CVS changes by file

review to branch (2009-08-25 to 2009-09-02) v214

• src/hg/archaeStuff/data/Genome-info-mods
  • 1.76 lines changed: 12, context: html, text, full: html, text
    add Name_chg to vibrChlo1
• src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
  • 1.19 lines changed: 10, context: html, text, full: html, text
    always print releaseDate
• src/hg/encode/encodeStatus/encodeStatus.pl
  • 1.9 lines changed: 1, context: html, text, full: html, text
    migrate to new mysqlbeta db server
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.127 lines changed: 169, context: html, text, full: html, text
    Added a few antibodies and added targetLink to antibodies
• src/hg/encode/encodeValidate/config/fields.ra
  • 1.19 lines changed: 5, context: html, text, full: html, text
    Added support for validationSettings
• src/hg/encode/encodeValidate/config/labs.ra
  • 1.8 lines changed: 3, context: html, text, full: html, text
    bye Mike!
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.189 lines changed: 62, context: html, text, full: html, text
    Added support for 'validateSettings' in the DAF
• src/hg/encode/encodeValidate/makefile
  • 1.18 lines changed: 1, context: html, text, full: html, text
    fix stray perl -c output
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • 1.25 lines changed: 26, context: html, text, full: html, text
    Added support for targetLink, lab and lots in antibodies
• src/hg/hgGene/hgGene.c
  • 1.117 lines changed: 3, context: html, text, full: html, text
    changed errAbort to hUserAbort to avoid stack dumps
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.499 lines changed: 2, context: html, text, full: html, text
    Removed the hide noncoding genes option.
  • 1.498 lines changed: 13, context: html, text, full: html, text
    Added code to call the vegaGeneUI function if the track is vegaGeneComposite. vegaGenUI() creates radio buttons to select accession, gene name, both or none for track item labels. It also adds a check box to select for noncoding genes not to be shown and the base colouring drop down menu.
  • 1.497 lines changed: 2, context: html, text, full: html, text
    let Reset to Defaults button appear on UI pages without views
• src/hg/hgTracks/chainTrack.c
  • 1.36 lines changed: 4, context: html, text, full: html, text
    For the three tracks that need normScoreAvailable detected, look into the trackDb instead of two describe queries to every chain track.
• src/hg/hgTracks/chromGraphTrack.c
  • 1.17 lines changed: 9, context: html, text, full: html, text
    Fixed a couple bugs and ensured ps-pdf code still works with IMAGEv2
• src/hg/hgTracks/expRatioTracks.c
  • 1.43 lines changed: 14, context: html, text, full: html, text
    Fixed a couple bugs and ensured ps-pdf code still works with IMAGEv2
• src/hg/hgTracks/hgTracks.c
  • 1.1595 lines changed: 86, context: html, text, full: html, text
    Fixed a couple bugs and ensured ps-pdf code still works with IMAGEv2
• src/hg/hgTracks/imageV2.c
  • 1.8 lines changed: 15, context: html, text, full: html, text
    Fixed default order when DRAG_REORDERING is off
  • 1.7 lines changed: 22, context: html, text, full: html, text
    Fixed a couple bugs and ensured ps-pdf code still works with IMAGEv2
• src/hg/hgTracks/imageV2.h
  • 1.5 lines changed: 3, context: html, text, full: html, text
    Fixed a couple bugs and ensured ps-pdf code still works with IMAGEv2
• src/hg/hgTracks/simpleTracks.c
  • 1.99 lines changed: 1, context: html, text, full: html, text
    Added code to vegaMethods() that calls loadGenePredWithConfiguredName on loading track items to interpret the radio button selections in the track UI.
  • 1.98 lines changed: 18, context: html, text, full: html, text
    Fixed a couple bugs and ensured ps-pdf code still works with IMAGEv2
  • 1.97 lines changed: 3, context: html, text, full: html, text
    a fix to prevent loading of composite subTracks that are set to on in the trackDb but are hidden by the view settings.
