All File Changes

v237_base to v238_preview (2010-08-03 to 2010-08-10) v238

• src/hg/encode/encodeLoad/doEncodeLoad.pl
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    change .bw to .bigWig
  • lines changed 4, context: html, text, full: html, text
    fix typos in preamble
• src/hg/encode/encodeLoad/doEncodeUnload.pl
  • lines changed 1, context: html, text, full: html, text
    change .bw to .bigWig
• src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes
  • lines changed 101, context: html, text, full: html, text
    updated to deal with the fact tha we don't have gbdb directories in the download directories any more and to deal with non-gz files
• src/hg/encode/encodeMkGeoPkg/encodeMkGeoPkg
  • lines changed 96, context: html, text, full: html, text
    fix raw/supp file calling, added fields requested by NCBI, added support for replicate
• src/hg/encode/encodeValidate/config/cv.ra
  • lines changed 8, context: html, text, full: html, text
    Updated SeqPlatform descriptions
  • lines changed 16, context: html, text, full: html, text
    Commented out documents, so that mouse cv can be released while documents can be released when a standard can be determined or mouse tracks are released.
  • lines changed 21, context: html, text, full: html, text
    Added first draft of pi.ra and cleaned up DataType
  • lines changed 3, context: html, text, full: html, text
    Updated Description typo in Fibroblast and termId and termUrl for WholeBrain
  • lines changed 348, context: html, text, full: html, text
    first draft of adding pi.ra to cv.ra
  • lines changed 9, context: html, text, full: html, text
    These are changed to accomodate ripTgtProtiens while we still have them and to make sure that there is a vendorId for every vendoerName in the cv.ra
  • lines changed 9, context: html, text, full: html, text
    Added rought descriptions for seqPlatforms, need to verify exact descriptions.
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • lines changed 2, context: html, text, full: html, text
    I am hoping to resolve a weird merge problem, I dont think there are changes
• src/hg/hgGene/hgGeneData/C_elegans/ce6/otherOrgs.ra
  • lines changed 1, context: html, text, full: html, text
    Reverting otherOrgs.ra files so that they match current values on RR one more time. blastTabs getting rebuilt once more.
• src/hg/hgGene/hgGeneData/D_melanogaster/dm3/otherOrgs.ra
  • lines changed 1, context: html, text, full: html, text
    Reverting otherOrgs.ra files so that they match current values on RR one more time. blastTabs getting rebuilt once more.
• src/hg/hgGene/hgGeneData/Human/hg19/otherOrgs.ra
  • lines changed 1, context: html, text, full: html, text
    Reverting otherOrgs.ra files so that they match current values on RR one more time. blastTabs getting rebuilt once more.
• src/hg/hgGene/hgGeneData/Mouse/mm9/otherOrgs.ra
  • lines changed 1, context: html, text, full: html, text
    Reverting otherOrgs.ra files so that they match current values on RR one more time. blastTabs getting rebuilt once more.
• src/hg/hgGene/hgGeneData/Rat/rn4/otherOrgs.ra
  • lines changed 1, context: html, text, full: html, text
    Reverting otherOrgs.ra files so that they match current values on RR one more time. blastTabs getting rebuilt once more.
• src/hg/hgGene/hgGeneData/S_cerevisiae/sacCer2/otherOrgs.ra
  • lines changed 1, context: html, text, full: html, text
    Reverting otherOrgs.ra files so that they match current values on RR one more time. blastTabs getting rebuilt once more.
• src/hg/hgTables/compositeTrack.c
  • lines changed 2, context: html, text, full: html, text
    Adding a trackHash parameter to a bunch of metadata routines so that they could find the track associated with a table. Fixing clipping bug in hgTracks.c for multiWig labels when in non-overlay mode due to a special case that seems to be obsolete (did fair bit of testing to make sure it's not used.)
• src/hg/hgTables/hgTables.c
  • lines changed 12, context: html, text, full: html, text
    Adding a trackHash parameter to a bunch of metadata routines so that they could find the track associated with a table. Fixing clipping bug in hgTracks.c for multiWig labels when in non-overlay mode due to a special case that seems to be obsolete (did fair bit of testing to make sure it's not used.)
