All File Changes

v244_preview2 to v244_base (2010-11-30 to 2010-12-07) v244

• src/hg/encode/DAFs/2.0/haibCnv.daf
  • lines changed 13, context: html, text, full: html, text
    commented out the trouble line and added longLabelswq
• src/hg/encode/DAFs/2.0/haibMethyl27.daf
  • lines changed 46, context: html, text, full: html, text
    This was changed to MethylBead
• src/hg/encode/DAFs/2.0/haibMethylBead.daf
  • lines changed 43, context: html, text, full: html, text
    This is trying to accommodate the Methyl450 data
• src/hg/encode/DAFs/2.0/stanfordMm9Hist.daf
  • lines changed 1, context: html, text, full: html, text
    Updated input typo in DAF to control
• src/hg/encode/DAFs/2.0/sunyRnaSeq.daf
  • lines changed 19, context: html, text, full: html, text
    yes to replicates, added ripTgtProtein back
• src/hg/encode/DAFs/2.0/sunySwitchgear.daf
  • lines changed 15, context: html, text, full: html, text
    changed to have ripTargetProtein again
• src/hg/encode/docId/docIdMetaShow/docIdMetaShow.c
  • lines changed 69, context: html, text, full: html, text
    resolve issues 1-4 in #1486
  • lines changed 261, context: html, text, full: html, text
    moved this to docIdView
• src/hg/encode/docId/docIdMetaShow/makefile
  • lines changed 17, context: html, text, full: html, text
    moved this to docIdView
• src/hg/encode/docId/docIdView/docIdView.c
  • lines changed 261, context: html, text, full: html, text
    rename docIdMetaShow to docIdView
  • lines changed 12, context: html, text, full: html, text
    fixes for #1486, note #9
• src/hg/encode/docId/docIdView/makefile
  • lines changed 17, context: html, text, full: html, text
    rename docIdMetaShow to docIdView
• src/hg/encode/encodeStatus/encodeStatus.pl
  • lines changed 13, context: html, text, full: html, text
    removed old error message from the approved status
• src/hg/hgTracks/hgTracks.c
  • lines changed 2, context: html, text, full: html, text
    Changed message wording as per Katrina's request in rm #1878
  • lines changed 0, context: html, text, full: html, text
    atthe is now at the. Thanks Katrina.
• src/hg/hgTracks/imageV2.c
  • lines changed 1, context: html, text, full: html, text
    add kindOfParent to ruler trackDbJson (fixes problem where ruler wasn't getting a modal config dialog)
  • lines changed 5, context: html, text, full: html, text
    add limitedVis to trackDbJson
  • lines changed 15, context: html, text, full: html, text
    Deal with the fact that the ruler isn't in the trackHash (fixes problem where trackDbJson was empty when requesting just the ruler)
• src/hg/hgTracks/simpleTracks.c
  • lines changed 3, context: html, text, full: html, text
    Updated omimGeneBuffer[] to avoid buffer overflow.
  • lines changed 27, context: html, text, full: html, text
    Refined processing of DECIPHER track per Angie's input.
  • lines changed 17, context: html, text, full: html, text
    Adding back some code for DECIPHER drawing that should not be deleted.
• src/hg/hgc/hgc.c
  • lines changed 12, context: html, text, full: html, text
    Refine DECIPHER processing to be genomic position specific.
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 13, context: html, text, full: html, text
    added AffyRnaLoc Hg19, redmine issue #58
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 19, context: html, text, full: html, text
    added tracksearch news item, archived some items
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 11, context: html, text, full: html, text
    Added Raney et al. NAR pub.
  • lines changed 2, context: html, text, full: html, text
    Updated a pubmed link per email from nihms.
• src/hg/htdocs/images/tracksearch.gif
  • lines changed 0, context: html, text, full: html, text
    image for tracksearch news item
  • lines changed 0, context: html, text, full: html, text
    rats, checked in wrong version...correcting.
