CVS changes by file

branch to review (2009-12-01 to 2009-12-09) v221

• src/blat/version.doc
  • 1.75 lines changed: 1, context: html, text, full: html, text
    fixing neg strand issue reported by user for pcr psl output
• src/hg/archaeStuff/tooltip/makefile
  • 1.1 lines changed: 21, context: html, text, full: html, text
    adding makefile
• src/hg/archaeStuff/tooltip/tooltip.c
  • 1.6 lines changed: 2, context: html, text, full: html, text
    removed gene prediction
  • 1.5 lines changed: 3, context: html, text, full: html, text
    commented out old prediction code
• src/hg/encode/DAFs/HAIBChIPseq.daf
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Added protocol and treatment terms
• src/hg/encode/DAFs/HAIBChIPseqExample.ddf
  • 1.1 lines changed: 9, context: html, text, full: html, text
    Example with protocol and treatment
• src/hg/encode/DAFs/HAIBRnaSeq.daf
  • 1.1 lines changed: 33, context: html, text, full: html, text
    first pass at DAF for Myers RNA-seq
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.152 lines changed: 55, context: html, text, full: html, text
    Added some treatments and protocols for HAIB
  • 1.151 lines changed: 44, context: html, text, full: html, text
    Switched Gliobla and Medullo
  • 1.150 lines changed: 7, context: html, text, full: html, text
    Add new grants from ARRA (stimulus) and other Mouse ENCODE (LICR)
  • 1.149 lines changed: 12, context: html, text, full: html, text
    Renamed 6 cell lines by request from Greg Crawford
  • 1.148 lines changed: 69, context: html, text, full: html, text
    Add organism setting to Cell Line entries (all existing ones are for Human)
  • 1.147 lines changed: 139, context: html, text, full: html, text
    Make targetLink handling symmetric with other links (remove special syntax). Splits targetLink setting into two -- targetId and targetUrl
  • 1.146 lines changed: 1, context: html, text, full: html, text
    add some words to the definition of total
• src/hg/encode/encodeValidate/config/fields.ra
  • 1.23 lines changed: 5, context: html, text, full: html, text
    Added protocol for HAIB
• src/hg/encode/encodeValidate/config/labs.ra
  • 1.11 lines changed: 16, context: html, text, full: html, text
    Add new grants from ARRA (stimulus) and other Mouse ENCODE (LICR)
• src/hg/encode/encodeValidate/config/pi.ra
  • 1.4 lines changed: 34, context: html, text, full: html, text
    Add new grants from ARRA (stimulus) and other Mouse ENCODE (LICR)
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.207 lines changed: 1, context: html, text, full: html, text
    Added protocol as another term
  • 1.206 lines changed: 36, context: html, text, full: html, text
    add support for SAM and BAM files (call validateFiles)
  • 1.205 lines changed: 3, context: html, text, full: html, text
    Update assembly in projects table (support for mouse and hg19)
  • 1.204 lines changed: 1, context: html, text, full: html, text
    add restrictionEnzyme to list of non-validated variables
• src/hg/encode/hgEncodeSubmit/app/controllers/pipeline_controller.rb
  • 1.94 lines changed: 24, context: html, text, full: html, text
    adding feature show_active which filters out the inactive things reaching a completed state
  • 1.93 lines changed: 13, context: html, text, full: html, text
    adding projects.db field and display, added show_daf and show_ddf
• src/hg/encode/hgEncodeSubmit/app/views/layouts/main.rhtml
  • 1.11 lines changed: 11, context: html, text, full: html, text
    adding feature show_active which filters out the inactive things reaching a completed state
• src/hg/encode/hgEncodeSubmit/app/views/pipeline/list.rhtml
  • 1.24 lines changed: 2, context: html, text, full: html, text
    adding projects.db field and display, added show_daf and show_ddf
• src/hg/encode/hgEncodeSubmit/app/views/pipeline/show.rhtml
  • 1.48 lines changed: 2, context: html, text, full: html, text
    making it a verb
  • 1.47 lines changed: 10, context: html, text, full: html, text
    added db field to show rhtml
  • 1.46 lines changed: 12, context: html, text, full: html, text
    adding projects.db field and display, added show_daf and show_ddf
• src/hg/encode/hgEncodeSubmit/app/views/pipeline/show_daf.rhtml
  • 1.1 lines changed: 8, context: html, text, full: html, text
    adding projects.db field and display, added show_daf and show_ddf
• src/hg/encode/hgEncodeSubmit/app/views/pipeline/show_ddf.rhtml
  • 1.1 lines changed: 8, context: html, text, full: html, text
    adding projects.db field and display, added show_daf and show_ddf
• src/hg/encode/hgEncodeSubmit/db/migrate/039_add_db_to_projects.rb
  • 1.1 lines changed: 9, context: html, text, full: html, text
    adding projects.db field and display, added show_daf and show_ddf
• src/hg/encode/hgEncodeSubmit/lib/pipeline_background.rb
  • 1.18 lines changed: 37, context: html, text, full: html, text
    adding projects.db field and display, added show_daf and show_ddf
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • 1.29 lines changed: 81, context: html, text, full: html, text
    1. Add support for 'organism' option (for mouse) 2. Cleanup (e.g. remove unused ifdef) 3. Add 'tag' option
  • 1.28 lines changed: 23, context: html, text, full: html, text
    Simplify by: 1) setting link style globally 2) removing special syntax in antibody targets
• src/hg/encode/validateFiles/validateFiles.c
  • 1.31 lines changed: 20, context: html, text, full: html, text
    add stubs for SAM and BAM format checking
  • 1.30 lines changed: 2, context: html, text, full: html, text
    when checking fasta sequence names, stop checking at space to allow extra stuff that folks often put after the sequence name
• src/hg/featureBits/featureBits.c
  • 1.57 lines changed: 2, context: html, text, full: html, text
    Fix usage message for chromSize argument
  • 1.56 lines changed: 3, context: html, text, full: html, text
    Really do not contact the database unless it is actually required
• src/hg/hgCustom/hgCustom.c
  • 1.135 lines changed: 37, context: html, text, full: html, text
    Added column to display remote ct errors (big*, bam). Fixed some stray </TD> tags. Uses new func javaScriptLiteralEncode().
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.509 lines changed: 2, context: html, text, full: html, text
    Omit cds-reference (fortunately the last element of the snp125Func variables) when version is 130 or greater.
• src/hg/hgTracks/chromGraphTrack.c
  • 1.20 lines changed: 1, context: html, text, full: html, text
    CONTEXT_MENU stuff; mostly turned off, except map area id's are live
• src/hg/hgTracks/config.c
  • 1.87 lines changed: 17, context: html, text, full: html, text
    Created static variable advancedJsEnabled to avoid excessive calls to look it up
• src/hg/hgTracks/cytoBandTrack.c
  • 1.12 lines changed: 8, context: html, text, full: html, text
    Tie the chrom imnnage drag jump feature to advancedJavascriptFeatures
• src/hg/hgTracks/expRatioTracks.c
  • 1.47 lines changed: 2, context: html, text, full: html, text
    CONTEXT_MENU stuff; mostly turned off, except map area id's are live
• src/hg/hgTracks/hgTracks.c
  • 1.1612 lines changed: 660, context: html, text, full: html, text
    Checkin for FLAT_TRACKS for dragReorder. Also several other features worked out or cleaned up
  • 1.1611 lines changed: 88, context: html, text, full: html, text
    CONTEXT_MENU stuff; mostly turned off, except map area id's are live
  • 1.1610 lines changed: 3, context: html, text, full: html, text
    Add lowetooltip.js inclusion on behalf of Andrew Holmes
• src/hg/hgTracks/imageV2.c
  • 1.17 lines changed: 273, context: html, text, full: html, text
    Checkin for FLAT_TRACKS for dragReorder. Also several other features worked out or cleaned up
  • 1.16 lines changed: 16, context: html, text, full: html, text
    CONTEXT_MENU stuff; mostly turned off, except map area id's are live
  • 1.15 lines changed: 2, context: html, text, full: html, text
    Fix bug in imageV2 maps to make them written in creation order
• src/hg/hgTracks/imageV2.h
  • 1.12 lines changed: 78, context: html, text, full: html, text
    Checkin for FLAT_TRACKS for dragReorder. Also several other features worked out or cleaned up
  • 1.11 lines changed: 8, context: html, text, full: html, text
    CONTEXT_MENU stuff; mostly turned off, except map area id's are live
• src/hg/hgTracks/rmskTrack.c
  • 1.13 lines changed: 1, context: html, text, full: html, text
    Removing details page when clicking on RepeatMasker but not on a specific repeat.
