CVS changes by file

review to branch (2009-04-21 to 2009-04-28) v205

• src/hg/archaeStuff/data/precomputed-tracks.tab
  • 1.1 lines changed: 30, context: html, text, full: html, text
    pull out precomputed track info from make-browser to separate file
• src/hg/archaeStuff/scripts/archaeBrowser/Constant.pm
  • 1.30 lines changed: 9, context: html, text, full: html, text
    use precomputed-tracks.tab for track info
• src/hg/archaeStuff/scripts/archaeBrowser/PrecomputedTrack.pm
  • 1.8 lines changed: 1, context: html, text, full: html, text
    ignore header line of precomputed track info file
  • 1.7 lines changed: 96, context: html, text, full: html, text
    use precomputed-tracks.tab for track info
• src/hg/archaeStuff/scripts/make-browser-2.0
  • 1.40 lines changed: 40, context: html, text, full: html, text
    use precomputed-tracks.tab for track info
• src/hg/bedItemOverlapCount/bedItemOverlapCount.c
  • 1.13 lines changed: 12, context: html, text, full: html, text
    modify code to support the normal two column chromSize file format
  • 1.12 lines changed: 28, context: html, text, full: html, text
    support -chromSize option
• src/hg/bedItemOverlapCount/makefile
  • 1.8 lines changed: 3, context: html, text, full: html, text
    add DESTDIR so we can add this to userApps
• src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
  • 1.11 lines changed: 5, context: html, text, full: html, text
    Okay, when type isn't found in trackDb, then just make it the file type.
  • 1.10 lines changed: 10, context: html, text, full: html, text
    Added lookup of metadata in fileDb.ra (if one exists in downloads directory)
  • 1.9 lines changed: 17, context: html, text, full: html, text
    Special case coding for Elnitski with her tables scattered across genomes.
  • 1.8 lines changed: 34, context: html, text, full: html, text
    dateSubmitted was not getting picked up as it should have been
  • 1.7 lines changed: 137, context: html, text, full: html, text
    Support for metadata setting from trackDb
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • 1.63 lines changed: 1, context: html, text, full: html, text
    add ENCODE prefix to shortlabel in pushQ entry to alert Q/A
• src/hg/encode/encodeStatus/encodeStatus.pl
  • 1.8 lines changed: 1, context: html, text, full: html, text
    fix typo
  • 1.7 lines changed: 1, context: html, text, full: html, text
    use hgsql --host option instead of doing a ssh
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.90 lines changed: 3, context: html, text, full: html, text
    add colors
• src/hg/encode/encodeValidate/config/labs.ra
  • 1.6 lines changed: 1, context: html, text, full: html, text
    aampp => aamp
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Andy is taking over Stam and Weng labs.
• src/hg/hgGenome/hgGenome.c
  • 1.65 lines changed: 1, context: html, text, full: html, text
    fixing cgis so that udcCache dir is set by new hg.conf setting udc.cacheDir=
• src/hg/hgTables/hgTables.c
  • 1.185 lines changed: 2, context: html, text, full: html, text
    fixing cgis so that udcCache dir is set by new hg.conf setting udc.cacheDir=
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.485 lines changed: 2, context: html, text, full: html, text
    moved explanation of yeast transReg scoring to Display Conventions section on details page
• src/hg/hgTracks/hgTracks.c
  • 1.1563 lines changed: 2, context: html, text, full: html, text
    fixing cgis so that udcCache dir is set by new hg.conf setting udc.cacheDir=
• src/hg/hgc/hgc.c
  • 1.1530 lines changed: 2, context: html, text, full: html, text
    fixing cgis so that udcCache dir is set by new hg.conf setting udc.cacheDir=
  • 1.1529 lines changed: 25, context: html, text, full: html, text
    GeneLynx.com is no longer available
  • 1.1528 lines changed: 1, context: html, text, full: html, text
    dont need to free hti because it comes from a cache
• src/hg/hgc/regMotif.c
  • 1.19 lines changed: 4, context: html, text, full: html, text
    changed CHIP/CHIP to ChIP-chip to conform to usual
• src/hg/inc/hui.h
  • 1.123 lines changed: 3, context: html, text, full: html, text
    fixing cgis so that udcCache dir is set by new hg.conf setting udc.cacheDir=
• src/hg/inc/trackDb.h
  • 1.47 lines changed: 13, context: html, text, full: html, text
    Add support for parsing out metadata settings.