• src/hg/htdocs/indexNews.html
  • lines changed 61, context: html, text, full: html, text
    added tracksearch news item, archived some items
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v244
• src/hg/js/hgTracks.js
  • lines changed 6, context: html, text, full: html, text
    modify too many items logic to use limitedVis
• src/hg/lib/knownToLocusLink.as
  • lines changed 6, context: html, text, full: html, text
    made new .as file to show that LocusLink is showing EntrezGene IDs in show table schema
• src/hg/lib/web.c
  • lines changed 73, context: html, text, full: html, text
    trying out phoneHome function
• src/hg/makeDb/doc/danRer7.txt
  • lines changed 195, context: html, text, full: html, text
    finishing off repeat masker
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeCaltechRnaSeq.release1.notes
  • lines changed 895, context: html, text, full: html, text
    added new releasenotes for Caltech
• src/hg/makeDb/doc/equCab2.txt
  • lines changed 42, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): work in progress: while waiting fordbSNP to re-dump allele frequencies, I'm automating the dbSNP process (doDbSnp.pl) and using equCab2 as a nice simple non-human test case. (I would use a higher-prio species but their dump files are out of date...) doDbSnp.pl doesn't run all the way through but I'm checking it in on a branch to save the work done so far.
  • lines changed 12, context: html, text, full: html, text
    doDbSnp.pl now runs successfully on equCab2 snp130. It still needsmore consistency checks, more info and guidance for the developer upon completion, and to add the new columns (allele freq + N, clinical bit, list of submitter handles.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 7, context: html, text, full: html, text
    trim unwanted chip-prefix from knownToU133 to be backwards compatible with hg17 and hg18
  • lines changed 2, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): work in progress: while waiting fordbSNP to re-dump allele frequencies, I'm automating the dbSNP process (doDbSnp.pl) and using equCab2 as a nice simple non-human test case. (I would use a higher-prio species but their dump files are out of date...) doDbSnp.pl doesn't run all the way through but I'm checking it in on a branch to save the work done so far.
  • lines changed 15, context: html, text, full: html, text
    darned data (database of rna-editing) for hg19 done
  • lines changed 12, context: html, text, full: html, text
    import of lsSnp hg19 data
  • lines changed 41, context: html, text, full: html, text
    make instructions for latest Agilent tracks
• src/hg/makeDb/doc/makeEnsembl.txt
  • lines changed 316, context: html, text, full: html, text
    version 60 update completed
• src/hg/makeDb/doc/mm9.txt
  • lines changed 21, context: html, text, full: html, text
    make instructions for latest Agilent tracks
• src/hg/makeDb/doc/rn4.txt
  • lines changed 22, context: html, text, full: html, text
    make instructions for latest Agilent tracks
• src/hg/makeDb/doc/susScr2.txt
  • lines changed 7, context: html, text, full: html, text
    Updated default position on RR.
• src/hg/makeDb/schema/all.joiner
  • lines changed 2, context: html, text, full: html, text
    Added rmdr, rmdrRaw to hg18 tablesIgnored.
  • lines changed 7, context: html, text, full: html, text
    Added rdmrGene identifier.
