CVS changes by file

review to branch (2009-05-05 to 2009-05-12) v206

• src/hg/archaeStuff/data/Genome-info-mods
  • 1.67 lines changed: 1, context: html, text, full: html, text
    add org_abr for natrMaga0
• src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
  • 1.12 lines changed: 168, context: html, text, full: html, text
    Now the page will be sorted on the defined sort order fields from the metadata.
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.181 lines changed: 8, context: html, text, full: html, text
    Fixed -quick, allow fragLength=0, removed obsolete trackDb.ra settings
• src/hg/hgLiftOver/hgLiftOver.c
  • 1.61 lines changed: 2, context: html, text, full: html, text
    Changed example double-lift from human to mouse, as we now have the direct lifts for the human example mentioned.
• src/hg/hgTables/mainPage.c
  • 1.143 lines changed: 3, context: html, text, full: html, text
    Free memory after restrictionDate lookup
• src/hg/hgTables/microarrayTables.c
  • 1.4 lines changed: 1, context: html, text, full: html, text
    fixed typo
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.488 lines changed: 11, context: html, text, full: html, text
    Call common API for showing downloads, schema and metadata links
  • 1.487 lines changed: 1, context: html, text, full: html, text
    Changed 'Track details..s' to 'Table metadata...'
  • 1.486 lines changed: 5, context: html, text, full: html, text
    Added call to show metadata if track is not a composite
• src/hg/hgTracks/hgTracks.c
  • 1.1565 lines changed: 2, context: html, text, full: html, text
    Quick fix for an interaction bug before the code release -- I hope a cleaner fix can be implemented afterwards. groupTracks() removes cart vars that are redundant with trackDb settings, which I think is good for reducing cart bloat. Unfortunately, something upstream of trackFromTrackDb, and also trackFromTrackDb itself, overwrite tdb->priority with the cart value, causing false detection of redundancy with trackDb here.
  • 1.1564 lines changed: 8, context: html, text, full: html, text
    Allow hg19 to click through to pre.ensembl.org with chr name translation
• src/hg/hgc/hgc.c
  • 1.1541 lines changed: 4, context: html, text, full: html, text
    Added h1n1_0511Seq (last time was h1n1b_0511Seq).
  • 1.1540 lines changed: 4, context: html, text, full: html, text
    Added h1n1_0511Seq.
  • 1.1539 lines changed: 2, context: html, text, full: html, text
    Call common API for showing downloads, schema and metadata links
  • 1.1538 lines changed: 8, context: html, text, full: html, text
    Added h1n1_0506Seq and h1n1b_0506Seq.
  • 1.1537 lines changed: 14, context: html, text, full: html, text
    doKomp: Added explicit inclusion of all targets for given gene, with the Design ID now appended to each gene name.
  • 1.1536 lines changed: 8, context: html, text, full: html, text
    Allow click through to NCBI entrez search for Contig names on ctgPos tracks
  • 1.1535 lines changed: 11, context: html, text, full: html, text
    Added the special case Ensembl Transcript Report link back in, due to tRNAs not having Ensembl IDs causing the trackDb.ra url setting to fail
  • 1.1534 lines changed: 5, context: html, text, full: html, text
    Added call to show metadata
  • 1.1533 lines changed: 27, context: html, text, full: html, text
    Removed obsolete special case code for ENCODE Gencode linking to VEGA and Ensembl, because this is now done with trackDB.ra url settin. Also made dataVersion and restriction date use metadata
• src/hg/hgc/hgc.h
  • 1.46 lines changed: 2, context: html, text, full: html, text
    Allow click through to NCBI entrez search for Contig names on ctgPos tracks
• src/hg/hgc/lowelab.c
  • 1.32 lines changed: 343, context: html, text, full: html, text
    fix hTableExist call for blastp track; change code to use centraldb name from hg.conf; add code to support blastx track
• src/hg/inc/ensFace.h
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Properly lift to Ensembl haplotype coordinates for Blue bar click through
  • 1.7 lines changed: 4, context: html, text, full: html, text
    Allow hg19 to click through to pre.ensembl.org with chr name translation
• src/hg/inc/hui.h
  • 1.128 lines changed: 3, context: html, text, full: html, text
    Added API for hgTrackUi and hgc to show schemaLink, Downlaods link and metadata
