CVS changes by file

review to branch (2010-01-26 to 2010-02-02) v224

• src/hg/archaeStuff/data/Genome-info-euk
  • 1.18 lines changed: 5, context: html, text, full: html, text
    change Ptric to v2.0
• src/hg/archaeStuff/data/Genome-info-mods
  • 1.96 lines changed: 1, context: html, text, full: html, text
    Fixed cren ordering
• src/hg/archaeStuff/scripts/archaeBrowser/Constant.pm
  • 1.39 lines changed: 9, context: html, text, full: html, text
    Made changes to move our /trackDb/lowelab/* structure from the kent CVS tree to the lowelab CVS tree
• src/hg/archaeStuff/scripts/archaeBrowser/OrganismDb.pm
  • 1.49 lines changed: 18, context: html, text, full: html, text
    Updated cytoband to handle plasmid-sized contigs better
  • 1.48 lines changed: 24, context: html, text, full: html, text
    Added cytoBand function to aid genome navigation
• src/hg/archaeStuff/scripts/archaeBrowser/Track.pm
  • 1.14 lines changed: 5, context: html, text, full: html, text
    Made changes to move our /trackDb/lowelab/* structure from the kent CVS tree to the lowelab CVS tree
• src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
  • 1.25 lines changed: 10, context: html, text, full: html, text
    Altered sort order. take only last matching line of metadata from fileDb.ra. Don't show antibody if its eq input
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.205 lines changed: 1, context: html, text, full: html, text
    Add label for reporting cosmetics
  • 1.204 lines changed: 111, context: html, text, full: html, text
    Added sex information for the human cell lines.
  • 1.203 lines changed: 22, context: html, text, full: html, text
    Minor adjustments to cell descriptions and officially added UCDavis as control type. This had been implied for some time.
  • 1.202 lines changed: 8, context: html, text, full: html, text
    Unify RNA-seq here for reporting -- will do for trackDb when convenient
  • 1.201 lines changed: 12, context: html, text, full: html, text
    Changed Mouse_IgG to IgG-mus and Rabbit_IgG to IgG-rab
• src/hg/encode/encodeValidate/config/pi.ra
  • 1.12 lines changed: 36, context: html, text, full: html, text
    Add synonmous entries for labs to accomodate inconsistent DAFs; Distinguish mouse labs
  • 1.11 lines changed: 1, context: html, text, full: html, text
    Tweak for consistency
• src/hg/encode/encodeValidate/doEncodeReport.pl
  • 1.14 lines changed: 27, context: html, text, full: html, text
    Fixes to lab handling and NHGRI factor reporting
  • 1.13 lines changed: 26, context: html, text, full: html, text
    Add support for additional NHGRI reporting fields
  • 1.12 lines changed: 11, context: html, text, full: html, text
    Tweak around trackDb insconsistencies
• src/hg/encode/encodeValidate/doReport.csh
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Wrapper for reporting, suitable for cron use, but still has some user-specific stuff
• src/hg/encode/encodeValidate/manual.all.txt
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Temp manual report for certain data types
• src/hg/encode/hgEncodeSubmit/app/controllers/pipeline_controller.rb
  • 1.97 lines changed: 4, context: html, text, full: html, text
    adding deadline setting instead of hardwiring it, tolerates missing deadline.yml
• src/hg/encode/hgEncodeSubmit/app/views/pipeline/new.rhtml
  • 1.14 lines changed: 3, context: html, text, full: html, text
    adding deadline setting instead of hardwiring it, tolerates missing deadline.yml
• src/hg/encode/hgEncodeSubmit/app/views/pipeline/show.rhtml
  • 1.53 lines changed: 4, context: html, text, full: html, text
    adding deadline setting instead of hardwiring it, tolerates missing deadline.yml
• src/hg/encode/hgEncodeSubmit/config/deadline.yml.sample
  • 1.1 lines changed: 0, context: html, text, full: html, text
    adding deadline setting instead of hardwiring it, tolerates missing deadline.yml
• src/hg/encode/hgEncodeSubmit/lib/pipeline_background.rb
  • 1.19 lines changed: 7, context: html, text, full: html, text
    adding deadline setting instead of hardwiring it, tolerates missing deadline.yml
• src/hg/hgTracks/searchTracks.c
  • 1.1 lines changed: 0, context: html, text, full: html, text
    very rough prototype for search tracks
• src/hg/hgc/hgc.c
  • 1.1595 lines changed: 11, context: html, text, full: html, text
    genericChainClick: fixed bug noticed by Katrina: we weren't checking the chainLinearGap trackDb setting, so when recalculating score-in-window, we used incorrect gap penalties unless the default loose penalties were used. Also, recalculating score-in-window had the unexpected side effect of clobbering the original chain's score when the whole chain fit in the window, because chainSubSetOnT was returning the original chain! I took out the score-in-window stuff for chains that fit in the window, and added a position link for the ref. genome (like we have on all of our other pages).