  • lines changed 3, context: html, text, full: html, text
    added rheMac2 > refSeqAnno to all.joiner
  • lines changed 13, context: html, text, full: html, text
    import of lsSnp hg19 data
• src/hg/makeDb/trackDb/cat/felCat3/description.html
  • lines changed 2, context: html, text, full: html, text
    fixed agencourt bioscience link
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 2, context: html, text, full: html, text
    Added two new cell protocols for the Bernstein lab
  • lines changed 12, context: html, text, full: html, text
    Approved a set of provisional entries
  • lines changed 2, context: html, text, full: html, text
    The antibody XRCC4 had somehow erroneously been renamed to WHIP, which is a completely different protein. Renamed it back to XRCC4
  • lines changed 1, context: html, text, full: html, text
    Fixed a typo: removed a second Y at the end of 'Universityy'
  • lines changed 6, context: html, text, full: html, text
    Added the Proteogenomics data type
  • lines changed 108, context: html, text, full: html, text
    Added several new cell types for the Crawford lab
  • lines changed 4, context: html, text, full: html, text
    Fixed a few bugs in the new cell type stanzas
• src/hg/makeDb/trackDb/drosophila/droAna2/description.html
  • lines changed 2, context: html, text, full: html, text
    Updated link to Agencourt, as it is now part of Beckman Coulter Genomics
• src/hg/makeDb/trackDb/drosophila/droAna2/gap.html
  • lines changed 1, context: html, text, full: html, text
    Updated link to Agencourt, as it is now part of Beckman Coulter Genomics
• src/hg/makeDb/trackDb/drosophila/droAna2/gold.html
  • lines changed 1, context: html, text, full: html, text
    Updated link to Agencourt, as it is now part of Beckman Coulter Genomics
• src/hg/makeDb/trackDb/drosophila/droEre1/description.html
  • lines changed 2, context: html, text, full: html, text
    Updated link to Agencourt, as it is now part of Beckman Coulter Genomics
• src/hg/makeDb/trackDb/drosophila/droEre1/gap.html
  • lines changed 1, context: html, text, full: html, text
    Updated link to Agencourt, as it is now part of Beckman Coulter Genomics
• src/hg/makeDb/trackDb/drosophila/droGri1/description.html
  • lines changed 2, context: html, text, full: html, text
    Updated link to Agencourt, as it is now part of Beckman Coulter Genomics
• src/hg/makeDb/trackDb/drosophila/droGri1/gap.html
  • lines changed 1, context: html, text, full: html, text
    Updated link to Agencourt, as it is now part of Beckman Coulter Genomics
• src/hg/makeDb/trackDb/drosophila/droMoj1/description.html
  • lines changed 2, context: html, text, full: html, text
    Updated link to Agencourt, as it is now part of Beckman Coulter Genomics
• src/hg/makeDb/trackDb/drosophila/droMoj2/description.html
  • lines changed 2, context: html, text, full: html, text
    Updated link to Agencourt, as it is now part of Beckman Coulter Genomics
• src/hg/makeDb/trackDb/drosophila/droMoj2/gap.html
  • lines changed 1, context: html, text, full: html, text
    Updated link to Agencourt, as it is now part of Beckman Coulter Genomics
• src/hg/makeDb/trackDb/drosophila/droVir1/description.html
  • lines changed 2, context: html, text, full: html, text
    Updated link to Agencourt, as it is now part of Beckman Coulter Genomics
• src/hg/makeDb/trackDb/drosophila/droVir2/description.html
  • lines changed 2, context: html, text, full: html, text
    Updated link to Agencourt, as it is now part of Beckman Coulter Genomics
• src/hg/makeDb/trackDb/drosophila/droVir2/gap.html
  • lines changed 1, context: html, text, full: html, text
    Updated link to Agencourt, as it is now part of Beckman Coulter Genomics
• src/hg/makeDb/trackDb/human/altSeqComposite.html
  • lines changed 164, context: html, text, full: html, text
    updated to include chain net discussion
  • lines changed 29, context: html, text, full: html, text
    rearranging html and making it more readable
  • lines changed 2, context: html, text, full: html, text
