makeDb/doc/ce6.txt
  • 1.18 lines changed: 62, context: html, text, full: html, text
    adding algBinding tracks
• src/hg/makeDb/doc/hg18.txt
  • 1.394 lines changed: 132, context: html, text, full: html, text
    Added NHGRI GWAS catalog track.
• src/hg/makeDb/doc/hg19.txt
  • 1.71 lines changed: 21, context: html, text, full: html, text
    vega Gene update done v36 for hg19 v37 for mm9
• src/hg/makeDb/doc/macEug1.txt
  • 1.2 lines changed: 44, context: html, text, full: html, text
    running genbank for Wallaby
• src/hg/makeDb/doc/mm9.txt
  • 1.120 lines changed: 19, context: html, text, full: html, text
    vega Gene update done v36 for hg19 v37 for mm9
• src/hg/makeDb/doc/oryCun2.txt
  • 1.4 lines changed: 61, context: html, text, full: html, text
    done with genbank for rabbit
• src/hg/makeDb/doc/sacCer2.txt
  • 1.15 lines changed: 13, context: html, text, full: html, text
    add liftOver to sacCer1
• src/hg/makeDb/doc/tetNig1.txt
  • 1.21 lines changed: 12, context: html, text, full: html, text
    liftOver to tetNig2 done
• src/hg/makeDb/doc/visiGene.txt
  • 1.13 lines changed: 9, context: html, text, full: html, text
    handling blank itemUrl
• src/hg/makeDb/genbank/doc/to-do.txt
  • 1.120 lines changed: 3, context: html, text, full: html, text
    added to-do case
• src/hg/makeDb/genbank/etc/genbank.conf
  • 1.357 lines changed: 14, context: html, text, full: html, text
    adding susScr1 Pig
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • 1.104 lines changed: 1, context: html, text, full: html, text
    adding tetNig2
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • 1.75 lines changed: 3, context: html, text, full: html, text
    adding susScr - Pig
• src/hg/makeDb/hgCgiData/Human/microarrayGroups.ra
  • 1.100 lines changed: 12, context: html, text, full: html, text
    
  • 1.99 lines changed: 11, context: html, text, full: html, text
    
• src/hg/makeDb/schema/all.joiner
  • 1.765 lines changed: 5, context: html, text, full: html, text
    added ALG Binding tables to ce tablesIgnored
  • 1.764 lines changed: 1, context: html, text, full: html, text
    add aplCal to the gbd variable
  • 1.763 lines changed: 1, context: html, text, full: html, text
    add aplCal to the xrg variable
  • 1.762 lines changed: 2, context: html, text, full: html, text
    added tetNig2 to Human Proteins rules
  • 1.761 lines changed: 2, context: html, text, full: html, text
    Added aplCal1 to the blastHg18* identifiers
• src/hg/makeDb/trackDb/README
  • 1.96 lines changed: 89, context: html, text, full: html, text
    Changing README per view-in-the-middle
• src/hg/makeDb/trackDb/blastHg18KG.html
  • 1.7 lines changed: 1, context: html, text, full: html, text
    changed reference to 'Known Genes track' to 'UCSC Genes track'
• src/hg/makeDb/trackDb/cat/felCat3/trackDb.ra
  • 1.25 lines changed: 6, context: html, text, full: html, text
    moved all canFam2 chainNets to composite and dropped individual tracks. canFam2 hg18 hg19 mm9 monDom4 ornAna1 panTro2 ponAbe2 rheMac2 are live on RR
• src/hg/makeDb/trackDb/cow/bosTau4/trackDb.ra
  • 1.20 lines changed: 7, context: html, text, full: html, text
    moved all canFam2 chainNets to composite and dropped individual tracks. canFam2 hg18 hg19 mm9 monDom4 ornAna1 panTro2 ponAbe2 rheMac2 are live on RR
• src/hg/makeDb/trackDb/dog/canFam2/trackDb.ra
  • 1.43 lines changed: 6, context: html, text, full: html, text
    moved all bosTau4 chainNets to composite and dropped individual tracks. hg19, hg18, mm9, canFam2, ornAna1 are live on RR
• src/hg/makeDb/trackDb/dog/trackDb.ra
  • 1.32 lines changed: 8, context: html, text, full: html, text
    moved all bosTau4 chainNets to composite and dropped individual tracks. hg19, hg18, mm9, canFam2, ornAna1 are live on RR
  • 1.31 lines changed: 28, context: html, text, full: html, text
    moved all bosTau1&2 chainNets to composite and dropped individual tracks. hg17, mm7 are live on RR
