CVS changes by file

review to branch (2009-10-20 to 2009-10-27) v218

• src/hg/archaeStuff/data/Genome-info-meta
  • 1.11 lines changed: 31, context: html, text, full: html, text
    add Nymph Lake metagenome
• src/hg/archaeStuff/scripts/archaeBrowser/Blast.pm
  • 1.27 lines changed: 4, context: html, text, full: html, text
    change to support Nymph Lake metagenome
• src/hg/archaeStuff/scripts/archaeBrowser/ConservedDomains.pm
  • 1.5 lines changed: 4, context: html, text, full: html, text
    change to support Nymph Lake metagenome
• src/hg/archaeStuff/scripts/archaeBrowser/OrganismDb.pm
  • 1.46 lines changed: 27, context: html, text, full: html, text
    change to support Nymph Lake metagenome
• src/hg/archaeStuff/scripts/archaeBrowser/RemovePriv.pm
  • 1.4 lines changed: 1, context: html, text, full: html, text
    change to support Nymph Lake metagenome
• src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
  • 1.20 lines changed: 1, context: html, text, full: html, text
    Don't display parentTable which is actually obsolete
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.140 lines changed: 7, context: html, text, full: html, text
    Vendor for H3K4me3 has changed.
  • 1.139 lines changed: 1, context: html, text, full: html, text
    Change BAFT to BATF
  • 1.138 lines changed: 110, context: html, text, full: html, text
    Added 10 new antibodies for Myers and one for Farnham and Myers
• src/hg/encode/encodeValidate/config/pi.ra
  • 1.1 lines changed: 94, context: html, text, full: html, text
    First cut of reporting script for ENCODE
• src/hg/encode/encodeValidate/doEncodeReport.pl
  • 1.1 lines changed: 318, context: html, text, full: html, text
    First cut of reporting script for ENCODE
• src/hg/hgGene/hgGeneData/Human/links.ra
  • 1.36 lines changed: 2, context: html, text, full: html, text
    Updating OMIM link to make it faster.
• src/hg/hgc/encodeClick.c
  • 1.10 lines changed: 63, context: html, text, full: html, text
    Details stuff for 5C tracks.
• src/hg/hgc/hgc.c
  • 1.1579 lines changed: 4, context: html, text, full: html, text
    Details stuff for 5C tracks.
• src/hg/hgc/hgc.h
  • 1.48 lines changed: 3, context: html, text, full: html, text
    Details stuff for 5C tracks.
• src/hg/inc/versionInfo.h
  • 1.158 lines changed: 1, context: html, text, full: html, text
    "New version number v218"
• src/hg/instinct/createDescriptionHTML/createSingleDescriptionHTML.pl
  • 1.2 lines changed: 3, context: html, text, full: html, text
    Printing of previous local_url bug fix
• src/hg/instinct/hgHeatmap2/hgHeatmap2.c
  • 1.80 lines changed: 4, context: html, text, full: html, text
    Added local url ability
• src/hg/instinct/hgHeatmap2/hgHeatmap2.h
  • 1.51 lines changed: 1, context: html, text, full: html, text
    Added local_url feature
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_etemadmoghadam2009.ra
  • 1.1 lines changed: 45, context: html, text, full: html, text
    
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_miller2005.ra
  • 1.1 lines changed: 99, context: html, text, full: html, text
    
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.ra
  • 1.31 lines changed: 6, context: html, text, full: html, text
    Fixed downsampling on new datasets
  • 1.30 lines changed: 83, context: html, text, full: html, text
    New datasets
• src/hg/instinct/hgHeatmap2/hgHeatmapFrontend/js/hgHeatmap.js
  • 1.76 lines changed: 4, context: html, text, full: html, text
    Added local url function
• src/hg/instinct/inc/hgHeatmapLib.h
  • 1.38 lines changed: 1, context: html, text, full: html, text
    Added local_url function
• src/hg/instinct/lib/hgHeatmapLib.c
  • 1.63 lines changed: 2, context: html, text, full: html, text
    Local url pointer added
• src/hg/js/hui.js
  • 1.41 lines changed: 27, context: html, text, full: html, text
    Added count of selected subtracks
  • 1.40 lines changed: 22, context: html, text, full: html, text
    Made vis changes work on 3-way matCBs
  • 1.39 lines changed: 6, context: html, text, full: html, text
    Temorarily readd hintOverSortableColumnHeader to avoid js errors.