• src/hg/hgTracks/simpleTracks.c
  • 1.116 lines changed: 35, context: html, text, full: html, text
    Checkin for FLAT_TRACKS for dragReorder. Also several other features worked out or cleaned up
  • 1.115 lines changed: 13, context: html, text, full: html, text
    CONTEXT_MENU stuff; mostly turned off, except map area id's are live
• src/hg/hgTracks/variation.c
  • 1.146 lines changed: 1, context: html, text, full: html, text
    CONTEXT_MENU stuff; mostly turned off, except map area id's are live
• src/hg/hgTracks/wigTrack.c
  • 1.99 lines changed: 5, context: html, text, full: html, text
    Checkin for FLAT_TRACKS for dragReorder. Also several other features worked out or cleaned up
• src/hg/hgc/hgc.c
  • 1.1582 lines changed: 2, context: html, text, full: html, text
    Added two more subtracks for Illumina SNP arrays.
  • 1.1581 lines changed: 2, context: html, text, full: html, text
    Added one line for Illumina snpArrayIlluminaHumanCytoSNP_12 chip.
• src/hg/inc/allpredictions.h
  • 1.1 lines changed: 67, context: html, text, full: html, text
    adding gene prediction
• src/hg/inc/customTrack.h
  • 1.57 lines changed: 1, context: html, text, full: html, text
    networkErrMsg field added to customTrack struct
• src/hg/js/hgTracks.js
  • 1.48 lines changed: 156, context: html, text, full: html, text
    Checkin for FLAT_TRACKS for dragReorder. Also several other features worked out or cleaned up
• src/hg/js/hui.js
  • 1.44 lines changed: 1, context: html, text, full: html, text
    Fix for bug Katrina found. All plus/minus buttons were failing when no matrix exists
• src/hg/js/jquery-ui.js
  • 1.2 lines changed: 9126, context: html, text, full: html, text
    checkin a minified version, with fixed MS-DOS line ends
  • 1.1 lines changed: 9134, context: html, text, full: html, text
    jQuery UI 1.7.2
• src/hg/js/jquery.jstore-all-min.js
  • 1.1 lines changed: 56, context: html, text, full: html, text
    jStore 1.2.0
• src/hg/js/lowetooltip.js
  • 1.1 lines changed: 300, context: html, text, full: html, text
    Adding lowe tooltip javascript
• src/hg/js/makefile
  • 1.12 lines changed: 4, context: html, text, full: html, text
    adding lowetooltip.js in ifdef lowelab
• src/hg/lib/allpredictions.c
  • 1.1 lines changed: 154, context: html, text, full: html, text
    adding all predictions
• src/hg/lib/cart.c
  • 1.114 lines changed: 109, context: html, text, full: html, text
    cartJustify has been added to clean up _imgOrd settings superceded by changed priorities
• src/hg/lib/customFactory.c
  • 1.112 lines changed: 47, context: html, text, full: html, text
    Added Catch around remote resource (big*, bam) loader when it tries to open the resource
• src/hg/lib/customTrack.c
  • 1.179 lines changed: 61, context: html, text, full: html, text
    splay remote errors if adding new cts. Unless hgCustom, filter out cts with load err (big*, bam) from ctList. Also improved add track list handling using slAddHead and slCat instead of slAddTail.
• src/hg/lib/hui.c
  • 1.251 lines changed: 1, context: html, text, full: html, text
    Fix for bug Katrina found. All plus/minus buttons were failing when no matrix exists
• src/hg/lib/retroMrnaInfo.sql
  • 1.2 lines changed: 1, context: html, text, full: html, text
    add XX to handle version number
• src/hg/lib/snpArrayIlluminaHuman660W_Quad.sql
  • 1.1 lines changed: 13, context: html, text, full: html, text
    Added 2 new tables for Illumina SNP array chips.
• src/hg/lib/snpArrayIlluminaHuman660W_QuadRaw.sql
  • 1.1 lines changed: 11, context: html, text, full: html, text
    Added table definition for 3 new Illumina SNP array chip raw data.
• src/hg/lib/snpArrayIlluminaHumanCytoSNP_12.sql
  • 1.1 lines changed: 13, context: html, text, full: html, text
    Added 1 table for an Illumina SNP array chip.
• src/hg/lib/snpArrayIlluminaHumanCytoSNP_12Raw.sql
  • 1.1 lines changed: 11, context: html, text, full: html, text
    Added table definition for 3 new Illumina SNP array chip raw data.
• src/hg/lib/snpArrayIlluminaHumanOmni1_Quad.sql
  • 1.1 lines changed: 13, context: html, text, full: html, text
    Added 2 new tables for Illumina SNP array chips.
• src/hg/lib/snpArrayIlluminaHumanOmni1_QuadRaw.sql
  • 1.1 lines changed: 11, context: html, text, full: html, text
    Added table definition for 3 new Illumina SNP array chip raw data.
• src/hg/lib/ucscRetroCds.sql
  • 1.4 lines changed: 1, context: html, text, full: html, text
    change cds from varchar(255) to longtext
  • 1.3 lines changed: 1, context: html, text, full: html, text
    change cds from varchar(255) to varchar(512)
  • 1.2 lines changed: 1, context: html, text, full: html, text
    changed cds from varchar(40) to varchar(255)
• src/hg/lib/wiggleCart.c
  • 1.35 lines changed: 37, context: html, text, full: html, text
    Restored viewLimitsCompositeOverride so that minLimit,maxLimit can be used to prompt range in view level cfg
• src/hg/makeDb/doc/encodeDccHg18/broadBernstein.txt
  • 1.10 lines changed: 120, context: html, text, full: html, text
    Some Rep2 tagAligns were missing.
• src/hg/makeDb/doc/encodeDccHg18/haibChipSeq.txt
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Keeping the record up to date
  • 1.4 lines changed: 131, context: html, text, full: html, text
    Backlog of work needing check-in
• src/hg/makeDb/doc/encodeDccHg18/uwChIPseq.release1.notes.txt
  • 1.3 lines changed: 2, context: html, text, full: html, text
    Removed one file that Richard noticed was replaced with differently named file
• src/hg/makeDb/doc/encodeDccHg18/uwStam.txt
  • 1.5 lines changed: 6, context: html, text, full: html, text
    Keeping the record up to date
  • 1.4 lines changed: 11, context: html, text, full: html, text
    Backlog check-in
• src/hg/makeDb/doc/encodeDccHg18/yaleDavisHarvardSnyder.txt
  • 1.13 lines changed: 49, context: html, text, full: html, text
    Keeping the record up to date
  • 1.12 lines changed: 306, context: html, text, full: html, text
    Finally most of Yale's tagAligns have been corrected.