• src/hg/inc/versionInfo.h
  • 1.145 lines changed: 1, context: html, text, full: html, text
    "New version number v205"
• src/hg/instinct/bioInt2/bioController.c
  • 1.8 lines changed: 40, context: html, text, full: html, text
    updated lots of stuff, will break older implementation of database
• src/hg/instinct/bioInt2/bioController.h
  • 1.5 lines changed: 6, context: html, text, full: html, text
    updated lots of stuff, will break older implementation of database
• src/hg/instinct/bioInt2/bioGeneLevel.c
  • 1.5 lines changed: 121, context: html, text, full: html, text
    updated lots of stuff, will break older implementation of database
• src/hg/instinct/bioInt2/bioIntDb.as
  • 1.5 lines changed: 31, context: html, text, full: html, text
    updated lots of stuff, will break older implementation of database
• src/hg/instinct/bioInt2/bioIntDb.c
  • 1.7 lines changed: 712, context: html, text, full: html, text
    updated lots of stuff, will break older implementation of database
• src/hg/instinct/bioInt2/bioIntDb.h
  • 1.6 lines changed: 395, context: html, text, full: html, text
    updated lots of stuff, will break older implementation of database
• src/hg/instinct/bioInt2/bioIntDb.sql
  • 1.5 lines changed: 34, context: html, text, full: html, text
    updated lots of stuff, will break older implementation of database
• src/hg/instinct/bioInt2/bioIntDriver.c
  • 1.3 lines changed: 797, context: html, text, full: html, text
    updated lots of stuff, will break older implementation of database
• src/hg/instinct/bioInt2/bioIntDriver.h
  • 1.5 lines changed: 70, context: html, text, full: html, text
    updated lots of stuff, will break older implementation of database
• src/hg/instinct/bioInt2/bioIntFrontend/bioIntStyle.css
  • 1.16 lines changed: 5, context: html, text, full: html, text
    Added cohort info panel
  • 1.15 lines changed: 10, context: html, text, full: html, text
    Added cohort selection button
• src/hg/instinct/bioInt2/bioIntFrontend/bioIntUI.js
  • 1.35 lines changed: 3, context: html, text, full: html, text
    Added plus icon for feature adding
  • 1.34 lines changed: 2, context: html, text, full: html, text
    Added shading to bars
  • 1.33 lines changed: 36, context: html, text, full: html, text
    Added cohort info panel
  • 1.32 lines changed: 8, context: html, text, full: html, text
    make
  • 1.31 lines changed: 1, context: html, text, full: html, text
    Fixed issue where getSuggest wasn't catching numbers
  • 1.30 lines changed: 3, context: html, text, full: html, text
    Fixed get correlated to now use type
  • 1.29 lines changed: 3, context: html, text, full: html, text
    Added cohort selection button
• src/hg/instinct/bioInt2/bioIntFrontend/index.html
  • 1.19 lines changed: 1, context: html, text, full: html, text
    Added plus icon for feature adding
  • 1.18 lines changed: 7, context: html, text, full: html, text
    Added cohort info panel
  • 1.17 lines changed: 1, context: html, text, full: html, text
    Added cohort selection button
• src/hg/instinct/bioInt2/bioIntUI.c
  • 1.20 lines changed: 98, context: html, text, full: html, text
    fixed gene drill down issues
  • 1.19 lines changed: 157, context: html, text, full: html, text
    added drill down into meta-genes
  • 1.18 lines changed: 37, context: html, text, full: html, text
    fixed correlation stuff
  • 1.17 lines changed: 52, context: html, text, full: html, text
    updated lots of stuff, will break older implementation of database
• src/hg/instinct/bioInt2/bioLevelI.c
  • 1.6 lines changed: 38, context: html, text, full: html, text
    updated lots of stuff, will break older implementation of database
• src/hg/instinct/bioInt2/bioSetLevel.c
  • 1.2 lines changed: 79, context: html, text, full: html, text
    updated lots of stuff, will break older implementation of database
• src/hg/instinct/bioInt2/cohortCorrelations.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    removed printf
  • 1.2 lines changed: 6, context: html, text, full: html, text
    updated lots of stuff, will break older implementation of database
• src/hg/instinct/bioInt2/createTables.c
  • 1.1 lines changed: 281, context: html, text, full: html, text
