All File Changes

v273_base to v274_preview (2012-09-18 to 2012-09-25) v274

• python/lib/ucscGb/qa/tables/positionalQa.py
  • lines changed 125, context: html, text, full: html, text
    Changed qaGbTracks so that it prints statistics about chromosome item counts to log file rather than the count of every chrom to a separate chrom file. See redmine #9075.
• python/lib/ucscGb/qa/tables/tableQa.py
  • lines changed 1, context: html, text, full: html, text
    Changed qaGbTracks so that it prints statistics about chromosome item counts to log file rather than the count of every chrom to a separate chrom file. See redmine #9075.
• src/blat/version.doc
  • lines changed 3, context: html, text, full: html, text
    added repMatch default values for tileSizes 16 to 18; also fixed and incremented version to 35x1
• src/hg/hgCustom/hgCustom.c
  • lines changed 2, context: html, text, full: html, text
    net.h needs to be included outside of #ifdef USE_BAM..., for mirror builds without special env vars.
• src/hg/hgTables/bam.c
  • lines changed 2, context: html, text, full: html, text
    Pauline found that hgTable's 'describe table schema' page was not showingthe track description for bigDataUrl track types. Hooked those up, and
    restricted a whitespace tweak to only descriptions that start with <H2>
    so plain text descriptions don't get squashed up against the section title.
    
• src/hg/hgTables/bigBed.c
  • lines changed 2, context: html, text, full: html, text
    Pauline found that hgTable's 'describe table schema' page was not showingthe track description for bigDataUrl track types. Hooked those up, and
    restricted a whitespace tweak to only descriptions that start with <H2>
    so plain text descriptions don't get squashed up against the section title.
    
• src/hg/hgTables/hgTables.h
  • lines changed 5, context: html, text, full: html, text
    Pauline found that hgTable's 'describe table schema' page was not showingthe track description for bigDataUrl track types. Hooked those up, and
    restricted a whitespace tweak to only descriptions that start with <H2>
    so plain text descriptions don't get squashed up against the section title.
    
• src/hg/hgTables/schema.c
  • lines changed 22, context: html, text, full: html, text
    Pauline found that hgTable's 'describe table schema' page was not showingthe track description for bigDataUrl track types. Hooked those up, and
    restricted a whitespace tweak to only descriptions that start with <H2>
    so plain text descriptions don't get squashed up against the section title.
    
• src/hg/hgTables/vcf.c
  • lines changed 3, context: html, text, full: html, text
    Pauline found that hgTable's 'describe table schema' page was not showingthe track description for bigDataUrl track types. Hooked those up, and
    restricted a whitespace tweak to only descriptions that start with <H2>
    so plain text descriptions don't get squashed up against the section title.
    
• src/hg/hgc/ccdsClick.c
  • lines changed 16, context: html, text, full: html, text
    link GENCODE to APPRIS and HGNC
• src/hg/hgc/ccdsClick.h
  • lines changed 9, context: html, text, full: html, text
    link GENCODE to APPRIS and HGNC
• src/hg/hgc/gencodeClick.c
  • lines changed 77, context: html, text, full: html, text
    link GENCODE to APPRIS and HGNC
  • lines changed 2, context: html, text, full: html, text
    fixed just introduced HTML table layout bug
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeUwDnase.release2.notes
  • lines changed 1475, context: html, text, full: html, text
    adding notes for uw dnase
• src/hg/makeDb/doc/hg19.txt
  • lines changed 6, context: html, text, full: html, text
    recipbest experiment to mm10
• src/hg/makeDb/doc/mm10.txt
  • lines changed 29, context: html, text, full: html, text
    adding the GRC Incident database track
• src/hg/makeDb/doc/proteins/120806.txt
  • lines changed 99, context: html, text, full: html, text
    finished (hopefully) building the proteome database (#7045)
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
  • lines changed 11, context: html, text, full: html, text
    add instructions to build track of Pfam domains in UCSC genes
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 93, context: html, text, full: html, text
    Adding targetClass where it is transitive, removing some old comments, dealing with capitalization for GeneCard listings and cleaning up urls
  • lines changed 176, context: html, text, full: html, text
    Removing unused antibodies
  • lines changed 1, context: html, text, full: html, text
    Qa fixes http://redmine.soe.ucsc.edu/issues/7907#note-28
  • lines changed 1, context: html, text, full: html, text
    Adding back a line that was accidentally erased
  • lines changed 13, context: html, text, full: html, text
    Trying to standardize on the Peptide mapping views
  • lines changed 1, context: html, text, full: html, text
    Solving merge issue with cv
  • lines changed 23, context: html, text, full: html, text
    Adding antibody validation docs in CV
  • lines changed 10, context: html, text, full: html, text
    Adding human antibody validation docs to CV
  • lines changed 1, context: html, text, full: html, text
    Changing CTCT to CTCF in CV
  • lines changed 1, context: html, text, full: html, text
    Adding antibody description
  • lines changed 56, context: html, text, full: html, text
    Updating the targets where there is an obvious capilatization or dash issue, or there is an obvious preference in HGNC. This should only be the target label.