• src/hg/makeDb/doc/galGal3.txt
  • 1.32 lines changed: 38, context: html, text, full: html, text
    add CA condor 454
  • 1.31 lines changed: 4, context: html, text, full: html, text
    Regenerated qual track to fix omission of chrUn_random.
• src/hg/makeDb/doc/hg18.txt
  • 1.390 lines changed: 87, context: html, text, full: html, text
    Added two more Illumina SNP array subtracks.
  • 1.389 lines changed: 43, context: html, text, full: html, text
    Added snpArrayIlluminaHumanCytoSNP_12 sub-track of SNP arrays track.
• src/hg/makeDb/doc/hg19.txt
  • 1.66 lines changed: 39, context: html, text, full: html, text
    Final loaded phastCons and phyloP for 46-way alignment
  • 1.65 lines changed: 15, context: html, text, full: html, text
    Added GeneNetowrk link for hg19 hgGene page.
• src/hg/makeDb/makefile
  • 1.42 lines changed: 2, context: html, text, full: html, text
    Adding trackDbPatch.
• src/hg/makeDb/trackDb/ancestor/borEut13/trackDb.ra
  • 1.8 lines changed: 61, context: html, text, full: html, text
    Fixing more dupes in trackDb.
• src/hg/makeDb/trackDb/ancestor/canHg12/trackDb.ra
  • 1.6 lines changed: 61, context: html, text, full: html, text
    Fixing more dupes in trackDb.
• src/hg/makeDb/trackDb/ancestor/catArr1/trackDb.ra
  • 1.5 lines changed: 61, context: html, text, full: html, text
    Fixing more dupes in trackDb.
• src/hg/makeDb/trackDb/ancestor/euaGli13/trackDb.ra
  • 1.4 lines changed: 61, context: html, text, full: html, text
    Fixing more dupes in trackDb.
• src/hg/makeDb/trackDb/ancestor/gliRes13/trackDb.ra
  • 1.4 lines changed: 61, context: html, text, full: html, text
    Fixing more dupes in trackDb.
• src/hg/makeDb/trackDb/ancestor/homIni13/trackDb.ra
  • 1.7 lines changed: 61, context: html, text, full: html, text
    Fixing more dupes in trackDb.
• src/hg/makeDb/trackDb/ancestor/homIni14/trackDb.ra
  • 1.6 lines changed: 73, context: html, text, full: html, text
    Fixing some duplicates found by tdbQuery
• src/hg/makeDb/trackDb/ancestor/priMat13/trackDb.ra
  • 1.6 lines changed: 61, context: html, text, full: html, text
    Fixing some duplicates found by tdbQuery
• src/hg/makeDb/trackDb/ancestor/rodEnt13/trackDb.ra
  • 1.4 lines changed: 61, context: html, text, full: html, text
    Fixing some duplicates found by tdbQuery
• src/hg/makeDb/trackDb/anopheles/trackDb.ra
  • 1.18 lines changed: 8, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/anopheles/visibility.ra
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/apis/apiMel2/trackDb.ra
  • 1.25 lines changed: 6, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/apis/apiMel2/visibility.ra
  • 1.3 lines changed: 2, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/armadillo/visibility.ra
  • 1.3 lines changed: 0, context: html, text, full: html, text
    Removing empty visibility.ra file.
• src/hg/makeDb/trackDb/chicken/galGal3/caCondor454.html
  • 1.2 lines changed: 17, context: html, text, full: html, text
    added references and credits
• src/hg/makeDb/trackDb/chicken/priority.ra
  • 1.9 lines changed: 42, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/chicken/trackDb.ra
  • 1.14 lines changed: 45, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
  • 1.13 lines changed: 0, context: html, text, full: html, text
    Little fixes to trackDb.ra
  • 1.12 lines changed: 8, context: html, text, full: html, text
    remove orphaned overrides for humanChainNet and horseChainNet
• src/hg/makeDb/trackDb/cow/bosTau2/trackDb.ra
  • 1.8 lines changed: 2, context: html, text, full: html, text
    all chains and nets on any Cow browser are now composites
• src/hg/makeDb/trackDb/cow/bosTau4/trackDb.ra
  • 1.18 lines changed: 8, context: html, text, full: html, text
    all chains and nets on any Cow browser are now composites
• src/hg/makeDb/trackDb/cow/trackDb.chainNet.ra
  • 1.2 lines changed: 9, context: html, text, full: html, text
    reversed priorities for chainNets on cow
  • 1.1 lines changed: 25, context: html, text, full: html, text
    all chains and nets on any Cow browser are now composites
• src/hg/makeDb/trackDb/cow/trackDb.ra
  • 1.4 lines changed: 7, context: html, text, full: html, text
    all chains and nets on any Cow browser are now composites
• src/hg/makeDb/trackDb/dog/canFam2/trackDb.ra
  • 1.39 lines changed: 25, context: html, text, full: html, text
    fixup duplicate chainCalJac1 and chainPanTro2 entries
• src/hg/makeDb/trackDb/dog/priority.ra
  • 1.8 lines changed: 66, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/dog/trackDb.ra
  • 1.26 lines changed: 29, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
  • 1.25 lines changed: 6, context: html, text, full: html, text
    remove orphaned overrides for humanChainNet and horseChainNet
  • 1.24 lines changed: 15, context: html, text, full: html, text
    fixup duplicate chainCalJac1 and chainPanTro2 entries
• src/hg/makeDb/trackDb/drosophila/dm2/trackDb.ra
  • 1.58 lines changed: 15, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/drosophila/dm2/visibility.ra
  • 1.2 lines changed: 12, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/drosophila/droAna2/trackDb.ra
  • 1.11 lines changed: 6, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/drosophila/droAna2/visibility.ra
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/drosophila/droEre1/trackDb.ra
  • 1.12 lines changed: 6, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/drosophila/droEre1/visibility.ra
  • 1.2 lines changed: 5, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/drosophila/droGri1/trackDb.ra
  • 1.7 lines changed: 7, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/drosophila/droGri1/visibility.ra
  • 1.2 lines changed: 5, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/elephant/loxAfr3/description.html
  • 1.4 lines changed: 1, context: html, text, full: html, text
    added whitespace around image
• src/hg/makeDb/trackDb/elephant/visibility.ra
  • 1.3 lines changed: 0, context: html, text, full: html, text
    Removing empty visibility.ra
• src/hg/makeDb/trackDb/fugu/priority.ra
  • 1.2 lines changed: 6, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/fugu/trackDb.ra
  • 1.63 lines changed: 4, context: html, text, full: html, text
    Fixing a few little places where the automatic rewrite left duplicate records.
  • 1.62 lines changed: 35, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
  • 1.61 lines changed: 0, context: html, text, full: html, text
    Little fixes to trackDb.ra
  • 1.60 lines changed: 4, context: html, text, full: html, text
    remove orphaned overrides for humanChainNet and horseChainNet
• src/hg/makeDb/trackDb/fugu/visibility.ra
  • 1.7 lines changed: 38, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/guineaPig/cavPor3/trackDb.ra
  • 1.7 lines changed: 32, context: html, text, full: html, text
    Eliminate duplicate definitions of chainHg18 and chainMm9 they are already overridden here
• src/hg/makeDb/trackDb/h1n1/h1n1/trackDb.ra
  • 1.12 lines changed: 1, context: html, text, full: html, text
    Fixing some duplicates found by tdbQuery
• src/hg/makeDb/trackDb/hiv/trackDb.ra
  • 1.5 lines changed: 321, context: html, text, full: html, text
    Moving around some subtracks that weren't directly under their parents. Adding some indentation to subtracks.