    initial commit
• src/hg/instinct/bioInt2/makefile
  • 1.8 lines changed: 10, context: html, text, full: html, text
    updated lots of stuff, will break older implementation of database
• src/hg/instinct/bioInt2/populateDb.c
  • 1.9 lines changed: 1, context: html, text, full: html, text
    added drill down into meta-genes
  • 1.8 lines changed: 16, context: html, text, full: html, text
    fixed memory leak
  • 1.7 lines changed: 642, context: html, text, full: html, text
    updated lots of stuff, will break older implementation of database
• src/hg/instinct/bioInt2/setCohorts.c
  • 1.5 lines changed: 20, context: html, text, full: html, text
    added drill down into meta-genes
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.TCGAcontrol.ra
  • 1.8 lines changed: 1, context: html, text, full: html, text
    fixed probe table for ovarian exon array
  • 1.7 lines changed: 20, context: html, text, full: html, text
    Added unc miRNA OV data
  • 1.6 lines changed: 19, context: html, text, full: html, text
    Added TCGA OV gene exon data
  • 1.5 lines changed: 8, context: html, text, full: html, text
    Changed tcga data groups around a bit
  • 1.4 lines changed: 77, context: html, text, full: html, text
    Added baylor OV mutation data
  • 1.3 lines changed: 20, context: html, text, full: html, text
    added mskcc 1x1M array
  • 1.2 lines changed: 20, context: html, text, full: html, text
    added mskcc set
• src/hg/instinct/lib/hgStatsLib.c
  • 1.13 lines changed: 4, context: html, text, full: html, text
    fixed bug with fishers meta
• src/hg/js/hui.js
  • 1.25 lines changed: 32, context: html, text, full: html, text
    Support for showing metadata in hgTrackUi
• src/hg/js/utils.js
  • 1.19 lines changed: 8, context: html, text, full: html, text
    Kate objects to exclamation marks.
• src/hg/lib/hui.c
  • 1.188 lines changed: 6, context: html, text, full: html, text
    Fix for min score being the same as trackDb default score, and eliminate drag and drop hint when cursor is over longLabel
  • 1.187 lines changed: 8, context: html, text, full: html, text
    fixing cgis so that udcCache dir is set by new hg.conf setting udc.cacheDir=
  • 1.186 lines changed: 175, context: html, text, full: html, text
    Support for showing metadata in hgTrackUi
• src/hg/lib/trackDbCustom.c
  • 1.63 lines changed: 59, context: html, text, full: html, text
    Add support for parsing out metadata settings.
• src/hg/lib/transRegCode.as
  • 1.4 lines changed: 1, context: html, text, full: html, text
    typo
  • 1.3 lines changed: 2, context: html, text, full: html, text
    changed CHIP/CHIP to ChIP-chip to conform to usual
• src/hg/lib/transRegCodeProbe.as
  • 1.5 lines changed: 1, context: html, text, full: html, text
    changed CHIP/CHIP to ChIP-chip to conform to usual
• src/hg/makeDb/doc/encodeDccHg18.txt
  • 1.1 lines changed: 9, context: html, text, full: html, text
    
• src/hg/makeDb/doc/h1n1.txt
  • 1.1 lines changed: 191, context: html, text, full: html, text
    Created h1n1.txt.
• src/hg/makeDb/doc/hg16.txt
  • 1.10 lines changed: 14, context: html, text, full: html, text
    liftOver to hg19 done
• src/hg/makeDb/doc/hg17.txt
  • 1.121 lines changed: 12, context: html, text, full: html, text
    liftOver to hg19 done
• src/hg/makeDb/doc/hg19.txt
  • 1.8 lines changed: 3, context: html, text, full: html, text
    done with swap of chain/net to panTro2
  • 1.7 lines changed: 18, context: html, text, full: html, text
    running swap to panTro2 and make gc5Base download file
  • 1.6 lines changed: 3, context: html, text, full: html, text
    Reset default position.
  • 1.5 lines changed: 7, context: html, text, full: html, text
    Changed default position.
• src/hg/makeDb/doc/mm9.txt
  • 1.92 lines changed: 15, context: html, text, full: html, text
    Updated MGI tracks (QTLs, transcripts, phenotype and allele).
• src/hg/makeDb/doc/panTro2.txt
  • 1.14 lines changed: 16, context: html, text, full: html, text
    hg19 chain/net swap done
• src/hg/makeDb/doc/ucscGenes/hg18.ucscGenes11.csh
  • 1.19 lines changed: 17, context: html, text, full: html, text
    Updated the processing step to build KEGG pathway tables for UCSC Genes.