• src/hg/hgc/lowelab.c
  • 1.43 lines changed: 139, context: html, text, full: html, text
    add doCRISPRs() for lowelab CRISPRs track
• src/hg/inc/versionInfo.h
  • 1.165 lines changed: 1, context: html, text, full: html, text
    "New version number v224"
• src/hg/instinct/hgGeneset/cluster.c
  • 1.1 lines changed: 0, context: html, text, full: html, text
    added clustering
• src/hg/instinct/hgGeneset/cluster.h
  • 1.1 lines changed: 0, context: html, text, full: html, text
    added clustering
• src/hg/instinct/hgGeneset/drawingCode.c
  • 1.4 lines changed: 243, context: html, text, full: html, text
    added labels/thumbnail
  • 1.3 lines changed: 12, context: html, text, full: html, text
    rotated maps
• src/hg/instinct/hgGeneset/frontend/css/hgHeatmapStyle.css
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Added start of file upload fxn
  • 1.4 lines changed: 22, context: html, text, full: html, text
    Dragging working
  • 1.3 lines changed: 33, context: html, text, full: html, text
    Got the pieces of the image in there
  • 1.2 lines changed: 41, context: html, text, full: html, text
    First cut, it's ugly but it works (kinda)
• src/hg/instinct/hgGeneset/frontend/css/uploadWidget.css
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Adding files necessary for upload widget
• src/hg/instinct/hgGeneset/frontend/genesetView.html
  • 1.4 lines changed: 9, context: html, text, full: html, text
    Dragging working
  • 1.3 lines changed: 30, context: html, text, full: html, text
    Got the pieces of the image in there
  • 1.2 lines changed: 37, context: html, text, full: html, text
    First cut, it's ugly but it works (kinda)
• src/hg/instinct/hgGeneset/frontend/img/XPButtonUploadText_61x22.png
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Adding files necessary for upload widget
• src/hg/instinct/hgGeneset/frontend/js/hgHeatmapGeneset.js
  • 1.5 lines changed: 9, context: html, text, full: html, text
    Added start of file upload fxn
  • 1.4 lines changed: 116, context: html, text, full: html, text
    Dragging working
  • 1.3 lines changed: 31, context: html, text, full: html, text
    Got the pieces of the image in there
  • 1.2 lines changed: 134, context: html, text, full: html, text
    First cut, it's ugly but it works (kinda)
• src/hg/instinct/hgGeneset/frontend/js/swfupload.cookies.js
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Adding files necessary for upload widget
• src/hg/instinct/hgGeneset/frontend/js/swfupload.js
  • 1.2 lines changed: 0, context: html, text, full: html, text
    Fixing bad line-endings
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Adding files necessary for upload widget
• src/hg/instinct/hgGeneset/frontend/js/swfuploadExtend.js
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Adding files necessary for upload widget
• src/hg/instinct/hgGeneset/frontend/swf/swfupload.swf
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Adding files necessary for upload widget
• src/hg/instinct/hgGeneset/frontend/uploadWidget.html
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Adding files necessary for upload widget
• src/hg/instinct/hgGeneset/hgGenesets.c
  • 1.14 lines changed: 33, context: html, text, full: html, text
    Added start of file upload fxn
  • 1.13 lines changed: 211, context: html, text, full: html, text
    added sorting
  • 1.12 lines changed: 168, context: html, text, full: html, text
    added search
  • 1.11 lines changed: 84, context: html, text, full: html, text
    updated json return
  • 1.10 lines changed: 6, context: html, text, full: html, text
    added labels/thumbnail
  • 1.9 lines changed: 27, context: html, text, full: html, text
    added 2D clustering
  • 1.8 lines changed: 4, context: html, text, full: html, text
    rotated maps
  • 1.7 lines changed: 37, context: html, text, full: html, text
    First cut, it's ugly but it works (kinda)
  • 1.6 lines changed: 7, context: html, text, full: html, text
    added option to grab first N genes in dataset
  • 1.5 lines changed: 116, context: html, text, full: html, text
    added clustering
• src/hg/instinct/hgGeneset/hgGenesets.h
  • 1.10 lines changed: 2, context: html, text, full: html, text
    Added start of file upload fxn
  • 1.9 lines changed: 12, context: html, text, full: html, text
    added sorting
  • 1.8 lines changed: 6, context: html, text, full: html, text
    added search
  • 1.7 lines changed: 23, context: html, text, full: html, text
    added labels/thumbnail
  • 1.6 lines changed: 1, context: html, text, full: html, text
    First cut, it's ugly but it works (kinda)
  • 1.5 lines changed: 1, context: html, text, full: html, text
    added option to grab first N genes in dataset
  • 1.4 lines changed: 2, context: html, text, full: html, text
    added clustering
• src/hg/instinct/hgGeneset/hgStats.c
  • 1.4 lines changed: 57, context: html, text, full: html, text
    added 2D clustering
  • 1.3 lines changed: 6, context: html, text, full: html, text
    fixed clustering
  • 1.2 lines changed: 2, context: html, text, full: html, text
    rotated maps
  • 1.1 lines changed: 65, context: html, text, full: html, text
    added clustering
• src/hg/instinct/hgGeneset/hgStats.h
  • 1.2 lines changed: 5, context: html, text, full: html, text
    added 2D clustering
  • 1.1 lines changed: 5, context: html, text, full: html, text
    added clustering
• src/hg/instinct/hgGeneset/makefile
  • 1.3 lines changed: 1, context: html, text, full: html, text
    added clustering
• src/hg/js/hui.js
  • 1.49 lines changed: 7, context: html, text, full: html, text
    Neglected 4 state subCBs in last check in
  • 1.48 lines changed: 9, context: html, text, full: html, text
    Changes to speed up matrix buttons
• src/hg/lib/customFactory.c
  • 1.115 lines changed: 19, context: html, text, full: html, text
    emergency fix for customTrash db server going offline
• src/hg/lib/hui.c
  • 1.255 lines changed: 9, context: html, text, full: html, text
    Show subId in metadata and hide antibody if it is really input.