• src/hg/makeDb/trackDb/horse/trackDb.ra
  • 1.15 lines changed: 16, context: html, text, full: html, text
    back to separate chain and net (chainNet is still release alpha).
  • 1.14 lines changed: 15, context: html, text, full: html, text
    using ChainNet instead
  • 1.13 lines changed: 3, context: html, text, full: html, text
    overrides for chain vars in chainNetOrnana1 track
  • 1.12 lines changed: 9, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/horse/visibility.ra
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    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/human/hg12/trackDb.ra
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    Fixing some duplicates found by tdbQuery
• src/hg/makeDb/trackDb/human/hg13/trackDb.ra
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    Fixing some duplicates found by tdbQuery
• src/hg/makeDb/trackDb/human/hg16/priority.ra
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    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/human/hg16/trackDb.ra
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    Merging visibility.ra and priority.ra files back into trackDb.ra
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    Removing unused track stanza with unusual tag.
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    Fixing some duplicates found by tdbQuery
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    Eliminate duplicate spanList definition
• src/hg/makeDb/trackDb/human/hg17/bosTau2.chainNet.html
  • 1.1 lines changed: 153, context: html, text, full: html, text
    Ancient chain and net has no axtChain command.
• src/hg/makeDb/trackDb/human/hg17/priority.ra
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    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/human/hg17/trackDb.encode.ra
  • 1.180 lines changed: 12, context: html, text, full: html, text
    Fixing dataversion that should be dataVersion.
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    Fixing some duplicates found by tdbQuery
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    eliminate a duplicate maxHeightPixels definition
• src/hg/makeDb/trackDb/human/hg17/trackDb.ra
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    Merging visibility.ra and priority.ra files back into trackDb.ra
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    removing unused track stanza with weird field.
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    Fixing some duplicates found by tdbQuery
• src/hg/makeDb/trackDb/human/hg18/trackDb.encodeChip.ra
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    Removing duplicate tags within same stanza.
• src/hg/makeDb/trackDb/human/hg18/trackDb.encodeChrom.ra
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    Removing duplicate tags within same stanza.
• src/hg/makeDb/trackDb/human/hg18/trackDb.encodeGenes.ra
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    Removing duplicate tags within same stanza.
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
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    Removed snpArrayIllumina650 per Illumina's request and added 3 new Illumina SNP arrary subtracks.
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    Fix bad metadata fields in UW CHIP-seq. Tweak track labels too for consistency
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    Moving around some subtracks that weren't directly under their parents. Adding some indentation to subtracks.
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    correcting altcolor to altColor
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    Little fixes to trackDb.ra
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
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    Added protocol and treatment to HAIB TFBS
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    add two letter codes to the CalTech RNA-seq short labels
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    put cell types in alphabetical order for RNA-seq tracks
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    change view terms *RawSig* to *_Raw_Signal
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    RNA-Seq to RNA-seq
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    take out unused views from settingsByView and defaults
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    Fix bad metadata fields in UW CHIP-seq. Tweak track labels too for consistency
  • 1.708 lines changed: 253, context: html, text, full: html, text
    Short label improvements to UW ChIP-seq by Thomas Juettemann
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    Replaced a bunch of viewLimitsMax vars with minLimit and maxLimit. Don't like it but will go along with the current.
  • 1.706 lines changed: 1, context: html, text, full: html, text
    change viewLimitsMax to viewLimits
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    fix some short labels
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    add some new cell and compartment types to the RNA-pet set
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    Fixing viewLimts that should be viewLimits
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    drop entry for wgEncodeGencode2WayV3 which is for hgwdev-gencode only
  • 1.701 lines changed: 1, context: html, text, full: html, text
    one was missing from the pushQ entry
  • 1.700 lines changed: 123, context: html, text, full: html, text
    removed alphas from Open Chromatin tracks ready for release
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    set autoscale to properly read autoscale
  • 1.698 lines changed: 24, context: html, text, full: html, text
    show mismatches in GIS Rna-seq alignments
  • 1.697 lines changed: 45, context: html, text, full: html, text
    show different bases in CSHL short RNA-seq track
  • 1.696 lines changed: 49, context: html, text, full: html, text
    don't do LOG transform on RNA-seq or RNA-pet tracks
  • 1.695 lines changed: 4, context: html, text, full: html, text
    relabel a couple of Yale tracks that should belong to YCD or Stanford
  • 1.694 lines changed: 6, context: html, text, full: html, text
    Removing duplicate tags within same stanza.
  • 1.693 lines changed: 81, context: html, text, full: html, text
    Added in 2 more experiments for HAIB TFSB
• src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMap.html
  • 1.28 lines changed: 1, context: html, text, full: html, text
    Fixed poorly worded release 2 note.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisRnaSeq.html
  • 1.4 lines changed: 2, context: html, text, full: html, text
    change in to on
• src/hg/makeDb/trackDb/human/hg19/cons46way.html
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Moved the multiz link one directory up.
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    added star to danRer6, as it's not out yet
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.73 lines changed: 20, context: html, text, full: html, text
    Added entry for RetroFinder Retroposed gene predictions.
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    Turned off tarsier, platypus, lizard, and stickleback in multiz default tracks, and turned on zebrafish.
  • 1.71 lines changed: 3, context: html, text, full: html, text
    Decluttering genes section. Hiding MGC genes by default. Putting hg19's RefSeq Genes back to dense.
• src/hg/makeDb/trackDb/human/hg19/ucscRetroAli.html
  • 1.1 lines changed: 66, context: html, text, full: html, text
    Renamed ucscRetroAli description file to have html file name extension instead of hmtl.
• src/hg/makeDb/trackDb/human/priority.ra
  • 1.11 lines changed: 232, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/human/trackDb.encode.ra
  • 1.100 lines changed: 26, context: html, text, full: html, text
    Removing duplicate track records at same level of directory hierarchy, in many cases by adding a missing release tag.
  • 1.99 lines changed: 5, context: html, text, full: html, text
    Removing duplicate tags within same stanza.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.476 lines changed: 225, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
  • 1.475 lines changed: 9, context: html, text, full: html, text
    Removing duplicate track records at same level of directory hierarchy, in many cases by adding a missing release tag.
• src/hg/makeDb/trackDb/human/wgEncodeGencode.html
  • 1.6 lines changed: 10, context: html, text, full: html, text
    add release notes for release 3c
• src/hg/makeDb/trackDb/lamprey/trackDb.ra
  • 1.5 lines changed: 4, context: html, text, full: html, text
    remove orphaned overrides for humanChainNet and horseChainNet
• src/hg/makeDb/trackDb/lizard/trackDb.ra
  • 1.6 lines changed: 0, context: html, text, full: html, text
    Little fixes to trackDb.ra
  • 1.5 lines changed: 4, context: html, text, full: html, text
    remove orphaned overrides for humanChainNet and horseChainNet
• src/hg/makeDb/trackDb/loadTracks
  • 1.18 lines changed: 1, context: html, text, full: html, text
    add root option to tdbQuery
  • 1.17 lines changed: 1, context: html, text, full: html, text
    Adding trackDbPatch.