  • lines changed 200, context: html, text, full: html, text
    Standardizing on the vendor names
  • lines changed 10, context: html, text, full: html, text
    Removing underbars in the label
  • lines changed 3, context: html, text, full: html, text
    Fixing typos found in ticket 9113
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeBroadChipSeq.ra
  • lines changed 923, context: html, text, full: html, text
    updating wgEncodeBroadChipSeq metadata (adding composite stanza, expId, & labVersion), removing UCSC Accession from sortOrder so it doesn't show up in hgFileUi (no ucsc Accessions for hg18), copying .new.ra to .ra and updating release tags to release sortOrder so Downloads link goes to hgFileUi rather than download dir
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeCshlLongRnaSeq.ra
  • lines changed 32, context: html, text, full: html, text
    releasing updated metadata (expIds added, All Raw Signal changed to Raw Signal per convention, expVars added), un-commenting fileSortOrder in trackDb .ra file so hgTrackUi Downloads link will go to hgFileUi
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeGisPet.ra
  • lines changed 387, context: html, text, full: html, text
    releasing updated metadata (added composite stanza & expIds and cfixed some view names) and uncommenting fileSortOrder so the hgTrackUi downloads link goes to hgFileUi
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeGisRnaSeq.ra
  • lines changed 36, context: html, text, full: html, text
    releasing updated metadata & uncommenting out fileSortOrder and removing md5sum from fileSortOrder
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeUwAffyExonArray.ra
  • lines changed 140, context: html, text, full: html, text
    releasing metdata updates and trackDB patch updates; also added file sort order so download link in hgTrackUi goes to hgFileUi
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeUwChIPSeq.ra
  • lines changed 710, context: html, text, full: html, text
    releasing metadata updates, uncommenting fileSortOrder to hgTrackUi Downloads link goes to hgFileUi (removed md5sum from fileSortOrder because it isn't that useful)
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeBroadChipSeq.ra
  • lines changed 923, context: html, text, full: html, text
    updating wgEncodeBroadChipSeq metadata (adding composite stanza, expId, & labVersion), removing UCSC Accession from sortOrder so it doesn't show up in hgFileUi (no ucsc Accessions for hg18), copying .new.ra to .ra and updating release tags to release sortOrder so Downloads link goes to hgFileUi rather than download dir
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeCshlLongRnaSeq.ra
  • lines changed 32, context: html, text, full: html, text
    releasing updated metadata (expIds added, All Raw Signal changed to Raw Signal per convention, expVars added), un-commenting fileSortOrder in trackDb .ra file so hgTrackUi Downloads link will go to hgFileUi
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeGisPet.ra
  • lines changed 387, context: html, text, full: html, text
    releasing updated metadata (added composite stanza & expIds and cfixed some view names) and uncommenting fileSortOrder so the hgTrackUi downloads link goes to hgFileUi
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeGisRnaSeq.ra
  • lines changed 36, context: html, text, full: html, text
    releasing updated metadata & uncommenting out fileSortOrder and removing md5sum from fileSortOrder
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeUwAffyExonArray.ra
  • lines changed 140, context: html, text, full: html, text
    releasing metdata updates and trackDB patch updates; also added file sort order so download link in hgTrackUi goes to hgFileUi
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeUwChIPSeq.ra
  • lines changed 710, context: html, text, full: html, text
    releasing metadata updates, uncommenting fileSortOrder to hgTrackUi Downloads link goes to hgFileUi (removed md5sum from fileSortOrder because it isn't that useful)
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    updating wgEncodeBroadChipSeq metadata (adding composite stanza, expId, & labVersion), removing UCSC Accession from sortOrder so it doesn't show up in hgFileUi (no ucsc Accessions for hg18), copying .new.ra to .ra and updating release tags to release sortOrder so Downloads link goes to hgFileUi rather than download dir
  • lines changed 2, context: html, text, full: html, text
    releasing metdata updates and trackDB patch updates; also added file sort order so download link in hgTrackUi goes to hgFileUi
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeq.new.ra
  • lines changed 1, context: html, text, full: html, text
    updating wgEncodeBroadChipSeq metadata (adding composite stanza, expId, & labVersion), removing UCSC Accession from sortOrder so it doesn't show up in hgFileUi (no ucsc Accessions for hg18), copying .new.ra to .ra and updating release tags to release sortOrder so Downloads link goes to hgFileUi rather than download dir