• src/hg/lib/trackDbCustom.c
  • 1.75 lines changed: 1, context: html, text, full: html, text
    fixed incorrect on-the-fly parse of superTrack setting
• src/hg/makeDb/doc/danRer6.txt
  • 1.16 lines changed: 20, context: html, text, full: html, text
    adding chromosomes/ download
• src/hg/makeDb/doc/hg18.txt
  • 1.396 lines changed: 24, context: html, text, full: html, text
    Renamed tables and added trackDb entry for the CRG mappability subtracks of the ENCODE Mapability track.
• src/hg/makeDb/doc/hg19.txt
  • 1.77 lines changed: 76, context: html, text, full: html, text
    Re-loading new data for the genomic segmental duplications track - in progress.
  • 1.76 lines changed: 27, context: html, text, full: html, text
    Renamed tables and added trackDb entry for the CRG mappability tracks as part of an ENCODE Mapability track.
• src/hg/makeDb/doc/sacCer2.txt
  • 1.16 lines changed: 16, context: html, text, full: html, text
    include definition of chain.csh script
• src/hg/makeDb/genbank/etc/align.dbs
  • 1.109 lines changed: 2, context: html, text, full: html, text
    disable ailMel1 (panda), as the genome is starting over
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • 1.113 lines changed: 2, context: html, text, full: html, text
    disable ailMel1 (panda), as the genome is starting over
• src/hg/makeDb/trackDb/chicken/galGal2/trackDb.chainNet.ra
  • 1.5 lines changed: 3, context: html, text, full: html, text
    moved all xenTro1 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/chicken/galGal2/trackDb.ra
  • 1.76 lines changed: 3, context: html, text, full: html, text
    moved all xenTro1 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/chicken/galGal3/trackDb.chainNet.ra
  • 1.4 lines changed: 6, context: html, text, full: html, text
    Changed horse chain and net shortLabels to match chainNet shortLabels.
  • 1.3 lines changed: 6, context: html, text, full: html, text
    Adding chain and net shortLabel overrides for opossum to match the chainNet overrides.
• src/hg/makeDb/trackDb/chicken/trackDb.ra
  • 1.19 lines changed: 7, context: html, text, full: html, text
    Removing trackDb.ra refs to ponAbe2 nets and chains -- these are in composites now.
• src/hg/makeDb/trackDb/chimp/panTro1/trackDb.chainNet.ra
  • 1.3 lines changed: 2, context: html, text, full: html, text
    changed animal name to o_Organism for several
• src/hg/makeDb/trackDb/chimp/panTro2/trackDb.ra
  • 1.51 lines changed: 6, context: html, text, full: html, text
    Removing trackDb.ra refs to ponAbe2 nets and chains -- these are in composites now.
• src/hg/makeDb/trackDb/chimp/trackDb.chainNet.ra
  • 1.11 lines changed: 6, context: html, text, full: html, text
    Adding chain and net shortLabel overrides for opossum to match the chainNet overrides.
• src/hg/makeDb/trackDb/chimp/trackDb.ra
  • 1.30 lines changed: 14, context: html, text, full: html, text
    moved all mm7 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/cow/bosTau1/trackDb.ra
  • 1.19 lines changed: 8, context: html, text, full: html, text
    moved all mm6 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/cow/bosTau2/trackDb.chainNet.ra
  • 1.4 lines changed: 6, context: html, text, full: html, text
    moved all mm7 chains and nets to composite and dropped individual tracks
  • 1.3 lines changed: 2, context: html, text, full: html, text
    changed animal name to o_Organism for several
• src/hg/makeDb/trackDb/dog/canFam1/trackDb.chainNet.ra
  • 1.4 lines changed: 6, context: html, text, full: html, text
    moved all mm7 chains and nets to composite and dropped individual tracks
  • 1.3 lines changed: 5, context: html, text, full: html, text
    changed animal name to o_Organism for several
• src/hg/makeDb/trackDb/dog/canFam1/trackDb.ra
  • 1.39 lines changed: 8, context: html, text, full: html, text
    moved all mm6 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/dog/canFam2/trackDb.chainNet.ra
  • 1.5 lines changed: 5, context: html, text, full: html, text
    Changed horse chain and net shortLabels to match chainNet shortLabels.
  • 1.4 lines changed: 3, context: html, text, full: html, text
    Removing override for chainNetMonDom4 shortLabel, as this is also done at the dog level.
• src/hg/makeDb/trackDb/dog/canFam2/trackDb.ra
  • 1.48 lines changed: 10, context: html, text, full: html, text
    Removed trackDb.ra refs to equCab1 net and chain -- these are in composites now.
• src/hg/makeDb/trackDb/dog/trackDb.chainNet.ra
  • 1.15 lines changed: 1, context: html, text, full: html, text
    moved all mm7 chains and nets to composite and dropped individual tracks
  • 1.14 lines changed: 6, context: html, text, full: html, text
    Adding chain and net shortLabel overrides for opossum to match the chainNet overrides.