• src/hg/hgTracks/variation.c
  • 1.143 lines changed: 23, context: html, text, full: html, text
    Fixed a couple bugs and ensured ps-pdf code still works with IMAGEv2
• src/hg/hgc/hgc.c
  • 1.1569 lines changed: 2, context: html, text, full: html, text
    Added check for table existence to printSnp125CodingAnnotations so an extra trackDb setting is ignored instead of errAborting.
  • 1.1568 lines changed: 5, context: html, text, full: html, text
    Added code to geneShowPosAndLinks() to write that there is no protein prediction for Vega gene if it is noncoding instead of having the sequence link.
  • 1.1567 lines changed: 119, context: html, text, full: html, text
    Added printEnsemblOrVegaCustomUrl() to create URL links like Ensembl for the Vega track details page to link to the Vega gene, transcript and protein reports. Only Vega uses this right now. Need to test for Ensembl.
• src/hg/hgc/mgcClick.c
  • 1.31 lines changed: 3, context: html, text, full: html, text
    sqlMustGetResult doesn't actually generate an error
• src/hg/inc/jksql.h
  • 1.84 lines changed: 16, context: html, text, full: html, text
    adding some handy comments
• src/hg/inc/versionInfo.h
  • 1.154 lines changed: 1, context: html, text, full: html, text
    "New version number v214"
• src/hg/instinct/bioInt2/bioController.c
  • 1.13 lines changed: 21, context: html, text, full: html, text
    Added beginnings of EM pathway analysis
• src/hg/instinct/bioInt2/bioController.h
  • 1.8 lines changed: 7, context: html, text, full: html, text
    Added beginnings of EM pathway analysis
• src/hg/instinct/bioInt2/bioPathway.h
  • 1.1 lines changed: 66, context: html, text, full: html, text
    Added beginnings of EM pathway analysis
• src/hg/instinct/bioInt2/bioPathwayLevel.c
  • 1.4 lines changed: 183, context: html, text, full: html, text
    Added beginnings of EM pathway analysis
• src/hg/instinct/bioInt2/bioPathwayLevelUsingEM.c
  • 1.1 lines changed: 391, context: html, text, full: html, text
    Added beginnings of EM pathway analysis
• src/hg/instinct/bioInt2/createTables.c
  • 1.3 lines changed: 14, context: html, text, full: html, text
    Added beginnings of EM pathway analysis
• src/hg/instinct/bioInt2/makeClusterFiles.c
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Added beginnings of EM pathway analysis
• src/hg/instinct/bioInt2/makefile
  • 1.13 lines changed: 1, context: html, text, full: html, text
    Added beginnings of EM pathway analysis
• src/hg/instinct/hgHeatmap2/hgAnnotations.c
  • 1.12 lines changed: 42, context: html, text, full: html, text
    added gene labels to geneset view
• src/hg/instinct/hgHeatmap2/hgHeatmap2.h
  • 1.50 lines changed: 1, context: html, text, full: html, text
    added gene labels to geneset view
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.ra
  • 1.16 lines changed: 2, context: html, text, full: html, text
    changed title/desc of basso dataset
  • 1.15 lines changed: 22, context: html, text, full: html, text
    added leukemia/lymphoma dataset
• src/hg/instinct/hgHeatmap2/hgHeatmapFrontend/hgHeatmapStyle.css
  • 1.16 lines changed: 3, context: html, text, full: html, text
    added gene labels to geneset view
• src/hg/instinct/hgHeatmap2/hgHeatmapFrontend/index.html
  • 1.34 lines changed: 1, context: html, text, full: html, text
    added link to user guide
• src/hg/js/hgTracks.js
  • 1.38 lines changed: 12, context: html, text, full: html, text
    removed some commented out garbage that was accidentally checked in
  • 1.37 lines changed: 95, context: html, text, full: html, text
    Now dynamically resizes height based up drag-scrolling over map areas (bed items)