• src/hg/makeDb/trackDb/horse/trackDb.ra
  • 1.22 lines changed: 8, context: html, text, full: html, text
    moved all canFam2 chainNets to composite and dropped individual tracks. canFam2 hg18 hg19 mm9 monDom4 ornAna1 panTro2 ponAbe2 rheMac2 are live on RR
• src/hg/makeDb/trackDb/human/hg17/trackDb.chainNet.ra
  • 1.10 lines changed: 3, context: html, text, full: html, text
    moved all bosTau1&2 chainNets to composite and dropped individual tracks. hg17, mm7 are live on RR
• src/hg/makeDb/trackDb/human/hg17/trackDb.ra
  • 1.436 lines changed: 20, context: html, text, full: html, text
    moved all canFam2 chainNets to composite and dropped individual tracks. canFam2 hg18 hg19 mm9 monDom4 ornAna1 panTro2 ponAbe2 rheMac2 are live on RR
  • 1.435 lines changed: 40, context: html, text, full: html, text
    moved all bosTau1&2 chainNets to composite and dropped individual tracks. hg17, mm7 are live on RR
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.453 lines changed: 22, context: html, text, full: html, text
    moved all canFam2 chainNets to composite and dropped individual tracks. canFam2 hg18 hg19 mm9 monDom4 ornAna1 panTro2 ponAbe2 rheMac2 are live on RR
  • 1.452 lines changed: 24, context: html, text, full: html, text
    moved all bosTau1&2 chainNets to composite and dropped individual tracks. hg17, mm7 are live on RR
  • 1.451 lines changed: 82, context: html, text, full: html, text
    Added personal genome variants that were lifted from hg18 to hg19.
  • 1.450 lines changed: 14, context: html, text, full: html, text
    Removed block for chainFelCat1. This table does not exist in the hg18 db, and there is no reference to it in the hg18 make doc.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.775 lines changed: 9, context: html, text, full: html, text
    Fixed some UCD(Farnham) metadata
  • 1.774 lines changed: 1, context: html, text, full: html, text
    forgot the big on the bed again...
  • 1.773 lines changed: 10, context: html, text, full: html, text
    ENCODE RIKEN CAGE Tags (longNonPolyA in H1-hESC cell) alignments
  • 1.772 lines changed: 61, context: html, text, full: html, text
    Added Yale UCD(Farnham)s 3 Jan 2010 submissions
  • 1.771 lines changed: 2, context: html, text, full: html, text
    oops... need a bigBed on that last commit
  • 1.770 lines changed: 41, context: html, text, full: html, text
    ENCODE RIKEN CAGE Tags (longNonPolyA in NHEK nucleus)
  • 1.769 lines changed: 21, context: html, text, full: html, text
    Riken CAGE Gm12878Nucleolus signals
  • 1.768 lines changed: 21, context: html, text, full: html, text
    ENCODE Riken CAGE H1hESC
  • 1.767 lines changed: 20, context: html, text, full: html, text
    CSHL short RNA-seq GM12878 K562 whole cell
  • 1.766 lines changed: 20, context: html, text, full: html, text
    add RIKEN CAGE plus and minus clusters for HUVEC cytosol
  • 1.765 lines changed: 11, context: html, text, full: html, text
    RIKEN Rna-seq GM12878 nucleolus
  • 1.764 lines changed: 11, context: html, text, full: html, text
    Riken RNA-seq HUVEC alignments
  • 1.763 lines changed: 51, context: html, text, full: html, text
    add CalTech RNA-seq NHEK directional 1x75
  • 1.762 lines changed: 30, context: html, text, full: html, text
    Caltech RNA-seq H1hesc paired end
  • 1.761 lines changed: 6, context: html, text, full: html, text
    Fix to Open Chromatin setting which had a tag problem
  • 1.760 lines changed: 1, context: html, text, full: html, text
    fix silly toed typo
  • 1.759 lines changed: 52, context: html, text, full: html, text
    adding H1hesc directional to Caltech RNA-seq
  • 1.758 lines changed: 12, context: html, text, full: html, text
    added viewLimits settings for the six new Open Chromatin tracks
  • 1.757 lines changed: 28, context: html, text, full: html, text
    Added one more Open Chromatin track
  • 1.756 lines changed: 136, context: html, text, full: html, text