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    Fixing some duplicates found by tdbQuery
• src/hg/makeDb/trackDb/lowelab/haloHalo1/trackDb.ra
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    Fixing some duplicates found by tdbQuery
• src/hg/makeDb/trackDb/lowelab/joseCoat_042308/trackDb.ra
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    Fixing some duplicates found by tdbQuery
• src/hg/makeDb/trackDb/lowelab/pyrFur2/trackDb.ra
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    Fixing some duplicates found by tdbQuery
• src/hg/makeDb/trackDb/lowelab/pyroArse1/trackDb.ra
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    Fixing some duplicates found by tdbQuery
• src/hg/makeDb/trackDb/lowelab/pyroIsla1/trackDb.ra
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    Fixing some duplicates found by tdbQuery
• src/hg/makeDb/trackDb/lowelab/trackDb.ra
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    Fixing some duplicates found by tdbQuery
• src/hg/makeDb/trackDb/malaria/falciparum/trackDb.ra
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    Little fixes to trackDb.ra
• src/hg/makeDb/trackDb/marmoset/calJac1/trackDb.ra
  • 1.13 lines changed: 3, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/marmoset/calJac1/visibility.ra
  • 1.2 lines changed: 3, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/marmoset/priority.ra
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    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/marmoset/trackDb.chainNet.ra
  • 1.2 lines changed: 25, context: html, text, full: html, text
    In same order as conservation track
  • 1.1 lines changed: 39, context: html, text, full: html, text
    All chain net tracks in Marmoset are now composite tracks
• src/hg/makeDb/trackDb/marmoset/trackDb.ra
  • 1.6 lines changed: 11, context: html, text, full: html, text
    All chain net tracks in Marmoset are now composite tracks
  • 1.5 lines changed: 14, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/medaka/priority.ra
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    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/medaka/trackDb.ra
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    Merging visibility.ra and priority.ra files back into trackDb.ra
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    Little fixes to trackDb.ra
  • 1.16 lines changed: 4, context: html, text, full: html, text
    remove orphaned overrides for humanChainNet and horseChainNet
• src/hg/makeDb/trackDb/mouse/mm7/bosTau2.chainNet.html
  • 1.1 lines changed: 153, context: html, text, full: html, text
    Ancient chain track has no axtChain
• src/hg/makeDb/trackDb/mouse/mm8/trackDb.ra
  • 1.59 lines changed: 25, context: html, text, full: html, text
    fix autoscale to read properly autoScale
• src/hg/makeDb/trackDb/mouse/priority.ra
  • 1.13 lines changed: 230, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • 1.163 lines changed: 178, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
  • 1.162 lines changed: 0, context: html, text, full: html, text
    Little fixes to trackDb.ra
  • 1.161 lines changed: 6, context: html, text, full: html, text
    remove orphaned overrides for humanChainNet and horseChainNet
  • 1.160 lines changed: 9, context: html, text, full: html, text
    Eliminate duplicate xenoRefGene entry
• src/hg/makeDb/trackDb/mouse/visibility.ra
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    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/opossum/trackDb.ra
  • 1.33 lines changed: 11, context: html, text, full: html, text
    remove orphaned overrides for humanChainNet and horseChainNet
  • 1.32 lines changed: 3, context: html, text, full: html, text
    Fixing some duplicates found by tdbQuery
• src/hg/makeDb/trackDb/platypus/ornAna1/priority.ra
  • 1.6 lines changed: 18, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/platypus/ornAna1/trackDb.ra
  • 1.15 lines changed: 6, context: html, text, full: html, text
    Moving horse c/n up a level. No combo chainNet track.
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    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/platypus/trackDb.ra
  • 1.8 lines changed: 29, context: html, text, full: html, text
    Moving horse c/n up a level. No combo chainNet track.
  • 1.7 lines changed: 7, context: html, text, full: html, text
    correctly ordering Opossum. overriding chain vars for Horse.
  • 1.6 lines changed: 0, context: html, text, full: html, text
    Little fixes to trackDb.ra
  • 1.5 lines changed: 10, context: html, text, full: html, text
    remove orphaned overrides for humanChainNet and horseChainNet
• src/hg/makeDb/trackDb/rabbit/ctgPos2.html
  • 1.1 lines changed: 8, context: html, text, full: html, text
    Adding ctgPos2 track for oryCun2
• src/hg/makeDb/trackDb/rabbit/trackDb.ra
  • 1.2 lines changed: 8, context: html, text, full: html, text
    Adding ctgPos2 track for oryCun2
  • 1.1 lines changed: 2, context: html, text, full: html, text
    Moving visibility.ra contents to new trackDb.ra file for rabbit.
• src/hg/makeDb/trackDb/rabbit/visibility.ra
  • 1.3 lines changed: 2, context: html, text, full: html, text
    Moving visibility.ra contents to new trackDb.ra file for rabbit.
• src/hg/makeDb/trackDb/rat/priority.ra
  • 1.6 lines changed: 112, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/rat/rn4/priority.ra
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    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
  • 1.44 lines changed: 2, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/rat/rn5/trackDb.ra
  • 1.2 lines changed: 47, context: html, text, full: html, text
    Obsolete genome at this time. May reappear sometime in the future
• src/hg/makeDb/trackDb/rat/trackDb.ra
  • 1.59 lines changed: 3, context: html, text, full: html, text
    Fixing a few little places where the automatic rewrite left duplicate records.
  • 1.58 lines changed: 127, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/rat/visibility.ra
  • 1.7 lines changed: 47, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/rhesus/priority.ra
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    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/rhesus/rheMac1/trackDb.ra
  • 1.7 lines changed: 12, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/rhesus/rheMac1/visibility.ra
  • 1.3 lines changed: 11, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.ra
  • 1.49 lines changed: 10, context: html, text, full: html, text
    eliminate duplicate entry for phastConsElements5way
• src/hg/makeDb/trackDb/rhesus/trackDb.ra
  • 1.13 lines changed: 14, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/sacCer/trackDb.ra
  • 1.44 lines changed: 1, context: html, text, full: html, text
    added dragAndDrop subTracks line to parent block of UW Footprints composite track to enable drag & reorder of subtracks
• src/hg/makeDb/trackDb/shrew/sorAra1/description.html
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Adding link to sequencing center project page
• src/hg/makeDb/trackDb/snp130.html
  • 1.11 lines changed: 2, context: html, text, full: html, text
    Removed mention of cds-reference since we no longer include that in the table (thx Katrina!).
• src/hg/makeDb/trackDb/squirt/ci1/trackDb.ra
  • 1.51 lines changed: 11, context: html, text, full: html, text
    Eliminate duplicate entry for blastzOikDio0
  • 1.50 lines changed: 1, context: html, text, full: html, text
    Eliminate a stray track definition line for blastzCioSav1
• src/hg/makeDb/trackDb/squirt/ci2/trackDb.ra
  • 1.8 lines changed: 12, context: html, text, full: html, text
    eliminate duplicate entries for blastzCioSav1 and blastzOikDio0
• src/hg/makeDb/trackDb/squirt/cioSav2/trackDb.ra
  • 1.7 lines changed: 12, context: html, text, full: html, text
    eliminate duplicate entries for blastzCioSav1 and blastzOikDio0
• src/hg/makeDb/trackDb/squirt/trackDb.ra
  • 1.13 lines changed: 5, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/squirt/visibility.ra
  • 1.2 lines changed: 3, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/stickleback/priority.ra
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    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/stickleback/trackDb.ra
  • 1.21 lines changed: 15, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
  • 1.20 lines changed: 0, context: html, text, full: html, text
    Little fixes to trackDb.ra
  • 1.19 lines changed: 4, context: html, text, full: html, text
    remove orphaned overrides for humanChainNet and horseChainNet
  • 1.18 lines changed: 14, context: html, text, full: html, text
    Fixing some duplicates found by tdbQuery
• src/hg/makeDb/trackDb/tagTypes.tab
  • 1.4 lines changed: 4, context: html, text, full: html, text
    Added 3 dimensionChecked terms and made subGroup6 allowed on any type
  • 1.3 lines changed: 9, context: html, text, full: html, text
    Making trackDb pass tdbQuery -check -alpha
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Moving around some subtracks that weren't directly under their parents. Adding some indentation to subtracks.