  • 1.127 lines changed: 3, context: html, text, full: html, text
    Moved metadata display to separate function to be called from hgc and hgTables
  • 1.126 lines changed: 2, context: html, text, full: html, text
    Clarified function comment
• src/hg/inc/trackDb.h
  • 1.48 lines changed: 4, context: html, text, full: html, text
    Added simple routine to find a metadata setting
• src/hg/inc/versionInfo.h
  • 1.146 lines changed: 1, context: html, text, full: html, text
    "New version number v206"
• src/hg/instinct/hgHeatmap2/drawingCode.c
  • 1.65 lines changed: 2, context: html, text, full: html, text
    Forced hg18 for genoLayChrom db to allow custom tracks
• src/hg/instinct/hgHeatmap2/hgHeatmap2.c
  • 1.75 lines changed: 23, context: html, text, full: html, text
    Added custom track loader
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_COSMIC.ra
  • 1.2 lines changed: 3, context: html, text, full: html, text
    Updated this dataset
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_balagurunathan2008.ra
  • 1.1 lines changed: 18, context: html, text, full: html, text
    
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_bardeesy2006.ra
  • 1.1 lines changed: 9, context: html, text, full: html, text
    
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_cutler2007.ra
  • 1.1 lines changed: 18, context: html, text, full: html, text
    
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_haverty2008.ra
  • 1.1 lines changed: 90, context: html, text, full: html, text
    
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_intgenOVBio.ra
  • 1.3 lines changed: 98, context: html, text, full: html, text
    Added new features
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_mullighan2008.ra
  • 1.1 lines changed: 27, context: html, text, full: html, text
    
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.ra
  • 1.9 lines changed: 120, context: html, text, full: html, text
    New Datasets
• src/hg/instinct/inc/hgHeatmapCustomDb.h
  • 1.1 lines changed: 247, context: html, text, full: html, text
    Adding autosql for the custom clinical db
• src/hg/instinct/inc/hgHeatmapLib.h
  • 1.36 lines changed: 2, context: html, text, full: html, text
    Adding autosql for the custom clinical db
• src/hg/instinct/lib/hgHeatmapCustomDb.c
  • 1.1 lines changed: 574, context: html, text, full: html, text
    Adding autosql for the custom clinical db
• src/hg/instinct/lib/hgHeatmapLib.c
  • 1.58 lines changed: 24, context: html, text, full: html, text
    Added platform and platform type for genesets
  • 1.57 lines changed: 38, context: html, text, full: html, text
    Added custom track handling
• src/hg/instinct/lib/makefile
  • 1.14 lines changed: 1, context: html, text, full: html, text
    Adding autosql for the custom clinical db
• src/hg/js/hui.js
  • 1.26 lines changed: 20, context: html, text, full: html, text
    Moved metadata display toggle code to utils to be called from hgc and hgTrackUi
• src/hg/js/utils.js
  • 1.21 lines changed: 21, context: html, text, full: html, text
    Moved metadata display toggle code to utils to be called from hgc and hgTrackUi
• src/hg/lib/ensFace.c
  • 1.11 lines changed: 28, context: html, text, full: html, text
    Properly lift to Ensembl haplotype coordinates for Blue bar click through
  • 1.10 lines changed: 28, context: html, text, full: html, text
    Allow hg19 to click through to pre.ensembl.org with chr name translation
• src/hg/lib/hui.c
  • 1.194 lines changed: 3, context: html, text, full: html, text
    Added a link to help on 'Filter by category' UI
  • 1.193 lines changed: 111, context: html, text, full: html, text
    Added API for hgTrackUi and hgc to show schemaLink, Downlaods link and metadata
  • 1.192 lines changed: 57, context: html, text, full: html, text
    Moved metadata display to separate function to be called from hgc and hgTables
  • 1.191 lines changed: 37, context: html, text, full: html, text
    Use metadata setting for controlled vocabulary look up and for restriction date lookup
• src/hg/lib/trackDbCustom.c
  • 1.64 lines changed: 22, context: html, text, full: html, text
    Added simple routine to find a metadata setting
• src/hg/makeDb/doc/h1n1.txt
  • 1.3 lines changed: 40, context: html, text, full: html, text
    Added h1n1_0506Seq track.