• src/hg/makeDb/trackDb/dog/trackDb.ra
  • 1.39 lines changed: 11, context: html, text, full: html, text
    moved all mm7 chains and nets to composite and dropped individual tracks
  • 1.38 lines changed: 6, context: html, text, full: html, text
    moved all mm6 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/elephant/trackDb.chainNet.ra
  • 1.3 lines changed: 1, context: html, text, full: html, text
    moved all mm7 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/human/hg16/trackDb.chainNet.ra
  • 1.6 lines changed: 6, context: html, text, full: html, text
    moved all mm7 chains and nets to composite and dropped individual tracks
  • 1.5 lines changed: 3, context: html, text, full: html, text
    moved all mm6 chains and nets to composite and dropped individual tracks
  • 1.4 lines changed: 3, context: html, text, full: html, text
    changed animal name to o_Organism for several
• src/hg/makeDb/trackDb/human/hg16/trackDb.ra
  • 1.584 lines changed: 8, context: html, text, full: html, text
    moved all mm6 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/human/hg17/trackDb.chainNet.ra
  • 1.17 lines changed: 6, context: html, text, full: html, text
    Changed bosTau2 chain and net shortLabels to match chainNet shortLabels.
  • 1.16 lines changed: 6, context: html, text, full: html, text
    moved all mm7 chains and nets to composite and dropped individual tracks
  • 1.15 lines changed: 9, context: html, text, full: html, text
    Added o_db shortLabels to panTro2 chainNet and chain and net.
  • 1.14 lines changed: 6, context: html, text, full: html, text
    Adding chain and net shortLabel overrides for opossum to match the chainNet overrides.
  • 1.13 lines changed: 4, context: html, text, full: html, text
    changed some explicit animal names to 0_Organism, including chainNetXenTro1 which shold not have said Tetraodon in the first place
• src/hg/makeDb/trackDb/human/hg17/trackDb.ra
  • 1.444 lines changed: 8, context: html, text, full: html, text
    moved all mm7 chains and nets to composite and dropped individual tracks
  • 1.443 lines changed: 6, context: html, text, full: html, text
    moved all mm6 chains and nets to composite and dropped individual tracks
  • 1.442 lines changed: 24, context: html, text, full: html, text
    Removed lingering release beta on panTro2 chain and net.
  • 1.441 lines changed: 22, context: html, text, full: html, text
    moved all xenTro1 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/human/hg18/trackDb.cancer2.ra
  • 1.3 lines changed: 438, context: html, text, full: html, text
    Organized some track.ra descriptions
• src/hg/makeDb/trackDb/human/hg18/trackDb.chainNet.ra
  • 1.14 lines changed: 5, context: html, text, full: html, text
    Changed horse chain and net shortLabels to match chainNet shortLabels.
  • 1.13 lines changed: 3, context: html, text, full: html, text
    moved all mm7 chains and nets to composite and dropped individual tracks
  • 1.12 lines changed: 6, context: html, text, full: html, text
    Adding chain and net shortLabel overrides for opossum to match the chainNet overrides.
  • 1.11 lines changed: 6, context: html, text, full: html, text
    Adding chain and net shortLabel overrides to match the chainNet shortLabel overrides.
  • 1.10 lines changed: 3, context: html, text, full: html, text
    moved all xenTro1 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/human/hg18/trackDb.instinct.ra
  • 1.46 lines changed: 464, context: html, text, full: html, text
    Organized some track.ra definitions
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.458 lines changed: 8, context: html, text, full: html, text
    moved all mm7 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.859 lines changed: 1701, context: html, text, full: html, text
    Add rank as separate from replicate to UW
  • 1.858 lines changed: 2, context: html, text, full: html, text
    shortened the short label of two subtracks
  • 1.857 lines changed: 3534, context: html, text, full: html, text
    Versioned a lot of Open Chromating Peaks and did some reorganization of the deck chairs
  • 1.856 lines changed: 2, context: html, text, full: html, text
    Fix lab and datatype metadata for Hannon lab tracks (short RNA)
  • 1.855 lines changed: 110, context: html, text, full: html, text
    Fix grant metadata in Caltech tracks
  • 1.854 lines changed: 51, context: html, text, full: html, text
    removed release alphas from ENCODE UW DNaseI HS release 2 new tables
  • 1.853 lines changed: 1, context: html, text, full: html, text
    fixed some metadata for Caltech GM12878
  • 1.852 lines changed: 1, context: html, text, full: html, text
    Added abbreviations to cell line titles in matrix for UW DNase.
  • 1.851 lines changed: 11, context: html, text, full: html, text
    Fix for mapability sort order
  • 1.850 lines changed: 1566, context: html, text, full: html, text
    Clean up of old crud. UW ChIP to UW Histone. Revoke 1 more for YDH
  • 1.849 lines changed: 1, context: html, text, full: html, text
    Moved the tag of subGroup1 for the CRG track.
  • 1.848 lines changed: 5, context: html, text, full: html, text
    Added wgEncode prefix to CRG Mapability subtrack table names for consistency.
  • 1.847 lines changed: 52, context: html, text, full: html, text
    Added subtracks for CRG's GEM Mapability data to the Mapability track.