  • 1.1 lines changed: 270, context: html, text, full: html, text
    Adding file that list all available tags and the types they can appear in.
• src/hg/makeDb/trackDb/tetraodon/priority.ra
  • 1.2 lines changed: 8, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/tetraodon/trackDb.ra
  • 1.42 lines changed: 11, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
  • 1.41 lines changed: 0, context: html, text, full: html, text
    Little fixes to trackDb.ra
  • 1.40 lines changed: 4, context: html, text, full: html, text
    remove orphaned overrides for humanChainNet and horseChainNet
• src/hg/makeDb/trackDb/tetraodon/visibility.ra
  • 1.2 lines changed: 3, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • 1.3 lines changed: 162, context: html, text, full: html, text
    All chain net tracks in Marmoset are now composite tracks
  • 1.2 lines changed: 82, context: html, text, full: html, text
    adding chainNetRn4 and chainNetHg18 for Cow bosTau browsers and setting appropriate release tags to separate from older individual tracks
  • 1.1 lines changed: 559, context: html, text, full: html, text
    Move all the chainNet definitions off to their own file
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.549 lines changed: 8, context: html, text, full: html, text
    All chain net tracks in Marmoset are now composite tracks
  • 1.548 lines changed: 8, context: html, text, full: html, text
    adding chainNetRn4 and chainNetHg18 for Cow bosTau browsers and setting appropriate release tags to separate from older individual tracks
  • 1.547 lines changed: 561, context: html, text, full: html, text
    Move all the chainNet definitions off to their own file
  • 1.546 lines changed: 1, context: html, text, full: html, text
    Adding a little more comment.
  • 1.545 lines changed: 5, context: html, text, full: html, text
    Fixing a few little places where the automatic rewrite left duplicate records.
  • 1.544 lines changed: 2, context: html, text, full: html, text
    fixup duplicate chainCalJac1 and chainPanTro2 entries
  • 1.543 lines changed: 31, context: html, text, full: html, text
    Removing duplicate track records at same level of directory hierarchy, in many cases by adding a missing release tag.
  • 1.542 lines changed: 1, context: html, text, full: html, text
    Removing duplicate tags within same stanza.
  • 1.541 lines changed: 3, context: html, text, full: html, text
    Decluttering genes section. Hiding MGC genes by default. Putting hg19's RefSeq Genes back to dense.
• src/hg/makeDb/trackDb/worm/caeJap1/trackDb.ra
  • 1.4 lines changed: 14, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/worm/caeJap1/visibility.ra
  • 1.2 lines changed: 14, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/worm/caePb2/trackDb.ra
  • 1.5 lines changed: 6, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/worm/caePb2/visibility.ra
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/worm/caeRem2/priority.ra
  • 1.2 lines changed: 15, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/worm/caeRem2/trackDb.ra
  • 1.8 lines changed: 15, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/worm/caeRem3/trackDb.ra
  • 1.4 lines changed: 9, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/worm/caeRem3/visibility.ra
  • 1.2 lines changed: 5, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/worm/ce2/trackDb.ra
  • 1.36 lines changed: 11, context: html, text, full: html, text
    eliminate duplicate definition for axtNetCb1
• src/hg/makeDb/trackDb/worm/ce4/trackDb.ra
  • 1.39 lines changed: 9, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/worm/ce4/visibility.ra
  • 1.2 lines changed: 5, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/worm/ce6/priority.ra
  • 1.2 lines changed: 17, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/worm/ce6/trackDb.ra
  • 1.16 lines changed: 42, context: html, text, full: html, text
    Some Fire Lab experiments
  • 1.15 lines changed: 21, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/worm/ce7/trackDb.ra
  • 1.5 lines changed: 3, context: html, text, full: html, text
    ensGene default pack
• src/hg/makeDb/trackDb/worm/priPac1/priority.ra
  • 1.2 lines changed: 5, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/worm/priPac1/trackDb.ra
  • 1.8 lines changed: 9, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/xenTro/priority.ra
  • 1.3 lines changed: 10, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/xenTro/trackDb.ra
  • 1.23 lines changed: 14, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
  • 1.22 lines changed: 2, context: html, text, full: html, text
    Fixing visibililty typo
  • 1.21 lines changed: 4, context: html, text, full: html, text
    remove orphaned overrides for humanChainNet and horseChainNet
• src/hg/makeDb/trackDb/xenTro/xenTro2/trackDb.ra
  • 1.18 lines changed: 8, context: html, text, full: html, text
    Fixing some duplicates found by tdbQuery
• src/hg/makeDb/trackDb/zebraFinch/trackDb.ra
  • 1.5 lines changed: 0, context: html, text, full: html, text
    Little fixes to trackDb.ra
  • 1.4 lines changed: 5, context: html, text, full: html, text
    remove orphaned overrides for humanChainNet and horseChainNet
• src/hg/makeDb/trackDb/zebrafish/danRer3/priority.ra
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/zebrafish/danRer3/trackDb.ra
  • 1.53 lines changed: 6, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
  • 1.52 lines changed: 3, context: html, text, full: html, text
    Fixing some duplicates found by tdbQuery
• src/hg/makeDb/trackDb/zebrafish/danRer4/priority.ra
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/zebrafish/danRer4/trackDb.ra
  • 1.36 lines changed: 6, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/zebrafish/danRer5/priority.ra
  • 1.7 lines changed: 26, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/zebrafish/danRer5/trackDb.ra
  • 1.24 lines changed: 30, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDb/zebrafish/trackDb.ra
  • 1.56 lines changed: 6, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
  • 1.55 lines changed: 4, context: html, text, full: html, text
    remove orphaned overrides for humanChainNet and horseChainNet
  • 1.54 lines changed: 0, context: html, text, full: html, text
    Fixing some duplicates found by tdbQuery
• src/hg/makeDb/trackDb/zebrafish/visibility.ra
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Merging visibility.ra and priority.ra files back into trackDb.ra
• src/hg/makeDb/trackDbPatch/trackDbPatch.c
  • 1.3 lines changed: 38, context: html, text, full: html, text
    Did some testing, took out debugging statements, and polished interface a little.
• src/hg/makefile
  • 1.154 lines changed: 4, context: html, text, full: html, text
    Adding tooltip CGI in ifdef LOWELAB
• src/hg/oneShot/freen/freen.c
  • 1.95 lines changed: 8, context: html, text, full: html, text
    Freen tests rqlStatementDump
• src/hg/oneShot/makeTrackDbTagVals/makeTrackDbTagVals.c
  • 1.1 lines changed: 109, context: html, text, full: html, text
    Utility to extract values of tags actually seen seems to work.
• src/hg/oneShot/makeTrackDbTagVals/makefile
  • 1.1 lines changed: 18, context: html, text, full: html, text
    Utility to extract values of tags actually seen seems to work.
• src/hg/oneShot/makeTrackDbTypeTags/makeTrackDbTypeTags.c
  • 1.1 lines changed: 110, context: html, text, full: html, text
    Utility to make first cut of tagTypes.tab seems to work.
• src/hg/oneShot/makeTrackDbTypeTags/makefile
  • 1.1 lines changed: 18, context: html, text, full: html, text
    Utility to make first cut of tagTypes.tab seems to work.
• src/hg/oneShot/tdbRewriteAddReplaces/makefile
  • 1.1 lines changed: 18, context: html, text, full: html, text
    Rewriter that adds 'replace' on track lines in subdirectories where are redefining an old track rather than defining a new track at that level.