• src/hg/makeDb/doc/hg18.txt
  • 1.361 lines changed: 13, context: html, text, full: html, text
    FOX2 clusters track from Gene Yeo
  • 1.360 lines changed: 39, context: html, text, full: html, text
    Add UCSC to Ensembl chrom name translation and haplotype lift tables for Blue Bar Ensembl click through
• src/hg/makeDb/doc/hg19.txt
  • 1.11 lines changed: 74, context: html, text, full: html, text
    Running Mouse Mm9 and Dog CanFam2 blastz
  • 1.10 lines changed: 230, context: html, text, full: html, text
    Document ctgPos table build, done with STS Markers, BAC Ends, and now working on FISH Clones
  • 1.9 lines changed: 1065, context: html, text, full: html, text
    STS Markers track done
• src/hg/makeDb/doc/mm9.txt
  • 1.93 lines changed: 26, context: html, text, full: html, text
    IKMC (komp): data update.
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • 1.98 lines changed: 1, context: html, text, full: html, text
    Added monDom5.
• src/hg/makeDb/hgCgiData/Human/microarrayGroups.ra
  • 1.75 lines changed: 86, context: html, text, full: html, text
    New Datasets
• src/hg/makeDb/schema/all.joiner
  • 1.713 lines changed: 1, context: html, text, full: html, text
    Added fox2ClipClusters to tables ignored.
  • 1.712 lines changed: 1, context: html, text, full: html, text
    added monDom5 as appropriate
  • 1.711 lines changed: 21, context: html, text, full: html, text
    removed all mention of affyHumanExon% tables (they are gone, never to return, says Andy)
• src/hg/makeDb/trackDb/README
  • 1.70 lines changed: 46, context: html, text, full: html, text
    Added description of scoreFilter and filterBy category
• src/hg/makeDb/trackDb/human/hg18/trackDb.instinct.ra
  • 1.40 lines changed: 76, context: html, text, full: html, text
    New datasets
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.293 lines changed: 16, context: html, text, full: html, text
    Changed the name of some Yale tables to be consistent
  • 1.292 lines changed: 518, context: html, text, full: html, text
    Had to regen some 1/2 of Yale Raw Signals. Since already release, made alpha/beta tracks.
  • 1.291 lines changed: 461, context: html, text, full: html, text
    Added Duke/Uta/Unc Raw signals back in, now that they have been regenerated.
  • 1.290 lines changed: 460, context: html, text, full: html, text
    Temprarily comment out Duke/Unc/Uta RawSignals while they are regenerated
  • 1.289 lines changed: 2, context: html, text, full: html, text
    Removed the Gencode url setting for auto-annotated track. tRNAs have no Ensembl ID so the link was broken.
  • 1.288 lines changed: 75, context: html, text, full: html, text
    Fixed some Yale metadata and make Gencode not a default track (as per Jim)
  • 1.287 lines changed: 232, context: html, text, full: html, text
    Added UW Affy Exon track and UW WERI-Rb-1 ChIP-seq subtrack.
  • 1.286 lines changed: 841, context: html, text, full: html, text
    Removed a lot of obsolete settings - values now in metadata. Should remove all these obsolete settings from non-released tracks
  • 1.285 lines changed: 14, context: html, text, full: html, text
    Marked the metadata of Yale's datasets that still have problems (peaks and signals)
  • 1.284 lines changed: 395, context: html, text, full: html, text
    Added 6 more datasets for Yale and changed the Peak controls
• src/hg/makeDb/trackDb/human/hg18/wgEncodeSangerGencode.html
  • 1.11 lines changed: 6, context: html, text, full: html, text
    Added Display Conventions section
• src/hg/makeDb/trackDb/human/hg19/ctgPos.html
  • 1.1 lines changed: 28, context: html, text, full: html, text
    Assembly description for hg19 is different
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.17 lines changed: 20, context: html, text, full: html, text
    Blocks that exist solely to pick up local html diffs are no longer needed.