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeq.ra
  • lines changed 1, context: html, text, full: html, text
    updating wgEncodeBroadChipSeq metadata (adding composite stanza, expId, & labVersion), removing UCSC Accession from sortOrder so it doesn't show up in hgFileUi (no ucsc Accessions for hg18), copying .new.ra to .ra and updating release tags to release sortOrder so Downloads link goes to hgFileUi rather than download dir
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlLongRnaSeq.ra
  • lines changed 1, context: html, text, full: html, text
    releasing updated metadata (expIds added, All Raw Signal changed to Raw Signal per convention, expVars added), un-commenting fileSortOrder in trackDb .ra file so hgTrackUi Downloads link will go to hgFileUi
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisPet.ra
  • lines changed 1, context: html, text, full: html, text
    releasing updated metadata (added composite stanza & expIds and cfixed some view names) and uncommenting fileSortOrder so the hgTrackUi downloads link goes to hgFileUi
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisRnaSeq.ra
  • lines changed 1, context: html, text, full: html, text
    releasing updated metadata & uncommenting out fileSortOrder and removing md5sum from fileSortOrder
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwAffyExonArray.patch.ra
  • lines changed 1, context: html, text, full: html, text
    releasing metdata updates and trackDB patch updates; also added file sort order so download link in hgTrackUi goes to hgFileUi
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwAffyExonArray.ra
  • lines changed 74, context: html, text, full: html, text
    releasing metdata updates and trackDB patch updates; also added file sort order so download link in hgTrackUi goes to hgFileUi
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwChIPSeq.ra
  • lines changed 1, context: html, text, full: html, text
    releasing metadata updates, uncommenting fileSortOrder to hgTrackUi Downloads link goes to hgFileUi (removed md5sum from fileSortOrder because it isn't that useful)
• src/hg/makeDb/trackDb/human/hg19/dhcVcfModern.html
  • lines changed 74, context: html, text, full: html, text
    Track #8886 (Denisova high-cov): description for Modern Human Variants.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 547, context: html, text, full: html, text
    added GEO accessions for BroadHistone and PsuDnase
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
  • lines changed 97, context: html, text, full: html, text
    added accessions for GisRnaPet and OpenChromChip
  • lines changed 14, context: html, text, full: html, text
    Adding notes about the 107c versus 105C confusion
  • lines changed 2, context: html, text, full: html, text
    Adding the md5sum back for the missing file
  • lines changed 39, context: html, text, full: html, text
    fixed a number of GEO issues with cricket for Gis RNA PET
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibBisulfate.ra
  • lines changed 229, context: html, text, full: html, text
    This is replaced by wgEncodeHaibMethylWgbs
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 118, context: html, text, full: html, text
    added accessions for GisRnaPet and OpenChromChip
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyAlbanyTiling.ra
  • lines changed 10, context: html, text, full: html, text
    added accessions for SUNY tiling
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 131, context: html, text, full: html, text
    added geo accessions for SydhTfbs (hg19 & mm9), SydhHist, and mm9 UwDgf. Also added fixed md5sums from double compression md5 fix for hg19 UwDgf
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 35, context: html, text, full: html, text
    added geo accessions for SydhTfbs (hg19 & mm9), SydhHist, and mm9 UwDgf. Also added fixed md5sums from double compression md5 fix for hg19 UwDgf
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeBroadHistone.ra
  • lines changed 547, context: html, text, full: html, text
    Adding Geo numbers for hg19 BroadHistone and mm9 PsuDnase for RM#9065
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeBuOrchid.ra
  • lines changed 2, context: html, text, full: html, text
    Adding GEO numbers to hg19 BuOrchid GisRnaPet and mm9 PsuTfbs for RM#9065
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeGisRnaPet.ra
  • lines changed 32, context: html, text, full: html, text
    Adding GEO numbers to hg19 BuOrchid GisRnaPet and mm9 PsuTfbs for RM#9065
  • lines changed 97, context: html, text, full: html, text
    releasing metadata changes, mostly the addition of GEO accessions
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeHaibTfbs.ra
  • lines changed 39, context: html, text, full: html, text
    releasing metadata changes, mostly the addition of GEO accessions