    Added 6 new Open Chromatin tracks
  • 1.755 lines changed: 344, context: html, text, full: html, text
    Added 9 more submissions (39 tables) for HAIB TFSB
  • 1.754 lines changed: 913, context: html, text, full: html, text
    Added 21 new submissions for HAIB TFSB
• src/hg/makeDb/trackDb/human/hg19/cons46way.html
  • 1.10 lines changed: 6, context: html, text, full: html, text
    added danRer6 links to new browser
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.83 lines changed: 26, context: html, text, full: html, text
    adding hg19 vegaGeneComposite track;
  • 1.82 lines changed: 27, context: html, text, full: html, text
    Added personal genome variants that were lifted from hg18 to hg19.
  • 1.81 lines changed: 10, context: html, text, full: html, text
    Added tRNAs track from Lowe Lab.
• src/hg/makeDb/trackDb/human/hg19/vegaGeneComposite.html
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Adding chromosome definitions for vegaGene on hg19
• src/hg/makeDb/trackDb/human/trackDb.chainNet.ra
  • 1.30 lines changed: 1, context: html, text, full: html, text
    moved all bosTau3 chainNets to composite and dropped individual tracks. hg18, mm8 are live on RR
  • 1.29 lines changed: 1, context: html, text, full: html, text
    moved all bosTau1&2 chainNets to composite and dropped individual tracks. hg17, mm7 are live on RR
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.493 lines changed: 13, context: html, text, full: html, text
    moved all canFam2 chainNets to composite and dropped individual tracks. canFam2 hg18 hg19 mm9 monDom4 ornAna1 panTro2 ponAbe2 rheMac2 are live on RR
  • 1.492 lines changed: 7, context: html, text, full: html, text
    moved all bosTau4 chainNets to composite and dropped individual tracks. hg19, hg18, mm9, canFam2, ornAna1 are live on RR
  • 1.491 lines changed: 6, context: html, text, full: html, text
    moved all bosTau3 chainNets to composite and dropped individual tracks. hg18, mm8 are live on RR
  • 1.490 lines changed: 6, context: html, text, full: html, text
    moved all bosTau1&2 chainNets to composite and dropped individual tracks. hg17, mm7 are live on RR
  • 1.489 lines changed: 81, context: html, text, full: html, text
    Added personal genome variants that were lifted from hg18 to hg19.
• src/hg/makeDb/trackDb/mouse/mm7/trackDb.chainNet.ra
  • 1.8 lines changed: 3, context: html, text, full: html, text
    moved all bosTau1&2 chainNets to composite and dropped individual tracks. hg17, mm7 are live on RR
• src/hg/makeDb/trackDb/mouse/mm7/trackDb.ra
  • 1.60 lines changed: 3, context: html, text, full: html, text
    moved all canFam2 chainNets to composite and dropped individual tracks. canFam2 hg18 hg19 mm9 monDom4 ornAna1 panTro2 ponAbe2 rheMac2 are live on RR
  • 1.59 lines changed: 3, context: html, text, full: html, text
    moved all bosTau1&2 chainNets to composite and dropped individual tracks. hg17, mm7 are live on RR
• src/hg/makeDb/trackDb/mouse/mm8/trackDb.chainNet.ra
  • 1.9 lines changed: 3, context: html, text, full: html, text
    moved all bosTau1&2 chainNets to composite and dropped individual tracks. hg17, mm7 are live on RR
• src/hg/makeDb/trackDb/mouse/mm8/trackDb.ra
  • 1.63 lines changed: 22, context: html, text, full: html, text
    moved all bosTau3 chainNets to composite and dropped individual tracks. hg18, mm8 are live on RR
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.chainNet.ra
  • 1.3 lines changed: 3, context: html, text, full: html, text
    moved all bosTau4 chainNets to composite and dropped individual tracks. hg19, hg18, mm9, canFam2, ornAna1 are live on RR
  • 1.2 lines changed: 3, context: html, text, full: html, text
    moved all bosTau3 chainNets to composite and dropped individual tracks. hg18, mm8 are live on RR
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • 1.75 lines changed: 10, context: html, text, full: html, text
    Added tRNAs track.