    removing last references to the 2nd patch. This way we won't have to keep on changing the html every time we release a new patch
  • lines changed 2, context: html, text, full: html, text
    taking out duplication of file path to ncbi
  • lines changed 1, context: html, text, full: html, text
    fixing link so that it links to a couple directories up from where it did before. Making link less patch2 specific
• src/hg/makeDb/trackDb/human/hg18/hg18ContigDiff.html
  • lines changed 1, context: html, text, full: html, text
    minor edits as requested in code review: http://redmine.soe.ucsc.edu/issues/1914
• src/hg/makeDb/trackDb/human/hg18/rdmr.html
  • lines changed 28, context: html, text, full: html, text
    Corrected grammar, reordered ref list, cleaned up html
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    change Neanderthal => Neandertal to be consistent with spelling in other tracks
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 3, context: html, text, full: html, text
    changed the Tier2 status of NHEK and H1-hESC where it is hard coded
• src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMap.ra
  • lines changed 1, context: html, text, full: html, text
    changed the Tier2 status of NHEK and H1-hESC where it is hard coded
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.new.ra
  • lines changed 18, context: html, text, full: html, text
    changed the Tier2 status of NHEK and H1-hESC where it is hard coded
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.ra
  • lines changed 4, context: html, text, full: html, text
    changed the Tier2 status of NHEK and H1-hESC where it is hard coded
• src/hg/makeDb/trackDb/human/hg19/ctgPos2.html
  • lines changed 1, context: html, text, full: html, text
    minor edits as requested in code review: http://redmine.soe.ucsc.edu/issues/1914
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 8825, context: html, text, full: html, text
    changed the subId on the resubmitted fastqs
  • lines changed 8825, context: html, text, full: html, text
    Revert "changed the subId on the resubmitted fastqs"I saved the wrong file This reverts commit 4d2ac33b15736e1f3db68e378bba797cecebabe7.
  • lines changed 47, context: html, text, full: html, text
    changing subId for fastq resubmissions
  • lines changed 53, context: html, text, full: html, text
    changed subId and date for resubmitted MCF-7
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 37, context: html, text, full: html, text
    fixed 025CH+, 025NL+, 025NP+, 026CH+, 026NL+, 026NP+ to not have +
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 39, context: html, text, full: html, text
    Changed name of one fastq
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
  • lines changed 135, context: html, text, full: html, text
    Added origAssembly metaData
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylSeq.ra
  • lines changed 577, context: html, text, full: html, text
    Revoked submission 1875 to fix meta-data problems.
  • lines changed 561, context: html, text, full: html, text
    Added fixed 1875 submission
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 5, context: html, text, full: html, text
    Removed errant origAssembly for HepG2 BHLHE40 experiment
  • lines changed 5, context: html, text, full: html, text
    Removed errant origAssembly for GM12878 SIX5 experiment
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 205, context: html, text, full: html, text
    Removed LHSR cell line data from the Open Chrom Faire and Dnase Seq composites.
  • lines changed 75, context: html, text, full: html, text
    Revoked all LHSR submissions
  • lines changed 667, context: html, text, full: html, text
    Re-loaded missing meta-data
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
  • lines changed 98, context: html, text, full: html, text
    Removed LHSR cell line data from the Open Chrom Faire and Dnase Seq composites.
  • lines changed 103, context: html, text, full: html, text
    Removed submission 1610 which is also LHSR cell line that was forgotten.