  • 1.846 lines changed: 84, context: html, text, full: html, text
    Removed 2 nonexistant tracks and revoked the 3 HUVECs for YDH
  • 1.845 lines changed: 46, context: html, text, full: html, text
    Re-pair 11 Yale experiments from IgG-rab to IgG-mus (temporary pairing)
  • 1.844 lines changed: 1, context: html, text, full: html, text
    Tweak metadata for reporting
  • 1.843 lines changed: 1, context: html, text, full: html, text
    Fix typo in freeze
  • 1.842 lines changed: 356, context: html, text, full: html, text
    Rearranged a lot of Yale metadata
  • 1.841 lines changed: 5, context: html, text, full: html, text
    change all HA methylSeq to PCR1X
  • 1.840 lines changed: 20, context: html, text, full: html, text
    ENCODE Riken Cage NHEK nucleus clusters
  • 1.839 lines changed: 1, context: html, text, full: html, text
    Added minGrayLevel to HAIB TFSB preaks, since they have scores below 100.
  • 1.838 lines changed: 39, context: html, text, full: html, text
    Added treatments to long labels of HAIB TFSB
  • 1.837 lines changed: 47, context: html, text, full: html, text
    Fixed a number of experiments which should have hade Rabbit_IgG protocol declared for Yale
  • 1.836 lines changed: 9, context: html, text, full: html, text
    Fixed HepG2/SREBP1 to HepG2/SREBP1/pravastatin for Yale
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlShortRnaSeq.html
  • 1.6 lines changed: 7, context: html, text, full: html, text
    fiddle with Credits some more
  • 1.5 lines changed: 9, context: html, text, full: html, text
    changes re: Carrie
• src/hg/makeDb/trackDb/human/hg19/trackDb.enc.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Created new genome-wide ENCODE trackDb.ra for hg19. Added Mapability track.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.87 lines changed: 45, context: html, text, full: html, text
    Added include for new genome-wide ENCODE trackDb.ra file and moved Mapability track to that file.
  • 1.86 lines changed: 44, context: html, text, full: html, text
    Added an ENCODE Mapability track with data from CRG's GEM Mapper aligner.
• src/hg/makeDb/trackDb/human/omimGene.html
  • 1.23 lines changed: 42, context: html, text, full: html, text
    moved diclaimer to top of description section
• src/hg/makeDb/trackDb/human/trackDb.chainNet.ra
  • 1.33 lines changed: 6, context: html, text, full: html, text
    Changed bosTau3 chain and net shortLabels to match chainNet shortLabels.
  • 1.32 lines changed: 3, context: html, text, full: html, text
    Removed release alpha/beta from rheMac1 nets, chains, chainNets and adjusted priority to match rheMac2.
  • 1.31 lines changed: 6, context: html, text, full: html, text
    Adding chain and net shortLabel overrides for chimp that match the chainNet overrides.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.502 lines changed: 8, context: html, text, full: html, text
    moved all mm7 chains and nets to composite and dropped individual tracks
  • 1.501 lines changed: 13, context: html, text, full: html, text
    moved all xenTro2 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/mouse/mm7/trackDb.chainNet.ra
  • 1.13 lines changed: 6, context: html, text, full: html, text
    Changed bosTau2 chain and net shortLabels to match chainNet shortLabels.
  • 1.12 lines changed: 6, context: html, text, full: html, text
    Added o_Organism shortLabel override to match the chainNet override.
  • 1.11 lines changed: 6, context: html, text, full: html, text
    Adding chain and net shortLabel overrides for chimp that match the chainNet overrides.
  • 1.10 lines changed: 6, context: html, text, full: html, text
    changed some explicit animal names to o_Organism, including chainNetXenTro1 which should not have said Tetraodon in the first place
• src/hg/makeDb/trackDb/mouse/mm7/trackDb.ra
  • 1.61 lines changed: 3, context: html, text, full: html, text
    Removed release alpha/beta from rheMac1 nets, chains, chainNets and adjusted priority to match rheMac2.
• src/hg/makeDb/trackDb/mouse/mm8/trackDb.chainNet.ra
  • 1.11 lines changed: 6, context: html, text, full: html, text
    Adding chain and net shortLabel overrides to match the chainNet shortLabel overrides.
  • 1.10 lines changed: 3, context: html, text, full: html, text
    moved all xenTro1 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/mouse/mm8/trackDb.ra
  • 1.64 lines changed: 3, context: html, text, full: html, text
    Removed individual chain and net settings for chicken, now that they have been moved into composite tracks.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.chainNet.ra
  • 1.7 lines changed: 6, context: html, text, full: html, text
    Changed bosTau3 chain and net shortLabels to match chainNet shortLabels.
  • 1.6 lines changed: 7, context: html, text, full: html, text
    Changed horse chain and net shortLabels to match chainNet shortLabels.
  • 1.5 lines changed: 6, context: html, text, full: html, text
    Adding chain and net shortLabel overrides for opossum to match the chainNet overrides.
• src/hg/makeDb/trackDb/mouse/trackDb.chainNet.ra
  • 1.30 lines changed: 1, context: html, text, full: html, text
    Removed redundant shortLabel on chainNetEquCab1.
  • 1.29 lines changed: 4, context: html, text, full: html, text
    moved all xenTro1 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • 1.192 lines changed: 26, context: html, text, full: html, text
    Removed release alpha/beta from rheMac1 nets, chains, chainNets and adjusted priority to match rheMac2.