  • 1.16 lines changed: 19, context: html, text, full: html, text
    Replaced visibility.ra settings for netPanTro2 and refGene tracks with track override visibility settings, and condensed chainPanTro2 block tojust the matrix and matrixHeader lines.
• src/hg/makeDb/trackDb/human/hg19/visibility.ra
  • 1.3 lines changed: 6, context: html, text, full: html, text
    Removing this file because visibility.ra and priority.ra have been superceded by track override in the regular trackDb.ra file.
• src/hg/makeDb/trackDb/opossum/monDom5/description.html
  • 1.2 lines changed: 11, context: html, text, full: html, text
    added image and info about photo from monDom4
• src/hg/makeDb/trackDb/opossum/monDom5/gold.html
  • 1.2 lines changed: 6, context: html, text, full: html, text
    changed the explanation of the type because chrM contains a contig that is type F
• src/hg/makeDb/trackDb/sacCer/sacCer2/trackDb.ra
  • 1.5 lines changed: 4, context: html, text, full: html, text
    turning off some tracks by default
• src/hg/pslFilterPrimers/pslFilterPrimers.c
  • 1.5 lines changed: 3, context: html, text, full: html, text
    The line files need to be opened with zTerm and the split is on tab
• src/hg/stsMarkers/epcrToPsl
  • 1.5 lines changed: 6, context: html, text, full: html, text
    Proper size on target chromosome
  • 1.4 lines changed: 103, context: html, text, full: html, text
    This functioned OK on hg19
• src/hg/stsMarkers/fixPrimersQueryGaps.pl
  • 1.1 lines changed: 62, context: html, text, full: html, text
    Initial source rescued from /cluster/bin/scripts
• src/hg/stsMarkers/liftFromSpec.pl
  • 1.1 lines changed: 60, context: html, text, full: html, text
    Initial source, worked with the ePCR results for hg19
• src/hg/utils/automation/HgAutomate.pm
  • 1.26 lines changed: 2, context: html, text, full: html, text
    Do not check swarm for workhorse idle machines, and add orfeomeGenes to genbank list of tables for makePushQSql.pl
  • 1.25 lines changed: 11, context: html, text, full: html, text
    Adding encodek and disable sanvol1
• src/hg/utils/automation/makeGenomeDb.pl
  • 1.21 lines changed: 3, context: html, text, full: html, text
    maybe this is better ncbi url to fetch the chrM seq with
• src/hg/utils/automation/makePushQSql.pl
  • 1.24 lines changed: 1, context: html, text, full: html, text
    Do not check swarm for workhorse idle machines, and add orfeomeGenes to genbank list of tables for makePushQSql.pl
• src/inc/common.h
  • 1.150 lines changed: 16, context: html, text, full: html, text
    convert slAddHead to an inline function, bitten one too many times by it being a macro
• src/lib/cheapcgi.c
  • 1.121 lines changed: 1, context: html, text, full: html, text
    Removed NO_VALUE define, as it is defined in the header file. Thanks Hiram
• src/lib/common.c
  • 1.130 lines changed: 16, context: html, text, full: html, text
    convert slAddHead to an inline function, bitten one too many times by it being a macro
• src/utils/qa/activeGenbank.csh
  • 1.7 lines changed: 1, context: html, text, full: html, text
    added sqlrr variable where needed to set up for new machine testing
• src/utils/qa/backupCentral.csh
  • 1.13 lines changed: 8, context: html, text, full: html, text
    added code to strip out directories a year old
  • 1.12 lines changed: 1, context: html, text, full: html, text
    added sqlrr variable where needed to set up for new machine testing
• src/utils/qa/blatPing.csh
  • 1.5 lines changed: 1, context: html, text, full: html, text
    added sqlrr variable where needed to set up for new machine testing
• src/utils/qa/checkCoverage.csh
  • 1.8 lines changed: 66, context: html, text, full: html, text
    added support for split tables and added a bit of protective logic
• src/utils/qa/checkMetaData.csh
  • 1.18 lines changed: 4, context: html, text, full: html, text