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeOpenChromChip.ra
  • lines changed 118, context: html, text, full: html, text
    releasing metadata changes, mostly the addition of GEO accessions
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeOpenChromSynth.ra
  • lines changed 19, context: html, text, full: html, text
    Adding Geo numbers for hg19 OpenChromSynth and mm9 SydhHist for RM#9065
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSydhTfbs.ra
  • lines changed 131, context: html, text, full: html, text
    releasing metadata changes, mostly the addition of GEO accessions
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwDgf.ra
  • lines changed 35, context: html, text, full: html, text
    added geo accessions for SydhTfbs (hg19 & mm9), SydhHist, and mm9 UwDgf. Also added fixed md5sums from double compression md5 fix for hg19 UwDgf
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeBroadHistone.ra
  • lines changed 547, context: html, text, full: html, text
    Adding Geo numbers for hg19 BroadHistone and mm9 PsuDnase for RM#9065
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeBuOrchid.ra
  • lines changed 2, context: html, text, full: html, text
    Adding GEO numbers to hg19 BuOrchid GisRnaPet and mm9 PsuTfbs for RM#9065
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeGisRnaPet.ra
  • lines changed 32, context: html, text, full: html, text
    Adding GEO numbers to hg19 BuOrchid GisRnaPet and mm9 PsuTfbs for RM#9065
  • lines changed 97, context: html, text, full: html, text
    releasing metadata changes, mostly the addition of GEO accessions
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeHaibTfbs.ra
  • lines changed 39, context: html, text, full: html, text
    releasing metadata changes, mostly the addition of GEO accessions
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeOpenChromChip.ra
  • lines changed 118, context: html, text, full: html, text
    releasing metadata changes, mostly the addition of GEO accessions
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeOpenChromFaire.ra
  • lines changed 2507, context: html, text, full: html, text
    Staging on public Open Chrom FAIRE (Release 2) RM#4142
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeOpenChromSynth.ra
  • lines changed 19, context: html, text, full: html, text
    Adding Geo numbers for hg19 OpenChromSynth and mm9 SydhHist for RM#9065
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeSydhTfbs.ra
  • lines changed 131, context: html, text, full: html, text
    releasing metadata changes, mostly the addition of GEO accessions
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwDgf.ra
  • lines changed 35, context: html, text, full: html, text
    Adding md5sum metaData for hg19 Univ Wash DGF RM#8477 for compression files fix
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    move Pfam in UCSC genes track to top level (#8968)
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    Staging on public Open Chrom FAIRE (Release 2) RM#4142
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release3.ra
  • lines changed 1, context: html, text, full: html, text
    Adding the GEO Accession column
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release3.html
  • lines changed 6, context: html, text, full: html, text
    Adding greater thans and fixing sanitation of emails
  • lines changed 13, context: html, text, full: html, text
    Trying to rearrange the contacts list
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release3.ra
  • lines changed 4, context: html, text, full: html, text
    Qa fixes http://redmine.soe.ucsc.edu/issues/7907#note-28
  • lines changed 19, context: html, text, full: html, text
    Fixing long labels
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV10.html
  • lines changed 38, context: html, text, full: html, text
    for GENCODE add description of problem biotypes and fix invalid HTML
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV11.html
  • lines changed 37, context: html, text, full: html, text
    for GENCODE add description of problem biotypes and fix invalid HTML
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV12.html
  • lines changed 36, context: html, text, full: html, text
    for GENCODE add description of problem biotypes and fix invalid HTML
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV13.html
  • lines changed 37, context: html, text, full: html, text
    for GENCODE add description of problem biotypes and fix invalid HTML
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV13.ra
  • lines changed 5, context: html, text, full: html, text
    link GENCODE to APPRIS and HGNC
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV7.html
  • lines changed 3, context: html, text, full: html, text
    for GENCODE add description of problem biotypes and fix invalid HTML
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV9.html
  • lines changed 1, context: html, text, full: html, text