  • lines changed 75, context: html, text, full: html, text
    Revoked all LHSR submissions
  • lines changed 257, context: html, text, full: html, text
    Re-loaded missing meta-data
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    staging wgEncodeHaibMethylRrbs on beta: removed release alpha lines (no release lines needed b/c this is 1st release) & staging metaDb on beta
  • lines changed 1, context: html, text, full: html, text
    staging caltechRnaSeq hg19 on hgwbeta, redmine #35
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeCaltechRnaSeq.ra
  • lines changed 9039, context: html, text, full: html, text
    staging caltechRnaSeq hg19 on hgwbeta, redmine #35
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeHaibMethylRrbs.ra
  • lines changed 2547, context: html, text, full: html, text
    staging wgEncodeHaibMethylRrbs on beta: removed release alpha lines (no release lines needed b/c this is 1st release) & staging metaDb on beta
  • lines changed 135, context: html, text, full: html, text
    Venkat added origAssembly to these data; I am pushing to beta
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    preparing AffyRnaLoc Hg19 for release, redmine issue #58
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeAffyRnaChip.ra
  • lines changed 1977, context: html, text, full: html, text
    preparing AffyRnaLoc Hg19 for release, redmine issue #58
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 12, context: html, text, full: html, text
    variables for alt sequence html page
  • lines changed 3, context: html, text, full: html, text
    Brain Histone track from UMassMed
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    added the SunySwitchgear .ra and .html for new track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAffyRnaChip.html
  • lines changed 12, context: html, text, full: html, text
    removed old signal tracks and removed pk from short labels
  • lines changed 12, context: html, text, full: html, text
    removed references to mutliple views in the html file and the views column in the ra file
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAffyRnaChip.ra
  • lines changed 286, context: html, text, full: html, text
    addressing note #30 from Track #58
  • lines changed 552, context: html, text, full: html, text
    removed old signal tracks and removed pk from short labels
  • lines changed 7, context: html, text, full: html, text
    extending shortLabels to have full cell names
  • lines changed 1, context: html, text, full: html, text
    removed references to mutliple views in the html file and the views column in the ra file
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.html
  • lines changed 81, context: html, text, full: html, text
    Georgis track description
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.ra
  • lines changed 26, context: html, text, full: html, text
    fixed the errant Paired view
  • lines changed 120, context: html, text, full: html, text
    short labels and long labels were too long, fixed
  • lines changed 148, context: html, text, full: html, text
    removed release alpha lines since it a first release, staging on hgwbeta, remine issue # 35
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencode.html
  • lines changed 1, context: html, text, full: html, text
    Corrected department name and link for Yale Uni link
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.html
  • lines changed 79, context: html, text, full: html, text
    from Jim. Needs to be converted to HTML
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.html
  • lines changed 5, context: html, text, full: html, text
    minor edits to html page: added mu, removed spaces, standardized the references
  • lines changed 4, context: html, text, full: html, text
    noticed another 'et al' was not in italics: changed it using the CSS and changed the other 'et al' I added to use CSS, too
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.ra
  • lines changed 119, context: html, text, full: html, text
    staging wgEncodeHaibMethylRrbs on beta: removed release alpha lines (no release lines needed b/c this is 1st release) & staging metaDb on beta
  • lines changed 1, context: html, text, full: html, text
    Fixed Tier 1 and Tier 2 labels from italic to parenthasis
  • lines changed 1, context: html, text, full: html, text
    Updated track configuration page to display treatment in sortable column
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylSeq.html
  • lines changed 16, context: html, text, full: html, text
    Fixed the email dispaly in track description to follow encrypted conventions.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylSeq.ra
  • lines changed 110, context: html, text, full: html, text
    Revoked submission 1875 to fix meta-data problems.
  • lines changed 112, context: html, text, full: html, text
    Added fixed 1875 submission
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
  • lines changed 422, context: html, text, full: html, text
    Made the HAIB longLabels uniform because the were irritating me.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.ra
  • lines changed 845, context: html, text, full: html, text
    Removed LHSR cell line data from the Open Chrom Faire and Dnase Seq composites.
  • lines changed 791, context: html, text, full: html, text
    Fixed removal of LHSR cell line data from the Open Chrome Dnase Seq composites.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.ra
  • lines changed 29, context: html, text, full: html, text
    Removed LHSR cell line data from the Open Chrom Faire and Dnase Seq composites.
  • lines changed 28, context: html, text, full: html, text
    Removed submission 1610 which is also LHSR cell line that was forgotten.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunySwitchgear.html
  • lines changed 155, context: html, text, full: html, text
    added the SunySwitchgear .ra and .html for new track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunySwitchgear.ra
  • lines changed 30, context: html, text, full: html, text
    added the SunySwitchgear .ra and .html for new track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.html
  • lines changed 1, context: html, text, full: html, text
    changed wording regarding mapper in methods section
  • lines changed 3, context: html, text, full: html, text
    Add cautionary note
• src/hg/makeDb/trackDb/human/numtSeq.html
  • lines changed 46, context: html, text, full: html, text
    Made some corections based on code review feedback. A couple grammar changes. Added a link in references. hard wrapped lines to 120 char.