  • 1.191 lines changed: 9, context: html, text, full: html, text
    moved all xenTro1 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/opossum/monDom1/trackDb.chainNet.ra
  • 1.4 lines changed: 6, context: html, text, full: html, text
    moved all mm7 chains and nets to composite and dropped individual tracks
  • 1.3 lines changed: 4, context: html, text, full: html, text
    moved all mm6 chains and nets to composite and dropped individual tracks
  • 1.2 lines changed: 1, context: html, text, full: html, text
    changed animal name to o_Organism for several
• src/hg/makeDb/trackDb/opossum/monDom1/trackDb.ra
  • 1.26 lines changed: 6, context: html, text, full: html, text
    moved all mm6 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/opossum/monDom4/trackDb.chainNet.ra
  • 1.10 lines changed: 6, context: html, text, full: html, text
    Adding chain and net shortLabel overrides to match the chainNet shortLabel overrides.
• src/hg/makeDb/trackDb/opossum/monDom5/trackDb.ra
  • 1.30 lines changed: 10, context: html, text, full: html, text
    moved all xenTro2 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/opossum/trackDb.ra
  • 1.44 lines changed: 6, context: html, text, full: html, text
    moved all mm6 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/pig/susScr1/description.html
  • 1.4 lines changed: 1, context: html, text, full: html, text
    change Sscrofa8 to Sscrofa9 since it is that
• src/hg/makeDb/trackDb/platypus/trackDb.chainNet.ra
  • 1.11 lines changed: 6, context: html, text, full: html, text
    Adding chain and net shortLabel overrides for opossum to match the chainNet overrides.
• src/hg/makeDb/trackDb/rabbit/oryCun2/trackDb.ra
  • 1.3 lines changed: 3, context: html, text, full: html, text
    transMap will not override viz
• src/hg/makeDb/trackDb/rabbit/trackDb.chainNet.ra
  • 1.3 lines changed: 1, context: html, text, full: html, text
    moved all mm7 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/rat/rn3/trackDb.chainNet.ra
  • 1.4 lines changed: 7, context: html, text, full: html, text
    moved all mm7 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
  • 1.52 lines changed: 22, context: html, text, full: html, text
    moved all mm7 chains and nets to composite and dropped individual tracks
  • 1.51 lines changed: 24, context: html, text, full: html, text
    moved all xenTro2 chains and nets to composite and dropped individual tracks
  • 1.50 lines changed: 22, context: html, text, full: html, text
    moved all xenTro1 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/rat/trackDb.chainNet.ra
  • 1.18 lines changed: 1, context: html, text, full: html, text
    moved all mm7 chains and nets to composite and dropped individual tracks
  • 1.17 lines changed: 6, context: html, text, full: html, text
    Adding chain and net shortLabel overrides to match the chainNet shortLabel overrides.
• src/hg/makeDb/trackDb/rat/trackDb.ra
  • 1.72 lines changed: 10, context: html, text, full: html, text
    moved all mm7 chains and nets to composite and dropped individual tracks
  • 1.71 lines changed: 12, context: html, text, full: html, text
    moved all xenTro2 chains and nets to composite and dropped individual tracks
  • 1.70 lines changed: 10, context: html, text, full: html, text
    moved all xenTro1 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/seaHare/trackDb.chainNet.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Adding correct alignment params for seaHare-human alignments.
• src/hg/makeDb/trackDb/seaHare/trackDb.ra
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Right now this is only needed for including trackDb.chainNet.ra -- would be cool for hgTrackDb to auto-include some filenames...
• src/hg/makeDb/trackDb/tagTypes.tab
  • 1.9 lines changed: 1, context: html, text, full: html, text
    minGrayLevel is for narrowPeaks too
• src/hg/makeDb/trackDb/tetraodon/trackDb.chainNet.ra
  • 1.10 lines changed: 1, context: html, text, full: html, text
    moved all mm7 chains and nets to composite and dropped individual tracks
  • 1.9 lines changed: 1, context: html, text, full: html, text
    moved all mm6 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/tetraodon/trackDb.ra
  • 1.50 lines changed: 9, context: html, text, full: html, text
    moved all mm7 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • 1.58 lines changed: 6, context: html, text, full: html, text
    moved all mm7 chains and nets to composite and dropped individual tracks
  • 1.57 lines changed: 3, context: html, text, full: html, text
    Removed release alpha/beta from rheMac1 nets, chains, chainNets and adjusted priority to match rheMac2.
  • 1.56 lines changed: 7, context: html, text, full: html, text
    reversed previous commit. not ready to do this and described it wrong
  • 1.55 lines changed: 7, context: html, text, full: html, text
    changed animal name to o_Organism for several
  • 1.54 lines changed: 7, context: html, text, full: html, text
    moved all mm6 chains and nets to composite and dropped individual tracks
  • 1.53 lines changed: 2, context: html, text, full: html, text
    Removed commented-out lines.
  • 1.52 lines changed: 3, context: html, text, full: html, text
    moved all xenTro2 chains and nets to composite and dropped individual tracks
  • 1.51 lines changed: 5, context: html, text, full: html, text
    moved all xenTro1 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.598 lines changed: 25, context: html, text, full: html, text
    moved all mm7 chains and nets to composite and dropped individual tracks
  • 1.597 lines changed: 25, context: html, text, full: html, text
    moved all mm6 chains and nets to composite and dropped individual tracks
  • 1.596 lines changed: 27, context: html, text, full: html, text
    moved all xenTro2 chains and nets to composite and dropped individual tracks
  • 1.595 lines changed: 27, context: html, text, full: html, text
    moved all xenTro1 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/worm/ce4/description.html
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Fixed broken links to wustl.