    for GENCODE add description of problem biotypes and fix invalid HTML
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.release2.ra
  • lines changed 1, context: html, text, full: html, text
    Fixed spelling error in the fileSortOrder
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.release2.ra
  • lines changed 38, context: html, text, full: html, text
    changed peaks back to normal
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.ra
  • lines changed 1, context: html, text, full: html, text
    Adding in the geoAccession column
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProtGenc.html
  • lines changed 35, context: html, text, full: html, text
    Adding in the description of the views and changing the score filters at Katrina s request
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProtGenc.ra
  • lines changed 4, context: html, text, full: html, text
    Adding in the description of the views and changing the score filters at Katrina s request
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding Mm10 Patch1 browser
• src/hg/makeDb/trackDb/marmoset/calJac1/description.html
  • lines changed 1, context: html, text, full: html, text
    Updated links on the marmoset gateway pages
• src/hg/makeDb/trackDb/marmoset/calJac3/description.html
  • lines changed 1, context: html, text, full: html, text
    Updated links on the marmoset gateway pages
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Removed lift from mm9 flag from mm10's ensGene track.
• src/hg/makeDb/trackDb/mouse/mm10Patch1/description.html
  • lines changed 63, context: html, text, full: html, text
    adding Mm10 Patch1 browser
• src/hg/makeDb/trackDb/mouse/mm10Patch1/gap.html
  • lines changed 29, context: html, text, full: html, text
    adding Mm10 Patch1 browser
• src/hg/makeDb/trackDb/mouse/mm10Patch1/gold.html
  • lines changed 34, context: html, text, full: html, text
    adding Mm10 Patch1 browser
• src/hg/makeDb/trackDb/mouse/mm10Patch1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    adding Mm10 Patch1 browser
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 9, context: html, text, full: html, text
    added accessions for raw data in mm9 Caltech RNA. Somehow these werent in there
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 61, context: html, text, full: html, text
    added accessions for the spikeins in mm9 CSHL, since they are renamed at GEO they hadnt matched correctly
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
  • lines changed 6, context: html, text, full: html, text
    added accessions for LicrHistone and LicrTfbs
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
  • lines changed 15, context: html, text, full: html, text
    added accessions for LicrHistone and LicrTfbs
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuDnase.ra
  • lines changed 14, context: html, text, full: html, text
    added GEO accessions for BroadHistone and PsuDnase
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
  • lines changed 5, context: html, text, full: html, text
    added accessions for the last few files in exp 2351 of PsuTfbs
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHist.ra
  • lines changed 55, context: html, text, full: html, text
    added geo accessions for SydhTfbs (hg19 & mm9), SydhHist, and mm9 UwDgf. Also added fixed md5sums from double compression md5 fix for hg19 UwDgf
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 151, context: html, text, full: html, text
    added geo accessions for SydhTfbs (hg19 & mm9), SydhHist, and mm9 UwDgf. Also added fixed md5sums from double compression md5 fix for hg19 UwDgf
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 117, context: html, text, full: html, text
    added geo accessions for SydhTfbs (hg19 & mm9), SydhHist, and mm9 UwDgf. Also added fixed md5sums from double compression md5 fix for hg19 UwDgf
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 141, context: html, text, full: html, text
    took treatment=none out
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeCaltechRnaSeq.ra
  • lines changed 9, context: html, text, full: html, text
    releasing metadata changes, mostly the addition of GEO accessions
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeCshlLongRnaSeq.ra
  • lines changed 61, context: html, text, full: html, text
    releasing metadata changes, mostly the addition of GEO accessions
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeLicrRnaSeq.ra
  • lines changed 2, context: html, text, full: html, text
    staging metadata changes with Cricket, mostly addition GEO accessions
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodePsuDnase.ra
  • lines changed 14, context: html, text, full: html, text
    Adding Geo numbers for hg19 BroadHistone and mm9 PsuDnase for RM#9065
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodePsuTfbs.ra
  • lines changed 56, context: html, text, full: html, text