• src/hg/oneShot/tdbRewriteAddReplaces/tdbRewriteAddReplaces.c
  • 1.2 lines changed: 16, context: html, text, full: html, text
    Getting rid of debugging statements.
  • 1.1 lines changed: 501, context: html, text, full: html, text
    Rewriter that adds 'replace' on track lines in subdirectories where are redefining an old track rather than defining a new track at that level.
• src/hg/oneShot/tdbRewriteReduceReplaces/makefile
  • 1.1 lines changed: 18, context: html, text, full: html, text
    Rewriter that will convert replacement records to override records when possible, and otherwise add comment that it is a replacement record seems to work.
• src/hg/oneShot/tdbRewriteReduceReplaces/tdbRewriteReduceReplaces.c
  • 1.1 lines changed: 572, context: html, text, full: html, text
    Rewriter that will convert replacement records to override records when possible, and otherwise add comment that it is a replacement record seems to work.
• src/hg/oneShot/tdbRewriteSortTags/makefile
  • 1.1 lines changed: 18, context: html, text, full: html, text
    Rewriter that alphabetizes tags after the first one in a stanza. Not totally sure I like result, but worth bouncing off other people.
• src/hg/oneShot/tdbRewriteSortTags/tdbRewriteSortTags.c
  • 1.1 lines changed: 172, context: html, text, full: html, text
    Rewriter that alphabetizes tags after the first one in a stanza. Not totally sure I like result, but worth bouncing off other people.
• src/hg/oneShot/tdbRewriteViewsToSubtracks/makefile
  • 1.1 lines changed: 17, context: html, text, full: html, text
    Rewriter to take out views and put in a new layer of hierarchy seems to work.
• src/hg/oneShot/tdbRewriteViewsToSubtracks/tdbRewriteViewsToSubtracks.c
  • 1.1 lines changed: 762, context: html, text, full: html, text
    Rewriter to take out views and put in a new layer of hierarchy seems to work.
• src/hg/qaPushQ/pushQ.as
  • 1.15 lines changed: 1, context: html, text, full: html, text
    oops get lockuser
• src/hg/qaPushQ/pushQ.c
  • 1.14 lines changed: 0, context: html, text, full: html, text
    oops get lockuser
• src/hg/qaPushQ/pushQ.h
  • 1.13 lines changed: 1, context: html, text, full: html, text
    oops get lockuser
• src/hg/qaPushQ/pushQ.sql
  • 1.14 lines changed: 1, context: html, text, full: html, text
    oops get lockuser
• src/hg/qaPushQ/qaPushQ.c
  • 1.115 lines changed: 6, context: html, text, full: html, text
    requested feature quicklinks to jump to sections ABCDL
• src/hg/snp/snpLoad/illuminaLookup1M.c
  • 1.2 lines changed: 9, context: html, text, full: html, text
    Updated illuminaLookup1M.c to make it work again for newer Illumina SNP array chips.
• src/hg/utils/automation/Encode.pm
  • 1.52 lines changed: 2, context: html, text, full: html, text
    move pairedTagAlign to bigBedTypes
  • 1.51 lines changed: 2, context: html, text, full: html, text
    Allow mouse
• src/hg/utils/makefile
  • 1.19 lines changed: 1, context: html, text, full: html, text
    Adding tdbQuery to build.
• src/hg/utils/phyloTrees/46way.dissect.txt
  • 1.1 lines changed: 637, context: html, text, full: html, text
    Initial contents
• src/hg/utils/phyloTrees/46way.nh
  • 1.1 lines changed: 21, context: html, text, full: html, text
    Initial contents
• src/hg/utils/phyloTrees/chainNet.pl
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Eliminate confusion from chainSelf tracks
  • 1.1 lines changed: 77, context: html, text, full: html, text
    Initial source appears to work OK
• src/hg/utils/phyloTrees/rerootTree.pl
  • 1.1 lines changed: 104, context: html, text, full: html, text
    Initial contents
• src/hg/utils/tdbQuery/makefile
  • 1.1 lines changed: 18, context: html, text, full: html, text
    Oops, forgot makefile in initial commit off of laptop.
• src/hg/utils/tdbQuery/tdbQuery.c
  • 1.24 lines changed: 1, context: html, text, full: html, text
    Fixed linux-specific compiler warning.
  • 1.23 lines changed: 4, context: html, text, full: html, text
    Avoiding generating a duplicate record for vis when there is both priority and vis.
  • 1.22 lines changed: 176, context: html, text, full: html, text
    Rewriting to get rid of visibility.ra and priority.ra files.
  • 1.21 lines changed: 51, context: html, text, full: html, text
    Starting to experiment with some rewriting. Not very far along.
  • 1.20 lines changed: 27, context: html, text, full: html, text
    Making tdbRecord have start and end lineIx, and also text representation of stanza.
  • 1.19 lines changed: 158, context: html, text, full: html, text
    Adding additional checks on child/parent relationships. Forcing children to be close to parent in file.
  • 1.18 lines changed: 27, context: html, text, full: html, text
    Making check for tag names in RQL query existing happen even without -check
  • 1.17 lines changed: 15, context: html, text, full: html, text
    When you do a -check also does check of query.
  • 1.16 lines changed: 8, context: html, text, full: html, text
    Adding -noBlank option
  • 1.15 lines changed: 48, context: html, text, full: html, text
    Fixing bug in -strict logic for parent tables.
  • 1.14 lines changed: 74, context: html, text, full: html, text
    Making -check do something, specifically look for tagTypes.tab and check tags against it.
  • 1.13 lines changed: 7, context: html, text, full: html, text
    Removing unimplemented 'file' option from usage statement.
  • 1.12 lines changed: 4, context: html, text, full: html, text
    Adding lm parameter to rqlEvalOnRecord since array operation uses memory.
  • 1.11 lines changed: 3, context: html, text, full: html, text
    Implementing limit clause.
  • 1.10 lines changed: 16, context: html, text, full: html, text
    Making -strict leave in parents when their children exist.
  • 1.9 lines changed: 70, context: html, text, full: html, text
    Adding in visibility.ra and priority.ra handling.
  • 1.8 lines changed: 243, context: html, text, full: html, text
    Massaging handling of duplicate record detection to handle a tricky case in danRer6 involving inheritence and inherited releases.
  • 1.7 lines changed: 2, context: html, text, full: html, text
    Improving usage message.
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Fixing linux compiler complaints.
  • 1.5 lines changed: 42, context: html, text, full: html, text
    Cleaning up debugging statements and also db and filePos pseudo-field handling.
  • 1.4 lines changed: 368, context: html, text, full: html, text
    Starting to work. Lots of debugging code still in.
  • 1.3 lines changed: 116, context: html, text, full: html, text
    Adding check for duplicate records including handling of different records for different releases. Merging together records from root/organism/assembly tree.
  • 1.2 lines changed: 63, context: html, text, full: html, text
    Handling include files. CHecking for duplicate tags (in non-include stanzas)
  • 1.1 lines changed: 245, context: html, text, full: html, text
    Initial commit of tdbQuery. Still has clones of some files from raSqlQuery that will eventually end up in library when more stable.
• src/hg/utils/tdbQuery/tdbQuery.doc
  • 1.3 lines changed: 22, context: html, text, full: html, text
    Improving docs.
  • 1.2 lines changed: 56, context: html, text, full: html, text
    Adding to documentation.
  • 1.1 lines changed: 12, context: html, text, full: html, text
    Removing unimplemented 'file' option from usage statement.