• src/hg/hgTables/hgTables.h
  • lines changed 1, context: html, text, full: html, text
    Adding a trackHash parameter to a bunch of metadata routines so that they could find the track associated with a table. Fixing clipping bug in hgTracks.c for multiWig labels when in non-overlay mode due to a special case that seems to be obsolete (did fair bit of testing to make sure it's not used.)
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 8, context: html, text, full: html, text
    Adding a trackHash parameter to a bunch of metadata routines so that they could find the track associated with a table. Fixing clipping bug in hgTracks.c for multiWig labels when in non-overlay mode due to a special case that seems to be obsolete (did fair bit of testing to make sure it's not used.)
  • lines changed 23, context: html, text, full: html, text
    Adding Nav links to composites with matrix
  • lines changed 8, context: html, text, full: html, text
    Adding cell abbreviation table to factorSource tracks.
  • lines changed 16, context: html, text, full: html, text
    add support for ajax option (serves up stripped down html)
  • lines changed 12, context: html, text, full: html, text
    Making it so reset to defaults option appears in hgTrackUi page for container wigs.
• src/hg/hgTracks/factorSource.c
  • lines changed 14, context: html, text, full: html, text
    show motif info only if TXCLUSTER_MOTIFS_TABLE is defined
• src/hg/hgTracks/hgTracks.c
  • lines changed 17, context: html, text, full: html, text
    Adding a trackHash parameter to a bunch of metadata routines so that they could find the track associated with a table. Fixing clipping bug in hgTracks.c for multiWig labels when in non-overlay mode due to a special case that seems to be obsolete (did fair bit of testing to make sure it's not used.)
  • lines changed 16, context: html, text, full: html, text
    Added checkboxes to searchTracks
• src/hg/hgTracks/imageV2.h
  • lines changed 1, context: html, text, full: html, text
    Turning on dragReorder in genome-test.
• src/hg/hgTracks/mainMain.c
  • lines changed 2, context: html, text, full: html, text
    Added checkboxes to searchTracks
  • lines changed 1, context: html, text, full: html, text
    include imageV2.h
• src/hg/hgTracks/searchTracks.c
  • lines changed 2, context: html, text, full: html, text
    Adding a trackHash parameter to a bunch of metadata routines so that they could find the track associated with a table. Fixing clipping bug in hgTracks.c for multiWig labels when in non-overlay mode due to a special case that seems to be obsolete (did fair bit of testing to make sure it's not used.)
  • lines changed 105, context: html, text, full: html, text
    Added checkboxes to searchTracks
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    draw in MG_BLACK, not 1 (which is white in 32-bit)
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    Adding a trackHash parameter to a bunch of metadata routines so that they could find the track associated with a table. Fixing clipping bug in hgTracks.c for multiWig labels when in non-overlay mode due to a special case that seems to be obsolete (did fair bit of testing to make sure it's not used.)
  • lines changed 7, context: html, text, full: html, text
    put gencode ensembl transcript id link in trackDb instead of hard-coding it
  • lines changed 52, context: html, text, full: html, text
    Added rdmr track.
• src/hg/hgc/peakClusters.c
  • lines changed 1, context: html, text, full: html, text
    Adding a trackHash parameter to a bunch of metadata routines so that they could find the track associated with a table. Fixing clipping bug in hgTracks.c for multiWig labels when in non-overlay mode due to a special case that seems to be obsolete (did fair bit of testing to make sure it's not used.)
  • lines changed 19, context: html, text, full: html, text
    Reworking a little how cell line abbreviation table appears, and moving some of the code for it to the library.
  • lines changed 69, context: html, text, full: html, text
    show motif info if TXCLUSTER_MOTIFS_TABLE is defined
• src/hg/htdocs/ENCODE/cellTypes.html
  • lines changed 1, context: html, text, full: html, text
    made tier three frame bigger
• src/hg/htdocs/ENCODE/cellTypesMouse.html
  • lines changed 6, context: html, text, full: html, text
    additional portal modifications in prep for release
• src/hg/htdocs/ENCODE/index.html
  • lines changed 1, context: html, text, full: html, text
    added link location that I had forgotten
  • lines changed 17, context: html, text, full: html, text
    additional portal modifications in prep for release
• src/hg/htdocs/ENCODE/newsarch.html
  • lines changed 2, context: html, text, full: html, text
    additional portal modifications in prep for release
• src/hg/htdocs/ENCODE/pubs.html
  • lines changed 8, context: html, text, full: html, text
    additional portal modifications in prep for release
• src/hg/htdocs/ENCODE/releaseLog.html
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 3, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 15, context: html, text, full: html, text
    "Encode release log update"
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 40, context: html, text, full: html, text
    Redid cat credits and added felCat4.