• src/hg/makeDb/genbank/etc/ignore.idx
  • 1.93 lines changed: 1, context: html, text, full: html, text
    
• src/hg/makeDb/genbank/etc/rr.dbs
  • 1.81 lines changed: 1, context: html, text, full: html, text
    added hg19
• src/hg/makeDb/genbank/src/extFileUpdate/extFileTool
  • 1.7 lines changed: 11, context: html, text, full: html, text
    global set of HGDB_CONF for hgsqlbeta
  • 1.6 lines changed: 4, context: html, text, full: html, text
    handle hgsqlbeta
• src/hg/makeDb/genbank/src/gbSanity/chkGbIndex.c
  • 1.5 lines changed: 3, context: html, text, full: html, text
    fixed bogus errors reported for NR refseqs
• src/hg/makeDb/genbank/src/gbSanity/chkMetaDataTbls.c
  • 1.13 lines changed: 10, context: html, text, full: html, text
    fixed bogus errors reported for NR refseqs
• src/hg/makeDb/genbank/src/gbSanity/chkSeqTbl.c
  • 1.3 lines changed: 4, context: html, text, full: html, text
    fixed bogus errors reported for NR refseqs
• src/hg/makeDb/hgCgiData/Human/microarrayGroups.ra
  • 1.73 lines changed: 11, context: html, text, full: html, text
    Added unc miRNA OV data
  • 1.72 lines changed: 13, context: html, text, full: html, text
    Added TCGA OV gene exon data
  • 1.71 lines changed: 30, context: html, text, full: html, text
    Added baylor OV mutation data
  • 1.70 lines changed: 10, context: html, text, full: html, text
    added mskcc 1x1M array
  • 1.69 lines changed: 3, context: html, text, full: html, text
    fixed harvard Ovarian array
  • 1.68 lines changed: 17, context: html, text, full: html, text
    updated TCGA ovarian datasets
• src/hg/makeDb/hgLoadBed/hgLoadBed.c
  • 1.69 lines changed: 3, context: html, text, full: html, text
    fix mysql 'Commands out of sync' problem
• src/hg/makeDb/schema/all.joiner
  • 1.709 lines changed: 25, context: html, text, full: html, text
    Added wgEncodeGencode tables
  • 1.708 lines changed: 3, context: html, text, full: html, text
    Added uwFootprints tables to tables ignored.
  • 1.707 lines changed: 1, context: html, text, full: html, text
    there is no netSelf table for hg19 - and Hiram does not intend to create one.
  • 1.706 lines changed: 1, context: html, text, full: html, text
    there is no netSelf table for hg19
  • 1.705 lines changed: 16, context: html, text, full: html, text
    Fixup rules for hg19 non-split tables and ignore gold
• src/hg/makeDb/trackDb/apis/apiMel1/description.html
  • 1.18 lines changed: 2, context: html, text, full: html, text
    Fixed honeybee links to Baylor.
  • 1.17 lines changed: 1, context: html, text, full: html, text
    Fixed link to Baylor conditions for use.
• src/hg/makeDb/trackDb/apis/apiMel2/description.html
  • 1.7 lines changed: 3, context: html, text, full: html, text
    Fixed honeybee links to Baylor.
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Fixed link to Baylor conditions for use.
• src/hg/makeDb/trackDb/apis/apiMel2/gold.html
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Fixed honeybee links to Baylor.
• src/hg/makeDb/trackDb/apis/apiMel2/scaffolds.html
  • 1.3 lines changed: 2, context: html, text, full: html, text
    Fixed honeybee links to Baylor.
• src/hg/makeDb/trackDb/chainHg19.html
  • 1.1 lines changed: 90, context: html, text, full: html, text
    For chains and nets of Hg19 on other organisms
• src/hg/makeDb/trackDb/chimp/panTro2/trackDb.ra
  • 1.34 lines changed: 1, context: html, text, full: html, text
    Added metadata to wgEncodeNhgriBip track
• src/hg/makeDb/trackDb/chimp/trackDb.ra
  • 1.16 lines changed: 24, context: html, text, full: html, text
    Adding hg19 chain and net to panTro2
• src/hg/makeDb/trackDb/cow/bosTau1/description.html
  • 1.16 lines changed: 2, context: html, text, full: html, text
    Got carried away with the http's. Fixed Baylor links again.
  • 1.15 lines changed: 2, context: html, text, full: html, text
    Fixed cow links to Baylor.
  • 1.14 lines changed: 1, context: html, text, full: html, text
    Fixed link to Baylor conditions for use.
• src/hg/makeDb/trackDb/cow/bosTau2/contigOrient.html
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Got carried away with the http's. Fixed Baylor links again.
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Fixed cow links to Baylor.
• src/hg/makeDb/trackDb/cow/bosTau2/description.html
  • 1.8 lines changed: 2, context: html, text, full: html, text
    Got carried away with the http's. Fixed Baylor links again.