• src/hg/lib/cart.c
  • 1.112 lines changed: 2, context: html, text, full: html, text
    do not need sqlTableOk now that sqlTableExists works right with innodb and myisam both
• src/hg/lib/hdb.c
  • 1.413 lines changed: 1, context: html, text, full: html, text
    fixed stupid commit
  • 1.412 lines changed: 19, context: html, text, full: html, text
    switch more sqlTableExists to hTableExists
  • 1.411 lines changed: 6, context: html, text, full: html, text
    converted gbSeq related sqlTableExists to hTableExists
• src/hg/lib/hgConfig.c
  • 1.21 lines changed: 12, context: html, text, full: html, text
    added hg.conf directive to delete variables
• src/hg/lib/hgSeq.c
  • 1.40 lines changed: 1, context: html, text, full: html, text
    making output more infomative
• src/hg/lib/hui.c
  • 1.233 lines changed: 9, context: html, text, full: html, text
    add (help) for tracks without views
• src/hg/lib/jksql.c
  • 1.134 lines changed: 5, context: html, text, full: html, text
    add in SQL_FETCH monitoring
  • 1.133 lines changed: 45, context: html, text, full: html, text
    added useful comments, put in fastest method found to determine if a table exists, added extention function sqlGetRestultsExt to help with testing and generally getting better error info out of mysql
• src/hg/lib/trackDbCustom.c
  • 1.69 lines changed: 2, context: html, text, full: html, text
    Support for noScoreFilter and bigBed in cfgTypeFromTdb
• src/hg/lib/web.c
  • 1.170 lines changed: 2, context: html, text, full: html, text
    Point Help on top bar to PB help page instead of GB help page.
• src/hg/makeDb/doc/hg19.txt
  • 1.36 lines changed: 302, context: html, text, full: html, text
    Added snp130: dbSNP's provisional mapping from b36 to GRCh37 coords. Also added orthologous allele table for snp130.
• src/hg/makeDb/doc/loxAfr3.txt
  • 1.4 lines changed: 20, context: html, text, full: html, text
    lastz alignments done between mouse and elephant
• src/hg/makeDb/doc/mm9.txt
  • 1.107 lines changed: 55, context: html, text, full: html, text
    lastz alignments done between mouse and elephant
• src/hg/makeDb/genbank/etc/dbload
  • 1.30 lines changed: 2, context: html, text, full: html, text
    updated to new machine names
• src/hg/makeDb/hgCgiData/Human/microarrayGroups.ra
  • 1.86 lines changed: 13, context: html, text, full: html, text
    added leukemia/lymphoma dataset
• src/hg/makeDb/schema/all.joiner
  • 1.733 lines changed: 1, context: html, text, full: html, text
    Adding minCheck to snp130Exceptions.name -- sometimes a snp can trigger an exception before we detect a real error and omit it from snp130.
  • 1.732 lines changed: 12, context: html, text, full: html, text
    new rules for new-style Vega Gene tracks for hg18 and mm9 (Rachel has blessed)
• src/hg/makeDb/schema/dbSnoop/dbSnoop.c
  • 1.14 lines changed: 2, context: html, text, full: html, text
    Need to back quote escape table names to avoid problems with tables that are SQL reserved words
• src/hg/makeDb/trackDb/drosophila/droYak1/description.html
  • 1.13 lines changed: 1, context: html, text, full: html, text
    Fixed broken link to wustl.
• src/hg/makeDb/trackDb/drosophila/droYak2/description.html
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Fixed broken link to wustl.
• src/hg/makeDb/trackDb/human/hg17/trackDb.ra
  • 1.426 lines changed: 1, context: html, text, full: html, text
    Turn on chainNormScoreAvailable for all the chainSelf tracks
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.415 lines changed: 1, context: html, text, full: html, text
    Added vegaPep to vegaGeneComposite trackDb entry.