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 3, context: html, text, full: html, text
    removed bad link
• src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html
  • lines changed 32, context: html, text, full: html, text
    added Overlay method and Transform function; consolidtaed 'y=0.0' and 'Draw indicator line at y'
• src/hg/htdocs/goldenPath/releaseLog.html
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
  • lines changed 3, context: html, text, full: html, text
    "Release log update"
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
  • lines changed 15, context: html, text, full: html, text
    "Release log update"
• src/hg/htdocs/images/Felis_catus4.jpg
  • lines changed 0, context: html, text, full: html, text
    removing felCat4 image due to copyright
  • lines changed 0, context: html, text, full: html, text
    new cat image for felCat4
• src/hg/htdocs/indexNews.html
  • lines changed 1, context: html, text, full: html, text
    added omitted 'of'
• src/hg/htdocs/style/jquery-ui.css
  • lines changed 10, context: html, text, full: html, text
    Added checkboxes to searchTracks
• src/hg/inc/hui.h
  • lines changed 4, context: html, text, full: html, text
    Adding a trackHash parameter to a bunch of metadata routines so that they could find the track associated with a table. Fixing clipping bug in hgTracks.c for multiWig labels when in non-overlay mode due to a special case that seems to be obsolete (did fair bit of testing to make sure it's not used.)
  • lines changed 4, context: html, text, full: html, text
    Adding Nav links to composites with matrix
  • lines changed 3, context: html, text, full: html, text
    Adding hPrintAbbreviationTable to library so can use it in both hgc and hgTrackUi.
• src/hg/inc/txCluster.h
  • lines changed 3, context: html, text, full: html, text
    add TXCLUSTER_MOTIFS_TABLE define
• src/hg/js/hgTracks.js
  • lines changed 110, context: html, text, full: html, text
    Added checkboxes to searchTracks
  • lines changed 2, context: html, text, full: html, text
    remove an alert that accidently got checked in
• src/hg/js/staticDoc.js
  • lines changed 3, context: html, text, full: html, text
    added the function for hgdownloads
• src/hg/lib/customFactory.c
  • lines changed 2, context: html, text, full: html, text
    add db setting to table browser custom tracks
  • lines changed 4, context: html, text, full: html, text
    checking incoming bed files for legal coordinates
• src/hg/lib/customTrack.c
  • lines changed 1, context: html, text, full: html, text
    was missing wibFile setting on track line for cts from table browser
• src/hg/lib/hui.c
  • lines changed 37, context: html, text, full: html, text
    Adding a trackHash parameter to a bunch of metadata routines so that they could find the track associated with a table. Fixing clipping bug in hgTracks.c for multiWig labels when in non-overlay mode due to a special case that seems to be obsolete (did fair bit of testing to make sure it's not used.)
  • lines changed 6, context: html, text, full: html, text
    Adding Nav links to composites with matrix
  • lines changed 23, context: html, text, full: html, text
    Adding hPrintAbbreviationTable to library so can use it in both hgc and hgTrackUi.
• src/hg/lib/jksql.c
  • lines changed 13, context: html, text, full: html, text
    fixed bug were attempt to allocated a connection cache entry with no-abort for a non-existant database would go very wrong
• src/hg/lib/rdmrRaw.sql
  • lines changed 15, context: html, text, full: html, text
    Added rdmr track.
• src/hg/lib/trackDbCustom.c
  • lines changed 1, context: html, text, full: html, text
    change back to old code
• src/hg/makeDb/doc/calJac3.txt
  • lines changed 21, context: html, text, full: html, text
    stalled by phlopP bug
• src/hg/makeDb/doc/ce6.txt
  • lines changed 6, context: html, text, full: html, text
    Rebuilt xxBlastTab tables for hg19, mm9, rn4, ce6, sacCer2, and dm3 using blast-2.2.11.
• src/hg/makeDb/doc/dm3.txt
  • lines changed 13, context: html, text, full: html, text
    Rebuilt xxBlastTab tables for hg19, mm9, rn4, ce6, sacCer2, and dm3 using blast-2.2.11.