  • 1.7 lines changed: 2, context: html, text, full: html, text
    Fixed cow links to Baylor.
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Fixed link to Baylor conditions for use.
• src/hg/makeDb/trackDb/cow/bosTau3/description.html
  • 1.8 lines changed: 3, context: html, text, full: html, text
    Got carried away with the http's. Fixed Baylor links again.
  • 1.7 lines changed: 3, context: html, text, full: html, text
    Fixed cow links to Baylor.
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Fixed link to Baylor conditions for use.
• src/hg/makeDb/trackDb/cow/bosTau3/scaffold.html
  • 1.3 lines changed: 2, context: html, text, full: html, text
    Got carried away with the http's. Fixed Baylor links again.
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Fixed cow links to Baylor.
• src/hg/makeDb/trackDb/cow/bosTau4/description.html
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Fixed cow links to Baylor.
• src/hg/makeDb/trackDb/cow/bosTau4/trackDb.ra
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Added metadata to wgEncodeNhgriBip track
• src/hg/makeDb/trackDb/dog/canFam2/trackDb.ra
  • 1.28 lines changed: 1, context: html, text, full: html, text
    Added metadata to wgEncodeNhgriBip track
• src/hg/makeDb/trackDb/drosophila/dm1/axtNetDp1.html
  • 1.7 lines changed: 2, context: html, text, full: html, text
    Fixed fly links to Baylor.
• src/hg/makeDb/trackDb/drosophila/dm1/netDp1.html
  • 1.8 lines changed: 2, context: html, text, full: html, text
    Fixed fly links to Baylor.
• src/hg/makeDb/trackDb/drosophila/dp2/description.html
  • 1.6 lines changed: 2, context: html, text, full: html, text
    Fixed fly links to Baylor.
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Fixed link to Baylor conditions for use.
• src/hg/makeDb/trackDb/drosophila/netDp2.html
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Fixed fly links to Baylor.
• src/hg/makeDb/trackDb/esRegGeneToMotif.html
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Edited link to Eran Segal's website
• src/hg/makeDb/trackDb/human/hg13/syntenyRat.html
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Fixed rat links to Baylor.
• src/hg/makeDb/trackDb/human/hg15/syntenyRat.html
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Fixed rat links to Baylor.
• src/hg/makeDb/trackDb/human/hg16/syntenyRn3.html
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Fixed rat links to Baylor.
• src/hg/makeDb/trackDb/human/hg17/ensRatMusHom.html
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Fixed rat links to Baylor.
• src/hg/makeDb/trackDb/human/hg17/syntenyRn3.html
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Fixed rat links to Baylor.
• src/hg/makeDb/trackDb/human/hg18/description.html
  • 1.22 lines changed: 1, context: html, text, full: html, text
    dropped an errant hyphen
• src/hg/makeDb/trackDb/human/hg18/phyloPConsLs44way.html
  • 1.1 lines changed: 67, context: html, text, full: html, text
    Add track description for Adam Siepel's lineage=specific phyloP
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.389 lines changed: 1, context: html, text, full: html, text
    changed priority of Alt Events track to keep it with other KG tracks
  • 1.388 lines changed: 1, context: html, text, full: html, text
    Label tweak for PhyloP track, by request of Adam
  • 1.387 lines changed: 1, context: html, text, full: html, text
    consistency tweak
  • 1.386 lines changed: 45, context: html, text, full: html, text
    1. Update phyloP LS track settings based on input from Adam 2. Add GERP cons for Javier at EBI (ENCODE-related)
• src/hg/makeDb/trackDb/human/hg18/trackDb.tcga1.ra
  • 1.17 lines changed: 62, context: html, text, full: html, text
    Added TCGA OV gene exon data
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.270 lines changed: 11, context: html, text, full: html, text
    some HAMethylSeq colors
  • 1.269 lines changed: 3, context: html, text, full: html, text
    add some colors
  • 1.268 lines changed: 46, context: html, text, full: html, text
    Update Elnitski BiP track and added new UW DNase tracks with Andy
  • 1.267 lines changed: 3, context: html, text, full: html, text
    Changed some shortLabels for ENCODE Gencode
  • 1.266 lines changed: 3, context: html, text, full: html, text
    Explicitly mark Gencode tracks as genePred so that encodeDownloadsPage.pl does the right thing
  • 1.265 lines changed: 9, context: html, text, full: html, text
    Fixed some metadata settings
  • 1.264 lines changed: 417, context: html, text, full: html, text
    Pull out raw signal from Riken (for now)
  • 1.263 lines changed: 1, context: html, text, full: html, text