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • 1.183 lines changed: 7, context: html, text, full: html, text
    Switched all chainFelCat3 and netFelCat3 tracks to be composite chainNetFelCat3 tracks.
  • 1.182 lines changed: 28, context: html, text, full: html, text
    moved all canFam2 chainNets to composite and dropped individual tracks. canFam2 hg18 hg19 mm9 monDom4 ornAna1 panTro2 ponAbe2 rheMac2 are live on RR
  • 1.181 lines changed: 7, context: html, text, full: html, text
    moved all bosTau3 chainNets to composite and dropped individual tracks. hg18, mm8 are live on RR
  • 1.180 lines changed: 30, context: html, text, full: html, text
    moved all bosTau1&2 chainNets to composite and dropped individual tracks. hg17, mm7 are live on RR
• src/hg/makeDb/trackDb/opossum/monDom5/trackDb.ra
  • 1.25 lines changed: 10, context: html, text, full: html, text
    moved all canFam2 chainNets to composite and dropped individual tracks. canFam2 hg18 hg19 mm9 monDom4 ornAna1 panTro2 ponAbe2 rheMac2 are live on RR
• src/hg/makeDb/trackDb/platypus/ornAna1/trackDb.ra
  • 1.17 lines changed: 4, context: html, text, full: html, text
    moved all bosTau4 chainNets to composite and dropped individual tracks. hg19, hg18, mm9, canFam2, ornAna1 are live on RR
• src/hg/makeDb/trackDb/rat/rn3/trackDb.ra
  • 1.66 lines changed: 22, context: html, text, full: html, text
    moved all canFam2 chainNets to composite and dropped individual tracks. canFam2 hg18 hg19 mm9 monDom4 ornAna1 panTro2 ponAbe2 rheMac2 are live on RR
• src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
  • 1.48 lines changed: 6, context: html, text, full: html, text
    moved all canFam2 chainNets to composite and dropped individual tracks. canFam2 hg18 hg19 mm9 monDom4 ornAna1 panTro2 ponAbe2 rheMac2 are live on RR
  • 1.47 lines changed: 10, context: html, text, full: html, text
    Added tRNAs track for rn4.
• src/hg/makeDb/trackDb/rat/trackDb.chainNet.ra
  • 1.15 lines changed: 1, context: html, text, full: html, text
    moved all bosTau1&2 chainNets to composite and dropped individual tracks. hg17, mm7 are live on RR
• src/hg/makeDb/trackDb/rat/trackDb.ra
  • 1.67 lines changed: 7, context: html, text, full: html, text
    moved all canFam2 chainNets to composite and dropped individual tracks. canFam2 hg18 hg19 mm9 monDom4 ornAna1 panTro2 ponAbe2 rheMac2 are live on RR
  • 1.66 lines changed: 8, context: html, text, full: html, text
    moved all bosTau3 chainNets to composite and dropped individual tracks. hg18, mm8 are live on RR
  • 1.65 lines changed: 6, context: html, text, full: html, text
    moved all bosTau1&2 chainNets to composite and dropped individual tracks. hg17, mm7 are live on RR
• src/hg/makeDb/trackDb/tRNAs.html
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Added tRNAs.html from Lowe Lab at the top level (applicable for all genomes).