• src/hg/makeDb/doc/encodeDccHg19/gencodeV4.txt
  • lines changed 9, context: html, text, full: html, text
    fix up some gencode table naming inconsistencies
• src/hg/makeDb/doc/hg19.txt
  • lines changed 7, context: html, text, full: html, text
    Rebuilt xxBlastTab tables for hg19, mm9, rn4, ce6, sacCer2, and dm3 using blast-2.2.11.
  • lines changed 19, context: html, text, full: html, text
    Re-built hg19 uniGene_3 track.
  • lines changed 7, context: html, text, full: html, text
    fixed checkTableCoords error
  • lines changed 48, context: html, text, full: html, text
    sestanBrainAtlas
  • lines changed 12, context: html, text, full: html, text
    snp131: fixed script loophole that allowed a function value to be empty instead of unknown.
  • lines changed 21, context: html, text, full: html, text
    complete sno/miRNA track
  • lines changed 34, context: html, text, full: html, text
    Updated genscan track build section to reflect corrections to .lft files.
• src/hg/makeDb/doc/mm9.txt
  • lines changed 12, context: html, text, full: html, text
    Rebuilt xxBlastTab tables for hg19, mm9, rn4, ce6, sacCer2, and dm3 using blast-2.2.11.
• src/hg/makeDb/doc/rn4.txt
  • lines changed 6, context: html, text, full: html, text
    Rebuilt xxBlastTab tables for hg19, mm9, rn4, ce6, sacCer2, and dm3 using blast-2.2.11.
• src/hg/makeDb/doc/sacCer2.txt
  • lines changed 13, context: html, text, full: html, text
    Rebuilt xxBlastTab tables for hg19, mm9, rn4, ce6, sacCer2, and dm3 using blast-2.2.11.
• src/hg/makeDb/genbank/etc/ignore.idx
  • lines changed 1, context: html, text, full: html, text
    added ignore entry
• src/hg/makeDb/schema/all.joiner
  • lines changed 14, context: html, text, full: html, text
    add association between hg19 Gencode class and GTF tables
• src/hg/makeDb/trackDb/cat/felCat4/description.html
  • lines changed 1, context: html, text, full: html, text
    changing to reference old cat photo because not sure of copyright status of the new photo
  • lines changed 1, context: html, text, full: html, text
    Oops, munged image
  • lines changed 42, context: html, text, full: html, text
    Edited the content for accuracy and readability.
• src/hg/makeDb/trackDb/cat/felCat4/trackDb.chainNet.ra
  • lines changed 5, context: html, text, full: html, text
    editing the default tracks to be pleasing to the eye
• src/hg/makeDb/trackDb/cat/felCat4/trackDb.ra
  • lines changed 16, context: html, text, full: html, text
    editing the default tracks to be pleasing to the eye
• src/hg/makeDb/trackDb/cat/trackDb.chainNet.ra
  • lines changed 9, context: html, text, full: html, text
    making visibilities hide by default and removing code to make short label be for mm9, since it doesn't seem to have any purpose
  • lines changed 15, context: html, text, full: html, text
    Put chain/net in phylogenetic order
• src/hg/makeDb/trackDb/human/hg18/haplotypeLocations.html
  • lines changed 9, context: html, text, full: html, text
    adding haplotype position tracks to hg19 and hg18 and lift over chain experiments
• src/hg/makeDb/trackDb/human/hg18/hg19ContigDiff.html
  • lines changed 31, context: html, text, full: html, text
    adding difference tracks hg18 to hg19 to hg18
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 73, context: html, text, full: html, text
    drop alignments from UCSF Brain Methyl since they aren't correct
  • lines changed 23, context: html, text, full: html, text
    adding haplotype position tracks to hg19 and hg18 and lift over chain experiments
  • lines changed 7, context: html, text, full: html, text
    adding difference tracks hg18 to hg19 to hg18
  • lines changed 9, context: html, text, full: html, text
    Added rdmr track.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    fix link out for Gencode V3
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    I am hoping to resolve a weird merge problem, I dont think there are changes
  • lines changed 1, context: html, text, full: html, text
    Making rainbow wigs packable.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaRnaSeq.html
  • lines changed 38, context: html, text, full: html, text
    mostly shortened run-on lines. added one EM tag pair around et al.