    Fix label for Riken
  • 1.262 lines changed: 1, context: html, text, full: html, text
    Tweak defaults on Riken CAGE
  • 1.261 lines changed: 169, context: html, text, full: html, text
    short labels and subtrack ordering adjustments to Riken CAGE
  • 1.260 lines changed: 13, context: html, text, full: html, text
    Change UW labels by request of John Stam
  • 1.259 lines changed: 39, context: html, text, full: html, text
    Restore mistakenly commented out UW Dnase K562 signal tracks
  • 1.258 lines changed: 8, context: html, text, full: html, text
    Added some missing color to newly added Open Chromatin tracks
  • 1.257 lines changed: 54, context: html, text, full: html, text
    Coloring and labels work for Riken CAGE
  • 1.256 lines changed: 130, context: html, text, full: html, text
    Added UNC HepG2/FAIRE
  • 1.255 lines changed: 26, context: html, text, full: html, text
    strand is not sure in helicos data
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncodeRikenRawSignal.ra
  • 1.1 lines changed: 436, context: html, text, full: html, text
    Pull out raw signal from Riken (for now)
• src/hg/makeDb/trackDb/human/hg18/wgEncodeAffyRnaChip.html
  • 1.11 lines changed: 4, context: html, text, full: html, text
    updated with RNA extract protocols
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Consistency
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.html
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Consistency
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHelicosRnaSeq.html
  • 1.5 lines changed: 3, context: html, text, full: html, text
    updated with RNA extract protocols
  • 1.4 lines changed: 1, context: html, text, full: html, text
    long rna not small
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.html
  • 1.10 lines changed: 2, context: html, text, full: html, text
    moved protocol dir
  • 1.9 lines changed: 2, context: html, text, full: html, text
    protocols for rna
  • 1.8 lines changed: 67, context: html, text, full: html, text
    Edit for clarity
  • 1.7 lines changed: 2, context: html, text, full: html, text
    minor text tweak
• src/hg/makeDb/trackDb/human/hg18/wgEncodeSangerGencode.html
  • 1.9 lines changed: 28, context: html, text, full: html, text
    Links, contact and Data release policy added
• src/hg/makeDb/trackDb/human/hg19/chainSelf.html
  • 1.1 lines changed: 92, context: html, text, full: html, text
    Fixup chainSelf business
• src/hg/makeDb/trackDb/human/hg19/description.html
  • 1.10 lines changed: 17, context: html, text, full: html, text
    Added an explanation of the chromosome names, plus an example search with the new chrUn_contigName chrom name.
  • 1.9 lines changed: 7, context: html, text, full: html, text
    Format bit about the PARs.
  • 1.8 lines changed: 2, context: html, text, full: html, text
    Changed PARs to match gold.fragStart and gold.fragEnd fields.
  • 1.7 lines changed: 8, context: html, text, full: html, text
    Commented out more missing pieces + minor edits.
  • 1.6 lines changed: 16, context: html, text, full: html, text
    removed some searches that don't work yet
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.12 lines changed: 15, context: html, text, full: html, text
    Fixup chainSelf business
• src/hg/makeDb/trackDb/human/hg19/visibility.ra
  • 1.2 lines changed: 3, context: html, text, full: html, text
    turned on chimp chain by default
  • 1.1 lines changed: 3, context: html, text, full: html, text
    made refGene visible by default
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.452 lines changed: 4, context: html, text, full: html, text
    Corrected hgdpFst and hgdpIhs view limits (thx Pauline).
• src/hg/makeDb/trackDb/lowelab/pyrAer1/trackDb.ra
  • 1.52 lines changed: 1, context: html, text, full: html, text
    Update multiz track
• src/hg/makeDb/trackDb/makefile
  • 1.265 lines changed: 1, context: html, text, full: html, text
    Added h1n1.
• src/hg/makeDb/trackDb/mouse/mm4/syntenyRn3.html
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Fixed rat links to Baylor.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • 1.44 lines changed: 1, context: html, text, full: html, text
    Added metadata to wgEncodeNhgriBip track
• src/hg/makeDb/trackDb/netHg19.html
  • 1.1 lines changed: 86, context: html, text, full: html, text
    For chains and nets of Hg19 on other organisms
• src/hg/makeDb/trackDb/rat/rn1/description.html
  • 1.3 lines changed: 2, context: html, text, full: html, text
    Fixed rat links to Baylor.
• src/hg/makeDb/trackDb/rat/rn1/ensRatMusHom.html
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Fixed rat links to Baylor.