• src/hg/makeDb/trackDb/worm/ce4/gap.html
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Fixed broken links to wustl.
• src/hg/makeDb/trackDb/worm/ce4/gold.html
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Fixed broken links to wustl.
• src/hg/makeDb/trackDb/worm/ce5/description.html
  • 1.4 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to wustl.
• src/hg/makeDb/trackDb/worm/ce5/gap.html
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Fixed broken links to wustl.
• src/hg/makeDb/trackDb/worm/ce5/gold.html
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Fixed broken links to wustl.
• src/hg/makeDb/trackDb/xenTro/trackDb.chainNet.ra
  • 1.9 lines changed: 1, context: html, text, full: html, text
    moved all mm7 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/xenTro/xenTro1/trackDb.ra
  • 1.43 lines changed: 8, context: html, text, full: html, text
    moved all mm7 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/xenTro/xenTro2/trackDb.chainNet.ra
  • 1.4 lines changed: 6, context: html, text, full: html, text
    Adding chain and net shortLabel overrides for opossum to match the chainNet overrides.
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Replaced hard-coded galGal2 with o_db variable.
• src/hg/makeDb/trackDb/xenTro/xenTro2/trackDb.ra
  • 1.23 lines changed: 18, context: html, text, full: html, text
    Removed individual chain and net settings for chicken, now that they have been moved into composite tracks.
• src/hg/makeDb/trackDb/zebrafish/danRer2/trackDb.ra
  • 1.36 lines changed: 17, context: html, text, full: html, text
    moved all mm6 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/zebrafish/danRer3/trackDb.chainNet.ra
  • 1.4 lines changed: 3, context: html, text, full: html, text
    changed animal name to o_Organism for several
• src/hg/makeDb/trackDb/zebrafish/danRer4/trackDb.chainNet.ra
  • 1.4 lines changed: 2, context: html, text, full: html, text
    changed animal name to o_Organism for several
• src/hg/makeDb/trackDb/zebrafish/trackDb.chainNet.ra
  • 1.13 lines changed: 1, context: html, text, full: html, text
    moved all mm7 chains and nets to composite and dropped individual tracks
• src/hg/makeDb/trackDb/zebrafish/trackDb.ra
  • 1.66 lines changed: 9, context: html, text, full: html, text
    moved all mm6 chains and nets to composite and dropped individual tracks
  • 1.65 lines changed: 28, context: html, text, full: html, text
    moved all xenTro2 chains and nets to composite and dropped individual tracks
• src/hg/overlapSelect/chromAnn.c
  • 1.16 lines changed: 2, context: html, text, full: html, text
    allow specifying location of name when specifying column indices so that -statsOutput is useful
• src/hg/overlapSelect/coordCols.c
  • 1.4 lines changed: 36, context: html, text, full: html, text
    allow specifying location of name when specifying column indices so that -statsOutput is useful
• src/hg/overlapSelect/coordCols.h
  • 1.3 lines changed: 15, context: html, text, full: html, text
    allow specifying location of name when specifying column indices so that -statsOutput is useful
• src/hg/overlapSelect/tests/expected/colSelectMerge.cluster
  • 1.3 lines changed: 4, context: html, text, full: html, text
    allow specifying location of name when specifying column indices so that -statsOutput is useful
• src/hg/overlapSelect/tests/expected/colStats.cluster
  • 1.1 lines changed: 0, context: html, text, full: html, text
    allow specifying location of name when specifying column indices so that -statsOutput is useful
• src/hg/overlapSelect/tests/input/gene.select
  • 1.3 lines changed: 4, context: html, text, full: html, text
    allow specifying location of name when specifying column indices so that -statsOutput is useful
• src/hg/overlapSelect/tests/makefile
  • 1.35 lines changed: 7, context: html, text, full: html, text
    allow specifying location of name when specifying column indices so that -statsOutput is useful
• src/hg/overlapSelect/usage.txt
  • 1.12 lines changed: 4, context: html, text, full: html, text
    allow specifying location of name when specifying column indices so that -statsOutput is useful
• src/hg/qaPushQ/qaPushQ.c
  • 1.121 lines changed: 23, context: html, text, full: html, text
    moved new greek byte function to kent/src/lib/obscure.c
  • 1.120 lines changed: 1, context: html, text, full: html, text
    activating D-queue link for encode
  • 1.119 lines changed: 35, context: html, text, full: html, text
    getting rid of redundant info at top, and adding Greek-Bytes B KB MB GB TB PB to totals displays
• src/hg/utils/automation/HgDb.pm
  • 1.8 lines changed: 4, context: html, text, full: html, text
    support PROFILE option
• src/hg/utils/mutationClassifier/makefile
  • 1.1 lines changed: 0, context: html, text, full: html, text
    first pass; currently only handles coding SNPs; still working on how to output mutation classifications
• src/hg/utils/mutationClassifier/mutationClassifier.c
  • 1.3 lines changed: 11, context: html, text, full: html, text
    remove some cruft in SPLICE_SITE code
  • 1.2 lines changed: 94, context: html, text, full: html, text
    use more and longer codes; start working on supporting indels; still not quite done
  • 1.1 lines changed: 107, context: html, text, full: html, text
    first pass; currently only handles coding SNPs; still working on how to output mutation classifications