  • 1.414 lines changed: 2, context: html, text, full: html, text
    Turn on chainNormScoreAvailable for all the chainSelf tracks
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.505 lines changed: 7, context: html, text, full: html, text
    adding metadata for Methyl27
  • 1.504 lines changed: 45, context: html, text, full: html, text
    wgEncodeGisRnaSeqSplitAlignH1esCytosolLongpolya
  • 1.503 lines changed: 37, context: html, text, full: html, text
    wgEncodeGisPetAlignmentsNhekNucleusLongpolya
  • 1.502 lines changed: 37, context: html, text, full: html, text
    add AffyRNA GM12878 nucleolus (sub: 452)
  • 1.501 lines changed: 82, context: html, text, full: html, text
    GIS, Affy, and Methyl27 changes/additions
  • 1.500 lines changed: 6, context: html, text, full: html, text
    Removed replicate information from metadata of each table of the wgEncodeHudsonalphaCnv composite track because it does not apply; sanctioned by Kate
  • 1.499 lines changed: 30, context: html, text, full: html, text
    some methylSeq changes to change the dimensions of the matrix
  • 1.498 lines changed: 28, context: html, text, full: html, text
    Removed alphas in prep for staging of encode caltech track.
• src/hg/makeDb/trackDb/human/hg18/vegaGeneComposite.html
  • 1.5 lines changed: 8, context: html, text, full: html, text
    Making it a bit easier to read.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaCnv.html
  • 1.11 lines changed: 2, context: html, text, full: html, text
    add link to Illumina's site
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethyl27.html
  • 1.13 lines changed: 23, context: html, text, full: html, text
    changed first paragraph to past tense
  • 1.12 lines changed: 11, context: html, text, full: html, text
    Minor edits
• src/hg/makeDb/trackDb/human/hg18/wgRna.html
  • 1.7 lines changed: 13, context: html, text, full: html, text
    moved reference to reference section
  • 1.6 lines changed: 4, context: html, text, full: html, text
    minor formatting changes
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.49 lines changed: 12, context: html, text, full: html, text
    Adding local overrides for snp130 (*provisional* b37 coord release by dbSNP).
  • 1.48 lines changed: 10, context: html, text, full: html, text
    change identifiers on subtracks to match those in container track for reordering fish. thanks, kayla
  • 1.47 lines changed: 1, context: html, text, full: html, text
    Turn on chainNormScoreAvailable for all the chainSelf tracks
• src/hg/makeDb/trackDb/mouse/mm9/miRNA.html
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Removed incorrect configuration information about the items being represented by thin blocks
• src/hg/makeDb/trackDb/mouse/mm9/vegaGeneComposite.html
  • 1.3 lines changed: 9, context: html, text, full: html, text
    Making it a bit easier to read.
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.527 lines changed: 24, context: html, text, full: html, text
    Remove the separate monDom5 chain and net entry
• src/hg/makeDb/trackDb/worm/caePb1/ctgPos2.html
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to WUSTL.
• src/hg/makeDb/trackDb/worm/caePb1/description.html
  • 1.8 lines changed: 3, context: html, text, full: html, text
    Fixed broken links to WUSTL.
• src/hg/makeDb/trackDb/worm/caePb1/gap.html
  • 1.4 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to WUSTL.
• src/hg/makeDb/trackDb/worm/caePb1/gold.html
  • 1.4 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to WUSTL.
• src/hg/makeDb/trackDb/worm/caePb2/ctgPos2.html
  • 1.4 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to WUSTL.
• src/hg/makeDb/trackDb/worm/caePb2/description.html
  • 1.8 lines changed: 3, context: html, text, full: html, text
    Fixed broken links to WUSTL.
• src/hg/makeDb/trackDb/worm/caePb2/gap.html
  • 1.4 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to WUSTL.