• src/hg/makeDb/trackDb/rat/rn2/description.html
  • 1.13 lines changed: 1, context: html, text, full: html, text
    Fixed rat links to Baylor.
• src/hg/makeDb/trackDb/rat/rn3/description.html
  • 1.20 lines changed: 2, context: html, text, full: html, text
    Fixed rat links to Baylor.
• src/hg/makeDb/trackDb/rat/rn3/ensRatMusHom.html
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Fixed rat links to Baylor.
• src/hg/makeDb/trackDb/rat/rn4/description.html
  • 1.3 lines changed: 2, context: html, text, full: html, text
    Fixed rat links to Baylor.
• src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
  • 1.33 lines changed: 1, context: html, text, full: html, text
    Added metadata to wgEncodeNhgriBip track
• src/hg/makeDb/trackDb/rhesus/rheMac1/description.html
  • 1.9 lines changed: 2, context: html, text, full: html, text
    Fixed rhesus links to Baylor.
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Fixed link to Baylor conditions for use.
• src/hg/makeDb/trackDb/rhesus/rheMac2/ctgPos.html
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Fixed rhesus links to Baylor.
• src/hg/makeDb/trackDb/rhesus/rheMac2/description.html
  • 1.10 lines changed: 2, context: html, text, full: html, text
    Fixed rhesus links to Baylor.
• src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.ra
  • 1.39 lines changed: 1, context: html, text, full: html, text
    Added metadata to wgEncodeNhgriBip track
• src/hg/makeDb/trackDb/sacCer/trackDb.ra
  • 1.35 lines changed: 15, context: html, text, full: html, text
    changed shortLabel for mRNA track (because it was too long before), and added new block for est (from top level) and changed shortLabel
  • 1.34 lines changed: 2, context: html, text, full: html, text
    changed CHIP/CHIP to ChIP-chip to conform to the usual
• src/hg/makeDb/trackDb/sacCer/transRegCode.html
  • 1.7 lines changed: 28, context: html, text, full: html, text
    moved explanation of yeast transReg scoring to Display Conventions section on details page
  • 1.6 lines changed: 9, context: html, text, full: html, text
    Made formatting edits
• src/hg/makeDb/trackDb/sacCer/transRegCodeProbe.html
  • 1.4 lines changed: 8, context: html, text, full: html, text
    Made formatting edits
• src/hg/makeDb/trackDb/sacCer/uwFootprints.html
  • 1.3 lines changed: 8, context: html, text, full: html, text
    Fixed typos and ref format.
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.502 lines changed: 1, context: html, text, full: html, text
    Turn off score filter for Eran Segal Regulatory Module esRegGeneToMotif on yeast browsers
  • 1.501 lines changed: 1, context: html, text, full: html, text
    hid venter
• src/hg/makeDb/trackDb/urchin/strPur1/description.html
  • 1.6 lines changed: 2, context: html, text, full: html, text
    Fixed urchin links to Baylor.
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Fixed link to Baylor conditions for use.
• src/hg/makeDb/trackDb/urchin/strPur2/description.html
  • 1.7 lines changed: 2, context: html, text, full: html, text
    Fixed urchin links to Baylor.
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Fixed link to Baylor conditions for use.
• src/hg/makeDb/trackDb/zebraFinch/nscanGene.html
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Slight tweaking of wording.
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Slight tweaking of punctuation.
• src/hg/makeDb/trackDb/zebraFinch/taeGut1/trackDb.ra
  • 1.3 lines changed: 1, context: html, text, full: html, text
    fixed typo in description
• src/hg/tcga/scripts/DataTypes.py
  • 1.5 lines changed: 213, context: html, text, full: html, text
    added U133A
• src/hg/tcga/scripts/GenericDataType.py
  • 1.5 lines changed: 33, context: html, text, full: html, text
    added U133A
• src/hg/tcga/scripts/processData.py
  • 1.8 lines changed: 39, context: html, text, full: html, text
    added U133A
  • 1.7 lines changed: 32, context: html, text, full: html, text
    Added pipeline for baylor OV data
• src/hg/utils/automation/makeDownloads.pl
  • 1.21 lines changed: 1, context: html, text, full: html, text
    Clarified the type of BED file for chromTrf.tar.gz.