    Adding GEO numbers to hg19 BuOrchid GisRnaPet and mm9 PsuTfbs for RM#9065
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeSydhHist.ra
  • lines changed 2, context: html, text, full: html, text
    Adding Geo numbers for hg19 OpenChromSynth and mm9 SydhHist for RM#9065
  • lines changed 55, context: html, text, full: html, text
    staging metadata changes with Cricket, mostly addition GEO accessions
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeSydhTfbs.ra
  • lines changed 151, context: html, text, full: html, text
    releasing metadata changes, mostly the addition of GEO accessions
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeUwDgf.ra
  • lines changed 117, context: html, text, full: html, text
    staging metadata changes with Cricket, mostly addition GEO accessions
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeUwDnase.ra
  • lines changed 141, context: html, text, full: html, text
    Matt made some changes to the metadata (redmine #4468)
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeUwRnaSeq.ra
  • lines changed 174, context: html, text, full: html, text
    staging metadata changes with Cricket, mostly addition GEO accessions
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeCaltechRnaSeq.ra
  • lines changed 9, context: html, text, full: html, text
    releasing metadata changes, mostly the addition of GEO accessions
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeCshlLongRnaSeq.ra
  • lines changed 61, context: html, text, full: html, text
    releasing metadata changes, mostly the addition of GEO accessions
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeLicrRnaSeq.ra
  • lines changed 2, context: html, text, full: html, text
    staging metadata changes with Cricket, mostly addition GEO accessions
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodePsuDnase.ra
  • lines changed 14, context: html, text, full: html, text
    Adding Geo numbers for hg19 BroadHistone and mm9 PsuDnase for RM#9065
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodePsuTfbs.ra
  • lines changed 56, context: html, text, full: html, text
    Adding GEO numbers to hg19 BuOrchid GisRnaPet and mm9 PsuTfbs for RM#9065
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeSydhHist.ra
  • lines changed 2, context: html, text, full: html, text
    Adding Geo numbers for hg19 OpenChromSynth and mm9 SydhHist for RM#9065
  • lines changed 55, context: html, text, full: html, text
    staging metadata changes with Cricket, mostly addition GEO accessions
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeSydhTfbs.ra
  • lines changed 151, context: html, text, full: html, text
    releasing metadata changes, mostly the addition of GEO accessions
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeUwDgf.ra
  • lines changed 117, context: html, text, full: html, text
    staging metadata changes with Cricket, mostly addition GEO accessions
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeUwRnaSeq.ra
  • lines changed 174, context: html, text, full: html, text
    staging metadata changes with Cricket, mostly addition GEO accessions
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    Staging UW DNaseI HS (Release 2) on beta (redmine #4468)
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechRnaSeq.release1.ra
  • lines changed 1, context: html, text, full: html, text
    Adding the GEO Accession column
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuDnase.ra
  • lines changed 1, context: html, text, full: html, text
    Adding the GEO Accession column
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHist.release2.ra
  • lines changed 1, context: html, text, full: html, text
    Adding in the geoAccession column
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.release2.html
  • lines changed 95, context: html, text, full: html, text
    Made corrections and cleaned up html (redmine #4468)
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.release2.ra
  • lines changed 3, context: html, text, full: html, text
    fixed some labels
  • lines changed 340, context: html, text, full: html, text
    qa label fixes
  • lines changed 13, context: html, text, full: html, text
    changed priority
  • lines changed 9, context: html, text, full: html, text
    more label fixes
  • lines changed 0, context: html, text, full: html, text
    even more labels
  • lines changed 270, context: html, text, full: html, text
    short label bonanza
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwRnaSeq.ra
  • lines changed 1, context: html, text, full: html, text
    Adding column for GEO accessions
• src/hg/makeDb/trackDb/orangutan/ponAbe2/description.html
  • lines changed 1, context: html, text, full: html, text
    Updated link on description page
• src/hg/makeDb/trackDb/rat/rn5/description.html
  • lines changed 2, context: html, text, full: html, text
    Changed link to NCBI to go to assembly/382928 (363128 stopped working).