• src/hg/lib/hui.c
  • 1.244 lines changed: 2, context: html, text, full: html, text
    Added count of selected subtracks
  • 1.243 lines changed: 56, context: html, text, full: html, text
    Moved dimension Z outside of matrix. Requested by Pauline and does make things clearer
  • 1.242 lines changed: 1, context: html, text, full: html, text
    Remove hintOverSortableColumnHeader which does nothing
• src/hg/makeDb/doc/encodeDccHg18/broadBernstein.txt
  • 1.8 lines changed: 74, context: html, text, full: html, text
    I guess I was sitting on these changes rather than checking them in
• src/hg/makeDb/doc/encodeDccHg18/broadChipSeq.notes.txt
  • 1.5 lines changed: 280, context: html, text, full: html, text
    I guess I was sitting on these changes rather than checking them in
• src/hg/makeDb/doc/encodeDccHg18/dnctRelease2.notes.txt
  • 1.1 lines changed: 819, context: html, text, full: html, text
    File list for Open Chromatin release 2
• src/hg/makeDb/doc/encodeDccHg18/dukeUtaUncCrawford.txt
  • 1.9 lines changed: 327, context: html, text, full: html, text
    Put release2 into the pushQ
• src/hg/makeDb/doc/encodeDccHg18/yaleDavisHarvardSnyder.txt
  • 1.10 lines changed: 19, context: html, text, full: html, text
    More submissions for Yale (post release2)
• src/hg/makeDb/doc/hg19.txt
  • 1.52 lines changed: 401, context: html, text, full: html, text
    Rerun the 4D site predictions with chrX only and non-ChrX others
  • 1.51 lines changed: 84, context: html, text, full: html, text
    Now working on phyloP business
  • 1.50 lines changed: 38, context: html, text, full: html, text
    Bring the msa_split procedure up to date
  • 1.49 lines changed: 670, context: html, text, full: html, text
    done with phastCons runs for the 46-way
• src/hg/makeDb/doc/makeEnsembl.txt
  • 1.14 lines changed: 24, context: html, text, full: html, text
    Rat rn4 v56 update done
• src/hg/makeDb/hgCgiData/Human/microarrayGroups.ra
  • 1.93 lines changed: 37, context: html, text, full: html, text
    new datasets
• src/hg/makeDb/trackDb/human/dgv.html
  • 1.6 lines changed: 18, context: html, text, full: html, text
    changed layout of color description to match SNP tracks and added color to the text
• src/hg/makeDb/trackDb/human/encodeAffyChIpHl60PvalStrict.html
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to atcc.org products.
• src/hg/makeDb/trackDb/human/encodeAffyChIpHl60SignalStrict.html
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to atcc.org products.
• src/hg/makeDb/trackDb/human/encodeAffyChIpHl60SitesStrict.html
  • 1.4 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to atcc.org products.
• src/hg/makeDb/trackDb/human/encodeGencodeGeneMar07.html
  • 1.15 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to atcc.org products.
• src/hg/makeDb/trackDb/human/encodeGencodeRaceFrags.html
  • 1.15 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to atcc.org products.
• src/hg/makeDb/trackDb/human/encodeStanfordChip.html
  • 1.3 lines changed: 3, context: html, text, full: html, text
    Fixed broken links to atcc.org products.
• src/hg/makeDb/trackDb/human/encodeStanfordChipSmoothed.html
  • 1.3 lines changed: 3, context: html, text, full: html, text
    Fixed broken links to atcc.org products.
• src/hg/makeDb/trackDb/human/encodeStanfordMeth.html
  • 1.5 lines changed: 8, context: html, text, full: html, text
    Fixed broken links to atcc.org products.
• src/hg/makeDb/trackDb/human/encodeStanfordMethSmoothed.html
  • 1.5 lines changed: 8, context: html, text, full: html, text
    Fixed broken links to atcc.org products.
• src/hg/makeDb/trackDb/human/encodeStanfordPromoters.html
  • 1.5 lines changed: 16, context: html, text, full: html, text
    Fixed broken links to atcc.org products.
• src/hg/makeDb/trackDb/human/encodeUvaDnaRepOrigins.html
  • 1.16 lines changed: 1, context: html, text, full: html, text
    Fixed broken links to atcc.org products.