  • lines changed 28, context: html, text, full: html, text
    moved last sentence to the second sentence; removed repeated sentence; broke into multiple lines
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaRnaSeq.ra
  • lines changed 13, context: html, text, full: html, text
    change Myers to HudsonAlpha
• src/hg/makeDb/trackDb/human/hg18/wgEncodeReg.html
  • lines changed 3, context: html, text, full: html, text
    further clarifications
  • lines changed 27, context: html, text, full: html, text
    edited for clarity and added data release policy
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRegDnaseClustered.html
  • lines changed 2, context: html, text, full: html, text
    changed DNAse to DNase
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRegMarkEnhH3k27ac.html
  • lines changed 7, context: html, text, full: html, text
    expanding on the descriptions of the histone mark tracks
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRegMarkEnhH3k4me1.html
  • lines changed 7, context: html, text, full: html, text
    expanding on the descriptions of the histone mark tracks
  • lines changed 1, context: html, text, full: html, text
    making a clarification in the description
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRegMarkEnhH3k4me3.html
  • lines changed 7, context: html, text, full: html, text
    expanding on the descriptions of the histone mark tracks
• src/hg/makeDb/trackDb/human/hg19/hg18ContigDiff.html
  • lines changed 31, context: html, text, full: html, text
    adding difference tracks hg18 to hg19 to hg18
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
  • lines changed 1, context: html, text, full: html, text
    metadata for hg19 gencodeV4
  • lines changed 1, context: html, text, full: html, text
    added wgEncodeMapability
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAffyRnaChip.ra
  • lines changed 105, context: html, text, full: html, text
    Upated metaData with origAssembly variable.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 400, context: html, text, full: html, text
    Standardized dataType ChIP-seq in the metadata
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 177, context: html, text, full: html, text
    Changed the prostate experiment to be short not total and have correct magic number
  • lines changed 3, context: html, text, full: html, text
    Changed the prostate experiment to be short not total
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencode.ra
  • lines changed 7, context: html, text, full: html, text
    add submission id for gencode
  • lines changed 89, context: html, text, full: html, text
    metadata for hg19 gencodeV4
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 394, context: html, text, full: html, text
    Standardized dataType ChIP-seq in the metadata
  • lines changed 377, context: html, text, full: html, text
    Added metaData for submission 1848, such that downloads page has correct metaData. Updted 3 files with incorrect protocol metaData
  • lines changed 25, context: html, text, full: html, text
    Added subId:1978 bam file metadata so that it can become available for AWG group as a control
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeMapability.ra
  • lines changed 85, context: html, text, full: html, text
    put this in metaDb
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 13, context: html, text, full: html, text
    Standardized dataType ChIP-seq in the metadata
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyAlbanyTiling.ra
  • lines changed 9, context: html, text, full: html, text
    Changed RipChip to RIP-chip
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyGeneST.ra
  • lines changed 22, context: html, text, full: html, text
    changed the RipChip to RIP-chip
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 64, context: html, text, full: html, text
    Standardized dataType ChIP-seq in the metadata
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 587, context: html, text, full: html, text
    Standardized dataType ChIP-seq in the metadata
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 1799, context: html, text, full: html, text
    Standardized dataType ChIP-seq in the metadata
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    adding the two chrM sequences to haplotype track
  • lines changed 2, context: html, text, full: html, text
    adding haplotype position tracks to hg19 and hg18 and lift over chain experiments
  • lines changed 7, context: html, text, full: html, text
    adding difference tracks hg18 to hg19 to hg18
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 3, context: html, text, full: html, text
    take out metadata for hg19 wgEncodeGencode
  • lines changed 1, context: html, text, full: html, text
    take out spurious url variable
  • lines changed 2, context: html, text, full: html, text
    fix up some gencode table naming inconsistencies
  • lines changed 1, context: html, text, full: html, text
    renamed to accomodate Katrina and tried to fix the matrix issue
  • lines changed 2, context: html, text, full: html, text
    put gencode ensembl transcript id link in trackDb instead of hard-coding it
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeCaltechRnaSeq.ra
  • lines changed 1327, context: html, text, full: html, text
    renamed to accomodate Katrina and tried to fix the matrix issue
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeSydhTfbs.ra
  • lines changed 1, context: html, text, full: html, text