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • 1.37 lines changed: 8, context: html, text, full: html, text
    moved all bosTau4 chainNets to composite and dropped individual tracks. hg19, hg18, mm9, canFam2, ornAna1 are live on RR
  • 1.36 lines changed: 4, context: html, text, full: html, text
    moved all bosTau3 chainNets to composite and dropped individual tracks. hg18, mm8 are live on RR
  • 1.35 lines changed: 7, context: html, text, full: html, text
    moved all bosTau1&2 chainNets to composite and dropped individual tracks. hg17, mm7 are live on RR
  • 1.34 lines changed: 2, context: html, text, full: html, text
    changed shortLabel chain and netBosTau1 o_db as it is only on dev
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.582 lines changed: 77, context: html, text, full: html, text
    moved all bosTau4 chainNets to composite and dropped individual tracks. hg19, hg18, mm9, canFam2, ornAna1 are live on RR
  • 1.581 lines changed: 27, context: html, text, full: html, text
    moved all bosTau3 chainNets to composite and dropped individual tracks. hg18, mm8 are live on RR
  • 1.580 lines changed: 29, context: html, text, full: html, text
    moved all bosTau1&2 chainNets to composite and dropped individual tracks. hg17, mm7 are live on RR
• src/hg/makeDb/trackDb/worm/ce6/algBinding.html
  • 1.2 lines changed: 50, context: html, text, full: html, text
    Edited this file for typos & style.
  • 1.1 lines changed: 50, context: html, text, full: html, text
    Adding ALG-1 Argonaute binding sites from the Yeo lab.
• src/hg/makeDb/trackDb/worm/ce6/trackDb.ra
  • 1.20 lines changed: 17, context: html, text, full: html, text
    appropriate visibility defaults for algBinding track
  • 1.19 lines changed: 170, context: html, text, full: html, text
    Adding ALG-1 Argonaute binding sites from the Yeo lab.
• src/hg/makeDb/trackDb/zebrafish/danRer6/description.html
  • 1.3 lines changed: 4, context: html, text, full: html, text
    removed collorabtors who did not add to this assembly
  • 1.2 lines changed: 68, context: html, text, full: html, text
    Edited the zv8 assembly description.
• src/hg/utils/automation/doEnsGeneUpdate.pl
  • 1.22 lines changed: 1, context: html, text, full: html, text
    proper .ra name for vegaGene
  • 1.21 lines changed: 37, context: html, text, full: html, text
    finish doCleanup for vegaGene
  • 1.20 lines changed: 122, context: html, text, full: html, text
    adding vegaGene processing option
• src/hg/utils/refreshNamedSessionCustomTracks/refreshNamedSessionCustomTracks.c
  • 1.11 lines changed: 24, context: html, text, full: html, text
    Added option -atime=N: if a session's lastUsed is older than N days, don't refresh its custom tracks.
• src/hg/visiGene/hgVisiGene/hgVisiGene.c
  • 1.102 lines changed: 2, context: html, text, full: html, text
    handling blank itemUrl
• src/hg/visiGene/hgVisiGene/printCaption.c
  • 1.27 lines changed: 8, context: html, text, full: html, text
    handling blank itemUrl
• src/lib/cheapcgi.c
  • 1.130 lines changed: 3, context: html, text, full: html, text
    Fixed another old assumption about cookie format that user's cookie has broken: ';' was assumed to always be followed by ' ', but it might not be.
  • 1.129 lines changed: 4, context: html, text, full: html, text
    parseCookies: fixed bug that caused us to errAbort if cookie string ends with ';'.
• src/lib/https.c
  • 1.4 lines changed: 1, context: html, text, full: html, text
    fix compile when USE_SSL is not set
• src/parasol/version.doc
  • 1.47 lines changed: 3, context: html, text, full: html, text
    added note on -env option
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.96 lines changed: 3, context: html, text, full: html, text
    v223 final build
• src/utils/qa/weeklybld/cvs-reports-d
  • 1.15 lines changed: 2, context: html, text, full: html, text
    trying to avoid erroring on temporary cvs lock

• lines changed: 4810
• files changed: 90