• src/hg/makeDb/trackDb/human/hg17/encodeNhgriDukeDnaseHs.html
  • 1.11 lines changed: 4, context: html, text, full: html, text
    Fixed broken links to atcc.org products.
• src/hg/makeDb/trackDb/human/hg17/encodeNhgriDukeDnaseHsFeb07.html
  • 1.6 lines changed: 4, context: html, text, full: html, text
    Fixed broken links to atcc.org products.
• src/hg/makeDb/trackDb/human/hg17/encodeYaleChipPval.html
  • 1.13 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to atcc.org products.
• src/hg/makeDb/trackDb/human/hg17/encodeYaleChipSig.html
  • 1.7 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to atcc.org products.
• src/hg/makeDb/trackDb/human/hg17/encodeYaleChipSignal.html
  • 1.10 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to atcc.org products.
• src/hg/makeDb/trackDb/human/hg17/encodeYaleChipSites.html
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to atcc.org products.
• src/hg/makeDb/trackDb/human/hg18/encodeNhgriDukeDnaseHs.html
  • 1.3 lines changed: 4, context: html, text, full: html, text
    Fixed broken links to atcc.org products.
• src/hg/makeDb/trackDb/human/hg18/encodeUvaDnaRepSuper.html
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Fixed broken links to atcc.org products.
• src/hg/makeDb/trackDb/human/hg18/encodeYaleChipPval.html
  • 1.4 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to atcc.org products.
• src/hg/makeDb/trackDb/human/hg18/encodeYaleChipSig.html
  • 1.4 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to atcc.org products.
• src/hg/makeDb/trackDb/human/hg18/encodeYaleChipSites.html
  • 1.4 lines changed: 2, context: html, text, full: html, text
    Fixed broken links to atcc.org products.
• src/hg/makeDb/trackDb/human/hg18/encodeYaleChipSuper.html
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Fixed broken links to atcc.org products.
• src/hg/makeDb/trackDb/human/hg18/knownGene.html
  • 1.30 lines changed: 5, context: html, text, full: html, text
    fixed typo and added color to the color key
• src/hg/makeDb/trackDb/human/hg18/trackDb.instinct.ra
  • 1.45 lines changed: 36, context: html, text, full: html, text
    New datasets
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.620 lines changed: 1, context: html, text, full: html, text
    fix up controlledVocabulary trackDb setting for CSHL long rna-seq
  • 1.619 lines changed: 16, context: html, text, full: html, text
    Remove download files for raw signal from metadata (not posting these for download)
  • 1.618 lines changed: 38, context: html, text, full: html, text
    Added 2 more submissions for UwDnase
  • 1.617 lines changed: 1, context: html, text, full: html, text
    Restore +1 too long label, as it was already released
  • 1.616 lines changed: 68, context: html, text, full: html, text
    Label consistency and length, sort order consistency for CSHL Long RNA track
  • 1.615 lines changed: 54, context: html, text, full: html, text
    Renamed an additional 28 tables for consistency of Open Chromatin tracks
  • 1.614 lines changed: 110, context: html, text, full: html, text
    restoring changes I made yesterday
  • 1.613 lines changed: 3, context: html, text, full: html, text
    In UwChIPSeq, replaced entries for 2HepG2 with 2HEPG2.