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    move Pfam in UCSC genes track to top level (#8968)
• src/hg/utils/automation/grcIncidentDb.pl
  • lines changed 1, context: html, text, full: html, text
    adding mm10 GRCm38 to the daily update
• src/hg/utils/automation/grcIncidentUpdate.sh
  • lines changed 13, context: html, text, full: html, text
    adding mm10 GRCm38 to the daily update
• src/hg/utils/automation/grcRunIncidentUpdate.sh
  • lines changed 4, context: html, text, full: html, text
    adding mm10 GRCm38 to the daily update
• src/hg/utils/decipher/buildDecipher
  • lines changed 34, context: html, text, full: html, text
    move decipher directory to be level with omim directory. (#8840)
• src/hg/utils/decipher/checkDecipher.sh
  • lines changed 93, context: html, text, full: html, text
    move decipher directory to be level with omim directory. (#8840)
• src/hg/utils/decipher/decipherWrapper.sh
  • lines changed 8, context: html, text, full: html, text
    move decipher directory to be level with omim directory. (#8840)
• src/inc/genoFind.h
  • lines changed 1, context: html, text, full: html, text
    added repMatch default values for tileSizes 16 to 18; also fixed and incremented version to 35x1
• src/jkOwnLib/genoFind.c
  • lines changed 7, context: html, text, full: html, text
    added repMatch default values for tileSizes 16 to 18; also fixed and incremented version to 35x1
• src/lib/net.c
  • lines changed 105, context: html, text, full: html, text
    code cleanup suggested by Angie
  • lines changed 1, context: html, text, full: html, text
    Fix for strict compiler warning: warn() needs a proper format string, not char * variable.
• src/utils/decipher/buildDecipher
  • lines changed 2, context: html, text, full: html, text
    checking in the scripts that Fan was actually using to update decipher (#8840)
  • lines changed 5, context: html, text, full: html, text
    got it working in /hive/data/outside/otto/decipher (#8840)
  • lines changed 34, context: html, text, full: html, text
    move decipher directory to be level with omim directory. (#8840)
• src/utils/decipher/checkDecipher.sh
  • lines changed 2, context: html, text, full: html, text
    checking in the scripts that Fan was actually using to update decipher (#8840)
  • lines changed 16, context: html, text, full: html, text
    got it working in /hive/data/outside/otto/decipher (#8840)
  • lines changed 93, context: html, text, full: html, text
    move decipher directory to be level with omim directory. (#8840)
• src/utils/decipher/decipherWrapper.sh
  • lines changed 8, context: html, text, full: html, text
    got it working in /hive/data/outside/otto/decipher (#8840)
  • lines changed 8, context: html, text, full: html, text
    move decipher directory to be level with omim directory. (#8840)
• src/utils/qa/qaGbTracks
  • lines changed 17, context: html, text, full: html, text
    Changed qaGbTracks so that it prints statistics about chromosome item counts to log file rather than the count of every chrom to a separate chrom file. See redmine #9075.

• lines changed: 16488
• files changed: 176