• src/hg/utils/bedExtendRanges/makefile
  • 1.4 lines changed: 2, context: html, text, full: html, text
    add BINDIR so we can add this to userApps
• src/hg/utils/makefile
  • 1.13 lines changed: 2, context: html, text, full: html, text
    positionalTblCheck wasn't being and had code rot
• src/hg/utils/positionalTblCheck/positionalTblCheck.c
  • 1.2 lines changed: 4, context: html, text, full: html, text
    positionalTblCheck wasn't being and had code rot
• src/inc/gff3.h
  • 1.1 lines changed: 211, context: html, text, full: html, text
    added initial implementation of gff3 parser. Still has some rough edges and problems due to ambiguities in the GFF3 specification
• src/lib/gff3.c
  • 1.1 lines changed: 914, context: html, text, full: html, text
    added initial implementation of gff3 parser. Still has some rough edges and problems due to ambiguities in the GFF3 specification
• src/lib/gifwrite.c
  • 1.7 lines changed: 1, context: html, text, full: html, text
    fix tiny buffer overflow bug discovered by user with ubuntu 8.10 and FORTIFY -- use strncpy instead of strcpy
• src/lib/makefile
  • 1.151 lines changed: 1, context: html, text, full: html, text
    added initial implementation of gff3 parser. Still has some rough edges and problems due to ambiguities in the GFF3 specification
• src/lib/tests/gff3Tester.c
  • 1.1 lines changed: 31, context: html, text, full: html, text
    added initial implementation of gff3 parser. Still has some rough edges and problems due to ambiguities in the GFF3 specification
• src/lib/tests/input/errorCasesTest.gff3
  • 1.1 lines changed: 28, context: html, text, full: html, text
    added initial implementation of gff3 parser. Still has some rough edges and problems due to ambiguities in the GFF3 specification
• src/lib/tests/input/sacCerTest.gff3
  • 1.1 lines changed: 43, context: html, text, full: html, text
    added initial implementation of gff3 parser. Still has some rough edges and problems due to ambiguities in the GFF3 specification
• src/lib/tests/input/specialCasesTest.gff3
  • 1.1 lines changed: 9, context: html, text, full: html, text
    added initial implementation of gff3 parser. Still has some rough edges and problems due to ambiguities in the GFF3 specification
• src/lib/tests/makefile
  • 1.35 lines changed: 21, context: html, text, full: html, text
    added initial implementation of gff3 parser. Still has some rough edges and problems due to ambiguities in the GFF3 specification
• src/parasol/gensub2/fancy.gsub
  • 1.1 lines changed: 3, context: html, text, full: html, text
    fix bug with lastDir2, made code more robust
• src/parasol/gensub2/fancy1.lst
  • 1.1 lines changed: 4, context: html, text, full: html, text
    fix bug with lastDir2, made code more robust
• src/parasol/gensub2/fancy2.lst
  • 1.1 lines changed: 4, context: html, text, full: html, text
    fix bug with lastDir2, made code more robust
• src/parasol/gensub2/gensub2.c
  • 1.13 lines changed: 11, context: html, text, full: html, text
    fix bug with lastDir2, made code more robust
• src/utils/qa/checkWigFiles.csh
  • 1.1 lines changed: 70, context: html, text, full: html, text
    Ensures that a table correlates with its associated wig file
• src/utils/qa/compareTableToFile.csh
  • 1.2 lines changed: 20, context: html, text, full: html, text
    if the file is of type wiggle, then call checkWigFiles script
  • 1.1 lines changed: 81, context: html, text, full: html, text
    This script checks download files against their corresponding table. It accepts a table name that has a file associated with it. It makes sure that the file corresponds correctly with its table by comparing total count as well as size (sum(chromEnd-chromStart)).
• src/utils/qa/doGenbankTests
  • 1.7 lines changed: 56, context: html, text, full: html, text
    Changed hard-coded tracknames to real ones from trackDb, added checks for mgcFullMrna and orfeomeMrna, changed echoes so that they reflect same command as is run, general cleanup.
• src/utils/qa/makefile
  • 1.105 lines changed: 2, context: html, text, full: html, text
    added two new scripts for comparing tables with their associated download files
• src/utils/qa/tableDumpDates.csh
  • 1.4 lines changed: 2, context: html, text, full: html, text
    Changed back to sourcing the qaConfig file using which, after specifying PATH in the crontab that was having problems running this script.
• src/utils/qa/updateTimes.csh
  • 1.24 lines changed: 3, context: html, text, full: html, text
    changed usage statement
• src/utils/qa/weeklybld/buildCvsReports.csh
  • 1.20 lines changed: 2, context: html, text, full: html, text
    move cvs stuff, dont copy it
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.56 lines changed: 3, context: html, text, full: html, text
    v205 final build

• lines changed: 9170
• files changed: 159