    added sqlrr variable where needed to set up for new machine testing
• src/utils/qa/compareHgFindSpecFast.csh
  • 1.6 lines changed: 2, context: html, text, full: html, text
    added sqlrr variable where needed to set up for new machine testing
• src/utils/qa/compareHgFindSpecs.csh
  • 1.10 lines changed: 1, context: html, text, full: html, text
    added sqlrr variable where needed to set up for new machine testing
• src/utils/qa/compareTrackDbAll.csh
  • 1.21 lines changed: 6, context: html, text, full: html, text
    clarified output so it is clear that "not real time" refers only to RR results
• src/utils/qa/compareTrackDbFast.csh
  • 1.8 lines changed: 1, context: html, text, full: html, text
    added sqlrr variable where needed to set up for new machine testing
• src/utils/qa/compareTrackDbs.csh
  • 1.28 lines changed: 1, context: html, text, full: html, text
    added sqlrr variable where needed to set up for new machine testing
• src/utils/qa/countPerChrom.csh
  • 1.7 lines changed: 50, context: html, text, full: html, text
    fixed interaction with split chroms. removed some unused variables. simplified logic and combined some variables. replaced long block with call to getChromFieldName.csh.
• src/utils/qa/databaseAday.csh
  • 1.10 lines changed: 1, context: html, text, full: html, text
    added sqlrr variable where needed to set up for new machine testing
• src/utils/qa/findBlatServer.csh
  • 1.11 lines changed: 2, context: html, text, full: html, text
    added sqlrr variable where needed to set up for new machine testing
• src/utils/qa/getChromFieldName.csh
  • 1.3 lines changed: 10, context: html, text, full: html, text
    added support for split tables
• src/utils/qa/getLiftOver.csh
  • 1.6 lines changed: 1, context: html, text, full: html, text
    added sqlrr variable where needed to set up for new machine testing
• src/utils/qa/getOrderKey.csh
  • 1.6 lines changed: 2, context: html, text, full: html, text
    added sqlrr variable where needed to set up for new machine testing
• src/utils/qa/getRRdatabases.csh
  • 1.11 lines changed: 1, context: html, text, full: html, text
    added sqlrr variable where needed to set up for new machine testing
• src/utils/qa/getSplit.csh
  • 1.9 lines changed: 2, context: html, text, full: html, text
    changed to accept hgsqlbeta instead of hgwbeta
  • 1.8 lines changed: 28, context: html, text, full: html, text
    adjusted so default is to dev and a few other cosmetic changes
• src/utils/qa/host.csh
  • 1.5 lines changed: 1, context: html, text, full: html, text
    added sqlrr variable where needed to set up for new machine testing
• src/utils/qa/kgTables
  • 1.2 lines changed: 4, context: html, text, full: html, text
    removed affyHumanExon* tables (they are gone sez Andy)
• src/utils/qa/qaConfig.bash
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Keeping in sync with qaConfig.tcsh.
• src/utils/qa/qaConfig.csh
  • 1.2 lines changed: 1, context: html, text, full: html, text
    added sqlrr variable where needed to set up for new machine testing
• src/utils/qa/sessionStats.csh
  • 1.6 lines changed: 9, context: html, text, full: html, text
    added sqlrr variable where needed to set up for new machine testing
• src/utils/qa/syncAday.csh
  • 1.8 lines changed: 3, context: html, text, full: html, text
    added sqlrr variable where needed to set up for new machine testing
• src/utils/qa/trackDbGlobal.csh
  • 1.30 lines changed: 2, context: html, text, full: html, text
    added sqlrr variable where needed to set up for new machine testing
• src/utils/qa/weeklybld/buildCvsReports.csh
  • 1.21 lines changed: 6, context: html, text, full: html, text
    fixing links
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.58 lines changed: 3, context: html, text, full: html, text
    v206 final build

• lines changed: 7613
• files changed: 89