  • lines changed 54, context: html, text, full: html, text
    Changed to 100 char with
• src/hg/makeDb/trackDb/human/trackDb.denisova.ra
  • lines changed 71, context: html, text, full: html, text
    adding Denisova bam tracks
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 55, context: html, text, full: html, text
    back out changes for Yale Brain.
  • lines changed 3, context: html, text, full: html, text
    adding Denisova bam tracks
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding danRer7 to alpha build
  • lines changed 13, context: html, text, full: html, text
    use ${CGI-BIN} instead of /usr/local/apache/cgi-bin
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
  • lines changed 401, context: html, text, full: html, text
    Added 3 Mouse Submissions
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 143, context: html, text, full: html, text
    Revoked submission 1353
  • lines changed 19, context: html, text, full: html, text
    Update CH12 and MEL meta-data for sex, age and strain.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 25, context: html, text, full: html, text
    Updated meta-data and subgroup information for the p300, CTCF and GATA-1 targets to be mapped to the correct antibodies that are registered in cv.ra.
  • lines changed 31, context: html, text, full: html, text
    Updated meta-data and file and table names to change Input from Std to Igg-rab
  • lines changed 31, context: html, text, full: html, text
    Updated meta-data, file and table names for Mel Rad21 and no treament experiments to updated control=std to control=IgG-rab
  • lines changed 29, context: html, text, full: html, text
    Updated meta-data, file and table names for Mel p300_n-15 to change the control from IgG-mus to IgG-rab
  • lines changed 59, context: html, text, full: html, text
    Update meta-data, file and table names for MEL c-Myb and Max experiments to replace the control Std and IgG-mus, respectivley, to IgG-rab
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    Updated meta-data, file and table names to change Input Standard DMSO treated experiments to Input IgG-Yale DMSO treated experiments.
  • lines changed 4, context: html, text, full: html, text
    Updated spelling error in controlId from Input to DMSO_2.0pct
  • lines changed 29, context: html, text, full: html, text
    Updated meta-data, file and tables names for MEL CTCF DMSO treated cell to used IgGYale control instead of Std
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    Updated meta-data, file and tables names for MEL Rad21 DMSO treated cell to used IgG-rab control instead of Std
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    Update CH12 and MEL meta-data for sex, age and strain.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.ra
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    Added 3 Mouse Submissions
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHist.html
  • lines changed 150, context: html, text, full: html, text
    Fixed the name of Description page to map to track name rather than file name
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    Fixed link in description page to reference the correct growth protocols
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHistone.html
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    Fixed the name of Description page to map to track name rather than file name
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHistone.ra
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    Updated defaults for P and Q value filters
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    Fixed typo in track longLabel to include / after ENCODE and after labto follow ENCODE track style guide
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    Added filterby option with matrix for treatment.
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    Updated Input reference in longLabels
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    Updated Comments in trackDb.
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    Updated the default view of Peaks from pack to dense.
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    Revoked submission 1353
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.html
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    Updated link to Mouse Cell Growth Protocols
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.ra
  • lines changed 8, context: html, text, full: html, text
    Fixed longLabel typo's and composite structure
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    Updated Track long label according to Track Setting Style Guide
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    Updated Long labels according to ENCODE Style Guide.
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    Updated Short Labels to be unique
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    Updated Input reference in longLabels
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    Fixed typo in 1 Input in longLabel
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    Updated order of columns and alphabetical order of factors
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    Set track defaults of subtracks selected
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    Updated meta-data and subgroup information for the p300, CTCF and GATA-1 targets to be mapped to the correct antibodies that are registered in cv.ra.