• src/hg/utils/mutationClassifier/test/test.bed
  • 1.1 lines changed: 0, context: html, text, full: html, text
    first pass; currently only handles coding SNPs; still working on how to output mutation classifications
• src/hg/visiGene/vgPrepImage/jp2Dec.c
  • 1.2 lines changed: 27, context: html, text, full: html, text
    trying to get it to compile, using dynamic libjpeg since static no longer easily available, changing jpeg2000 dependency to default off since most people will not need it, using jpgTilesX.h as a minimal include file removes the conflict over "boolean" between common.h and libjpeg.h
• src/hg/visiGene/vgPrepImage/jpgTiles.c
  • 1.4 lines changed: 2, context: html, text, full: html, text
    trying to get it to compile, using dynamic libjpeg since static no longer easily available, changing jpeg2000 dependency to default off since most people will not need it, using jpgTilesX.h as a minimal include file removes the conflict over "boolean" between common.h and libjpeg.h
• src/hg/visiGene/vgPrepImage/jpgTiles.h
  • 1.2 lines changed: 1, context: html, text, full: html, text
    trying to get it to compile, using dynamic libjpeg since static no longer easily available, changing jpeg2000 dependency to default off since most people will not need it, using jpgTilesX.h as a minimal include file removes the conflict over "boolean" between common.h and libjpeg.h
• src/hg/visiGene/vgPrepImage/jpgTilesX.h
  • 1.1 lines changed: 0, context: html, text, full: html, text
    trying to get it to compile, using dynamic libjpeg since static no longer easily available, changing jpeg2000 dependency to default off since most people will not need it, using jpgTilesX.h as a minimal include file removes the conflict over "boolean" between common.h and libjpeg.h
• src/hg/visiGene/vgPrepImage/makefile
  • 1.6 lines changed: 9, context: html, text, full: html, text
    trying to get it to compile, using dynamic libjpeg since static no longer easily available, changing jpeg2000 dependency to default off since most people will not need it, using jpgTilesX.h as a minimal include file removes the conflict over "boolean" between common.h and libjpeg.h
• src/hg/visiGene/vgPrepImage/vgPrepImage.c
  • 1.5 lines changed: 1, context: html, text, full: html, text
    trying to get it to compile, using dynamic libjpeg since static no longer easily available, changing jpeg2000 dependency to default off since most people will not need it, using jpgTilesX.h as a minimal include file removes the conflict over "boolean" between common.h and libjpeg.h
• src/inc/common.mk
  • 1.75 lines changed: 3, context: html, text, full: html, text
    if lowelab is defined, set SCRIPTS to /cse/grads/pchan/scripts since lowelab does not use /cluster/bin
• src/inc/obscure.h
  • 1.36 lines changed: 3, context: html, text, full: html, text
    moved new greek byte function to kent/src/lib/obscure.c
• src/lib/bbiWrite.c
  • 1.12 lines changed: 13, context: html, text, full: html, text
    Fixing it so that while you have to be sorted within a chromosome, the chromosomes themselves need not be sorted.
  • 1.11 lines changed: 10, context: html, text, full: html, text
    Adding more error checking on input.
• src/lib/obscure.c
  • 1.53 lines changed: 19, context: html, text, full: html, text
    moved new greek byte function to kent/src/lib/obscure.c
• src/utils/bedGraphToBigWig/emptyItem.bedGraph
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Adding another test case
• src/utils/bedGraphToBigWig/endThenStart.bedGraph
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Adding another error test case.
• src/utils/bedToBigBed/bedToBigBed.c
  • 1.21 lines changed: 1, context: html, text, full: html, text
    gcc34 and some other compilers complained. but we should have the cast around the full expression anyways
• src/utils/qa/countPerChrom.csh
  • 1.17 lines changed: 1, context: html, text, full: html, text
    reversed previous change. the hap chrom breaks the histogram if two assemblies have different hap sets. fix is too complicated for right now
  • 1.16 lines changed: 1, context: html, text, full: html, text
    added back the haplotype chroms at ann's request
• src/utils/qa/findLevel.csh
  • 1.19 lines changed: 20, context: html, text, full: html, text
    added logic to find all cases of the track in it's different release alpha/beta and staging locations
  • 1.18 lines changed: 4, context: html, text, full: html, text
    added a -alpha flag to the tdbQuery call to get tracks that are restricted to alpha. added release to the output, so we can see if they are restricted to one machine or the other.
• src/utils/qa/getRRtables.csh
  • 1.7 lines changed: 1, context: html, text, full: html, text
    variable needed quoting
• src/utils/qa/graph.csh
  • 1.4 lines changed: 5, context: html, text, full: html, text
    added support for datasets where the largest data value is smaller than the width of graph. graph then shrinks to width of largest value
• src/utils/qa/qaEncodeTracks.csh
  • 1.6 lines changed: 5, context: html, text, full: html, text
    we don't need that much output in the index check (thanks Brooke)
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.98 lines changed: 3, context: html, text, full: html, text
    v224 final build

• lines changed: 12306
• files changed: 154