    Missed spelled display of factor ZNF274 as ZNF27 in composite subGroup, corrected error.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.ra
  • lines changed 42, context: html, text, full: html, text
    Fixed the check boxes, set default tracks on, changed the matrix to have 400 and 200 included
  • lines changed 1327, context: html, text, full: html, text
    renamed to accomodate Katrina and tried to fix the matrix issue
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.ra
  • lines changed 58, context: html, text, full: html, text
    Changed the matrix, the short label, a typo
  • lines changed 63, context: html, text, full: html, text
    changed the short labels, fixed some typos, changed the matrix
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 1230, context: html, text, full: html, text
    Standardized dataType ChIP-seq in the metadata
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 13031, context: html, text, full: html, text
    Standardized dataType ChIP-seq in the metadata
• src/hg/makeDb/trackDb/tagTypes.tab
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    put gencode ensembl transcript id link in trackDb instead of hard-coding it
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
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    felCat4 chain/nets are not quite right. Adding a release alpha, beta tag so don't go out to the RR in their current state. Also added a release alpha to felCatVIe so that these chain/nets never go out to beta or the RR
• src/hg/regulate/regCluster/regCluster.c
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    Making score an int rather than floating point in regCluster bed output.
• src/hg/snp/snpLoad/snpNcbiToUcsc.c
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    Error out if a string value is empty instead of one of the join-codes for missing. An empty func value from a script loophole caused a SNP to be invisible from hgTracks display (GB - Bug #75).
• src/hg/useCount/useCount.c
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    use proper dateTime result string
• src/hg/utils/automation/Encode.pm
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    added die statement to check if there is no matching composite expVars.ra
• src/hg/utils/automation/EnsGeneAutomate.pm
  • lines changed 168, context: html, text, full: html, text
    updated with v59 definitions
• src/hg/utils/automation/doHgNearBlastp.pl
  • lines changed 1, context: html, text, full: html, text
    Changed blastPath to point to /scratch/data/blast which is now a symlink to the preferred version of blast.
• src/hg/utils/automation/doSameSpeciesLiftOver.pl
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    fixing code again for overlap
  • lines changed 3, context: html, text, full: html, text
    fixing code for overlap
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    correcting overlap so that blat chunk will not exceed 5000
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    using an overlap of 500 bases during the 5K split
• src/hg/utils/motifFinder/motifFinder.c
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    add prior and priorBackoff command line parameters
• src/hg/utils/phyloTrees/chainNet.pl
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    should be oviAri not oviAra on newAssembliesList
• src/inc/cheapcgi.h
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    cgiClientBrowser() macro checked in
• src/lib/errCatch.c
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    Updated comment to avoid advising people to generate a compiler error.
• src/product/scripts/trashCleanMonitor.csh
  • lines changed 2, context: html, text, full: html, text
    remove the safety exit 0, this is now live
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    finalized versions ready to go
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    omit reference to my location
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    trash cleaner now in two parts to verify OK
• src/product/scripts/trashCleaner.csh
  • lines changed 49, context: html, text, full: html, text
    finalized versions ready to go
  • lines changed 27, context: html, text, full: html, text
    trash cleaner now in two parts to verify OK
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    initial contents of single trash cleaner all in one
• src/product/scripts/trashCleaning.sh
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    removed older trashCleaning.sh script
• src/utils/qa/checkGenomeMysql
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    adding better comments to the script
• src/utils/qa/weeklybld/buildEnv.csh
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    v238 preview
• src/utils/qa/weeklybld/buildUtils.csh
  • lines changed 2, context: html, text, full: html, text
    trying to speed up 32bit utils build
• src/utils/qa/weeklybld/coBranch.csh
  • lines changed 1, context: html, text, full: html, text
    adding chmod g+w for build scripts that clone kent dirs
• src/utils/qa/weeklybld/doJavaUtilBuild.csh
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    adding chmod g+w for build scripts that clone kent dirs
• src/utils/qa/weeklybld/doRobots.csh
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    adding note about search robot
• src/utils/qa/weeklybld/makeUserApps.csh
  • lines changed 1, context: html, text, full: html, text
    adding chmod g+w for build scripts that clone kent dirs

• lines changed: 24082
• files changed: 193