• src/hg/makeDb/trackDb/worm/caePb2/gold.html
  • 1.7 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to WUSTL.
• src/hg/makeDb/trackDb/worm/cb3/description.html
  • 1.8 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to WUSTL.
• src/hg/makeDb/trackDb/worm/cb3/gap.html
  • 1.3 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to WUSTL.
• src/hg/makeDb/trackDb/worm/cb3/gold.html
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to WUSTL.
• src/hg/oneShot/freen/freen.c
  • 1.88 lines changed: 10, context: html, text, full: html, text
    Testing strptime function.
• src/hg/snp/snpLoad/snpNcbiToUcsc.c
  • 1.11 lines changed: 10, context: html, text, full: html, text
    If refNCBI is wrong size (or snp coords are wrong), make an error instead of aborting. Don't abort on between+in-del -- between size is 0, min observed size can be 0 (-).
• src/hg/utils/automation/makePushQSql.pl
  • 1.27 lines changed: 3, context: html, text, full: html, text
    migrate to new mysqlbeta db server
• src/inc/apacheLog.h
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Updating runTime to be milliseconds not seconds in comment.
  • 1.2 lines changed: 2, context: html, text, full: html, text
    somebody not me forgot to check in the .h file
• src/lib/apacheLog.c
  • 1.4 lines changed: 7, context: html, text, full: html, text
    Making it accept times in seconds or microseconds.
  • 1.3 lines changed: 8, context: html, text, full: html, text
    Adding more time parsing.
  • 1.2 lines changed: 15, context: html, text, full: html, text
    Checking for zero chromosome coordinate (supposed to be 1-based coordinates)
• src/lib/bigBed.c
  • 1.21 lines changed: 20, context: html, text, full: html, text
    Checking for zero chromosome coordinate (supposed to be 1-based coordinates)
• src/lib/bwgCreate.c
  • 1.15 lines changed: 2, context: html, text, full: html, text
    Making zero coordinate error message handle negative coords too.
  • 1.14 lines changed: 9, context: html, text, full: html, text
    Checking for zero chromosome coordinate (supposed to be 1-based coordinates)
• src/makefile
  • 1.62 lines changed: 1, context: html, text, full: html, text
    adding bedGraphToBigWig
• src/product/ex.hg.conf
  • 1.17 lines changed: 5, context: html, text, full: html, text
    added hg.conf directive to delete variables
• src/utils/gtfToGenePred/gtfToGenePred.c
  • 1.7 lines changed: 18, context: html, text, full: html, text
    don't dereference NULL if an annotation doesn't have an exon'
• src/utils/qa/makeTouchCommands.csh
  • 1.3 lines changed: 2, context: html, text, full: html, text
    dropped unneeded line and dropped # in output
  • 1.2 lines changed: 1, context: html, text, full: html, text
    tweak to usage statement
  • 1.1 lines changed: 70, context: html, text, full: html, text
    script to generate touch commands for changing table timestamps
• src/utils/qa/makefile
  • 1.113 lines changed: 1, context: html, text, full: html, text
    script to generate touch commands for changing table timestamps
• src/utils/qa/qaConfig.bash
  • 1.3 lines changed: 2, context: html, text, full: html, text
    Removed spaces around variable assignment. This wasn't working! Also changed hgsqlbeta to mysqlbeta.
• src/utils/qa/qaConfig.csh
  • 1.3 lines changed: 1, context: html, text, full: html, text
    changed hqsqlbeta to mysqlbeta.
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.75 lines changed: 3, context: html, text, full: html, text
    v214 final build
• src/utils/qa/weeklybld/makeUserApps.csh
  • 1.4 lines changed: 4, context: html, text, full: html, text
    trying to get clean
• src/utils/twoBitToFa/twoBitToFa.c
  • 1.13 lines changed: 67, context: html, text, full: html, text
    Added -bed option

• lines changed: 2709
• files changed: 93