• src/hg/utils/tdbQuery/tdbRecord.c
  • 1.5 lines changed: 3, context: html, text, full: html, text
    Fixing bug that limited to no more than 4 settings in a settingsByLimit for any view. Sharpening line number reporting in error messages.
  • 1.4 lines changed: 16, context: html, text, full: html, text
    Making tdbRecord have start and end lineIx, and also text representation of stanza.
  • 1.3 lines changed: 3, context: html, text, full: html, text
    Adding in visibility.ra and priority.ra handling.
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Fixing linux compiler complaints.
  • 1.1 lines changed: 156, context: html, text, full: html, text
    Initial commit of tdbQuery. Still has clones of some files from raSqlQuery that will eventually end up in library when more stable.
• src/hg/utils/tdbQuery/tdbRecord.h
  • 1.2 lines changed: 12, context: html, text, full: html, text
    Making tdbRecord have start and end lineIx, and also text representation of stanza.
  • 1.1 lines changed: 47, context: html, text, full: html, text
    Initial commit of tdbQuery. Still has clones of some files from raSqlQuery that will eventually end up in library when more stable.
• src/inc/cheapcgi.h
  • 1.69 lines changed: 7, context: html, text, full: html, text
    added new func javaScriptLiteralEncode
  • 1.68 lines changed: 4, context: html, text, full: html, text
    Added a couple color defines
• src/inc/localmem.h
  • 1.9 lines changed: 4, context: html, text, full: html, text
    Adding lmCloneSomeWord.
  • 1.8 lines changed: 3, context: html, text, full: html, text
    Adding lmCloneFirstWord
• src/inc/ra.h
  • 1.8 lines changed: 6, context: html, text, full: html, text
    Adding optional dyString parameter.
• src/inc/rql.h
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Adding in whereVarList to rqlStatement
  • 1.5 lines changed: 4, context: html, text, full: html, text
    Adding lm parameter to rqlEvalOnRecord since array operation uses memory.
  • 1.4 lines changed: 17, context: html, text, full: html, text
    Making rqlParser handle arrays and field-separating-dots. Evaluation handles arrays but not dots yet.
  • 1.3 lines changed: 4, context: html, text, full: html, text
    Adding integer unary minus.
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Adding limit clause to RQL parsing.
  • 1.1 lines changed: 118, context: html, text, full: html, text
    Adding rql parser and evaluator to library.
• src/jkOwnLib/gfPcrLib.c
  • 1.12 lines changed: 12, context: html, text, full: html, text
    fixing neg strand issue reported by user for pcr psl output
• src/lib/cheapcgi.c
  • 1.126 lines changed: 58, context: html, text, full: html, text
    added new func javaScriptLiteralEncode
• src/lib/localmem.c
  • 1.13 lines changed: 17, context: html, text, full: html, text
    Adding lmCloneSomeWord.
  • 1.12 lines changed: 14, context: html, text, full: html, text
    Adding lmCloneFirstWord
• src/lib/makefile
  • 1.157 lines changed: 1, context: html, text, full: html, text
    Adding rql parser and evaluator to library.
• src/lib/options.c
  • 1.29 lines changed: 1, context: html, text, full: html, text
    Fixing bug where options was no longer handling -this=that, just this=that.
  • 1.28 lines changed: 12, context: html, text, full: html, text
    Making the this=that option parsing smart about not trying to parse code, filenames, and other things as option. Previously it knew not to treat URLs with = as options.
• src/lib/ra.c
  • 1.17 lines changed: 25, context: html, text, full: html, text
    Making it so that don't lose blank terminating lines in raNextTagVal. Simplifying logic in raSkipLeadingEmptyLines.
  • 1.16 lines changed: 17, context: html, text, full: html, text
    Fixing some problems with the new dyString parameter to the ra readers.
  • 1.15 lines changed: 37, context: html, text, full: html, text
    Adding optional dyString parameter.
• src/lib/rqlEval.c
  • 1.4 lines changed: 28, context: html, text, full: html, text
    Adding lm parameter to rqlEvalOnRecord since array operation uses memory.
  • 1.3 lines changed: 91, context: html, text, full: html, text
    Making rqlParser handle arrays and field-separating-dots. Evaluation handles arrays but not dots yet.
  • 1.2 lines changed: 6, context: html, text, full: html, text
    Adding integer unary minus.
  • 1.1 lines changed: 289, context: html, text, full: html, text
    Adding rql parser and evaluator to library.
• src/lib/rqlParse.c
  • 1.7 lines changed: 20, context: html, text, full: html, text
    Adding whereVarList to rqlStatement structure.
  • 1.6 lines changed: 16, context: html, text, full: html, text
    Adding lm parameter to rqlEvalOnRecord since array operation uses memory.
  • 1.5 lines changed: 77, context: html, text, full: html, text
    Making rqlParser handle arrays and field-separating-dots. Evaluation handles arrays but not dots yet.
  • 1.4 lines changed: 12, context: html, text, full: html, text
    Adding integer unary minus.
  • 1.3 lines changed: 36, context: html, text, full: html, text
    Adding limit clause to RQL parsing.
  • 1.2 lines changed: 26, context: html, text, full: html, text
    Adding rqlStatementFree.
  • 1.1 lines changed: 643, context: html, text, full: html, text
    Adding rql parser and evaluator to library.
• src/lib/tests/udcTest.c
  • 1.1 lines changed: 285, context: html, text, full: html, text
    New test for udc: interleave accesses from two open udcFile * handles to the same part of a URL/file. Fairly reliably fails on hgwdev. I'm not hooking it into makefile until udc passes.
• src/parasol/inc/paraLib.h
  • 1.26 lines changed: 5, context: html, text, full: html, text
    added -cpu and -ram to the parasol add jobs command
• src/parasol/lib/paraLib.c
  • 1.33 lines changed: 34, context: html, text, full: html, text
    added -cpu and -ram to the parasol add jobs command
• src/parasol/para/para.c
  • 1.107 lines changed: 36, context: html, text, full: html, text
    added -cpu and -ram to the parasol add jobs command
• src/parasol/parasol/parasol.c
  • 1.49 lines changed: 23, context: html, text, full: html, text
    added -cpu and -ram to the parasol add jobs command
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.91 lines changed: 2, context: html, text, full: html, text
    v221 preview
• src/utils/raSqlQuery/makefile
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Librarifying RQL parser and interpreter.
• src/utils/raSqlQuery/raRecord.c
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Fixing bug that limited to no more than 4 settings in a settingsByLimit for any view.
  • 1.9 lines changed: 13, context: html, text, full: html, text
    Librarifying RQL parser and interpreter.
• src/utils/raSqlQuery/raSqlQuery.c
  • 1.26 lines changed: 3, context: html, text, full: html, text
    Adding lm parameter to rqlEvalOnRecord since array operation uses memory.
  • 1.25 lines changed: 12, context: html, text, full: html, text
    Librarifying RQL parser and interpreter.
• src/utils/raSqlQuery/rql.h
  • 1.3 lines changed: 99, context: html, text, full: html, text
    Librarifying RQL parser and interpreter.
• src/utils/raSqlQuery/rqlEval.c
  • 1.3 lines changed: 288, context: html, text, full: html, text
    Librarifying RQL parser and interpreter.
• src/utils/raSqlQuery/rqlParse.c
  • 1.9 lines changed: 643, context: html, text, full: html, text
    Librarifying RQL parser and interpreter.
• src/utils/raSqlQuery/test.ra
  • 1.2 lines changed: 3, context: html, text, full: html, text
    Adding lm parameter to rqlEvalOnRecord since array operation uses memory.

• lines changed: 37943
• files changed: 272