  • 1.612 lines changed: 291, context: html, text, full: html, text
    Added 10 new subtracks under UwChIPSeq
  • 1.611 lines changed: 24, context: html, text, full: html, text
    11 more name changes
  • 1.610 lines changed: 114, context: html, text, full: html, text
    Renamed 3 tables in Duke
  • 1.609 lines changed: 15, context: html, text, full: html, text
    add bounds information to bigWig
  • 1.608 lines changed: 33, context: html, text, full: html, text
    some short label edits and defaults for CSHL long RNA-seq
  • 1.607 lines changed: 60, context: html, text, full: html, text
    take out old CSHL long RNA-seq track
  • 1.606 lines changed: 17, context: html, text, full: html, text
    seom fixups for the CSHL long rna track
  • 1.605 lines changed: 1296, context: html, text, full: html, text
    Added a bunch of new UW Chip seq tracks
  • 1.604 lines changed: 47, context: html, text, full: html, text
    Added V2 notes to Open Chromatin
  • 1.603 lines changed: 220, context: html, text, full: html, text
    add CSHL long rna back in, now with compartment and rnaExtract
  • 1.602 lines changed: 33, context: html, text, full: html, text
    Add TFBS validation track from Weng lab, with first dataset
  • 1.601 lines changed: 170, context: html, text, full: html, text
    remove CSHL long rna
  • 1.600 lines changed: 32, context: html, text, full: html, text
    Added one more for UwDnase
  • 1.599 lines changed: 1, context: html, text, full: html, text
    Fixed one longLabel
  • 1.598 lines changed: 89, context: html, text, full: html, text
    Added 3 UwDnase sets
  • 1.597 lines changed: 4, context: html, text, full: html, text
    Made the long labels for the Broad Chip Seq controls consistent with each other
  • 1.596 lines changed: 21, context: html, text, full: html, text
    Added Yale HeLa E2F6.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeq.html
  • 1.20 lines changed: 23, context: html, text, full: html, text
    Added Mapability reference to Broad
• src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMap.html
  • 1.24 lines changed: 76, context: html, text, full: html, text
    Added release 2 notes
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlLongRnaSeq.html
  • 1.3 lines changed: 4, context: html, text, full: html, text
    more text
  • 1.2 lines changed: 124, context: html, text, full: html, text
    more text
  • 1.1 lines changed: 8, context: html, text, full: html, text
    first pass
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDGF.html
  • 1.4 lines changed: 50, context: html, text, full: html, text
    Reorganized the wording on the page to make the description a bit nicer.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeYalePolIISignal.html
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Fixed broken links to atcc.org products.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeYalePolIISites.html
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Fixed broken links to atcc.org products.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleStat1Signal.html
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Fixed broken links to atcc.org products.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleStat1Sites.html
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Fixed broken links to atcc.org products.
• src/hg/makeDb/trackDb/human/hg19/knownGene.html
  • 1.2 lines changed: 5, context: html, text, full: html, text
    fixed typo and added color to the color key
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.55 lines changed: 2, context: html, text, full: html, text
    Get the other phastCons46way tracks set to bigWig
• src/hg/makeDb/trackDb/lowelab/nympLake0708_PGA2009_1/multizSulfolobales.html
  • 1.1 lines changed: 161, context: html, text, full: html, text
    Details page for multiz track
• src/hg/makeDb/trackDb/lowelab/nympLake0708_PGA2009_1/trackDb.ra
  • 1.1 lines changed: 30, context: html, text, full: html, text
    Update multiz track
• src/hg/utils/automation/Encode.pm
  • 1.48 lines changed: 27, context: html, text, full: html, text
    Add functions used by reporting script
• src/hg/utils/automation/EnsGeneAutomate.pm
  • 1.20 lines changed: 172, context: html, text, full: html, text
    Adding version 56 definitions
• src/hg/utils/automation/doBlastzChainNet.pl
  • 1.30 lines changed: 3, context: html, text, full: html, text
    Add the removal of the /err/ parasol directories during cleanUp
• src/hg/utils/automation/doEnsGeneUpdate.pl
  • 1.19 lines changed: 4, context: html, text, full: html, text
    fixup password string given to FTP server to be correct
• src/hg/utils/fiveCToBed/exampleFiveC.txt
  • 1.1 lines changed: 3, context: html, text, full: html, text
    Added a little converter for 5C data.
• src/hg/utils/fiveCToBed/fiveCToBed.c
  • 1.1 lines changed: 141, context: html, text, full: html, text
    Added a little converter for 5C data.
• src/hg/utils/fiveCToBed/makefile
  • 1.1 lines changed: 21, context: html, text, full: html, text
    Added a little converter for 5C data.
• src/hg/visiGene/vgProbeTrack/vgProbeTrack.c
  • 1.17 lines changed: 2, context: html, text, full: html, text
    slightly faster
• src/utils/faRenameRecords/faRenameRecords.c
  • 1.1 lines changed: 57, context: html, text, full: html, text
    New utility to do renaming of all sequences in fasta file seems to work.
• src/utils/faRenameRecords/makefile
  • 1.1 lines changed: 18, context: html, text, full: html, text
    New utility to do renaming of all sequences in fasta file seems to work.
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.85 lines changed: 5, context: html, text, full: html, text
    Starting build v218

• lines changed: 7640
• files changed: 83