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    Updated meta-data and file and table names to change Input from Std to Igg-rab
  • lines changed 4, context: html, text, full: html, text
    Updated meta-data, file and table names for Mel Rad21 and no treament experiments to updated control=std to control=IgG-rab
  • lines changed 4, context: html, text, full: html, text
    Updated meta-data, file and table names for Mel p300_n-15 to change the control from IgG-mus to IgG-rab
  • lines changed 8, context: html, text, full: html, text
    Update meta-data, file and table names for MEL c-Myb and Max experiments to replace the control Std and IgG-mus, respectivley, to IgG-rab
  • lines changed 4, context: html, text, full: html, text
    Updated meta-data, file and table names to change Input Standard DMSO treated experiments to Input IgG-Yale DMSO treated experiments.
  • lines changed 2, context: html, text, full: html, text
    Updated the label for Input IgG-Yale DMSO treatment experiment from facotor=input standard to factor=input IgGyale
  • lines changed 4, context: html, text, full: html, text
    Updated meta-data, file and tables names for MEL CTCF DMSO treated cell to used IgGYale control instead of Std
  • lines changed 4, context: html, text, full: html, text
    Updated meta-data, file and tables names for MEL Rad21 DMSO treated cell to used IgG-rab control instead of Std
• src/hg/makeDb/trackDb/rhesus/refSeqAnno.html
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    corrected some grammar
• src/hg/makeDb/trackDb/tagTypes.tab
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    allow matrix, matrixHeader, chainMinScore and chainLinearGap on psl types because of composites
• src/hg/makeDb/trackDb/zebrafish/danRer7/description.html
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    adding danRer7 to alpha build
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    finalize descriptions for gateway page and gold,gap tracks
• src/hg/makeDb/trackDb/zebrafish/danRer7/gap.html
  • lines changed 64, context: html, text, full: html, text
    adding danRer7 to alpha build
  • lines changed 44, context: html, text, full: html, text
    finalize descriptions for gateway page and gold,gap tracks
• src/hg/makeDb/trackDb/zebrafish/danRer7/gold.html
  • lines changed 23, context: html, text, full: html, text
    adding danRer7 to alpha build
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    finalize descriptions for gateway page and gold,gap tracks
• src/hg/makeDb/trackDb/zebrafish/danRer7/trackDb.ra
  • lines changed 40, context: html, text, full: html, text
    adding danRer7 to alpha build
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    adding ctgPos2
• src/hg/snp/snpLoad/snpNcbiToUcsc.c
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    For some species (e.g. horse), dbSNP has absolutely no validationinfo, so in snpNNN.sql, the valid column is a set containing only 'unknown'. In that case, we need not to include a comma after 'unknown' or mysql barfs.
• src/hg/utils/automation/doDbSnp.pl
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    Track #1684 (SNPs 132 (dbSNP)): work in progress: while waiting fordbSNP to re-dump allele frequencies, I'm automating the dbSNP process (doDbSnp.pl) and using equCab2 as a nice simple non-human test case. (I would use a higher-prio species but their dump files are out of date...) doDbSnp.pl doesn't run all the way through but I'm checking it in on a branch to save the work done so far.
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    Some small fixes to doDbSnp.pl to get it to run a bit farther.Currently dies when hgLoadSqlTab complains about mysql warnings, of which there are a zillion with dbSNP's dump files that have empty values in numeric columns.
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    doDbSnp.pl now runs successfully on equCab2 snp130. It still needsmore consistency checks, more info and guidance for the developer upon completion, and to add the new columns (allele freq + N, clinical bit, list of submitter handles.
• src/lib/genomeRangeTree.c
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    fixed memory leak
• src/product/README.mysql.setup
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    eliminate the example hg.conf to refer to ex.hg.conf instead
• src/product/scripts/updateHtml.sh
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    fix usage message about ignored directories and indicate in the log file what the rsync command is
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    did not have enough - on the exclude trash, how did it work before ?
• src/utils/decipher/buildDecipher
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    Created to check, download, and process DECIPHER data.
• src/utils/decipher/checkDecipher.sh
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    Created to check, download, and process DECIPHER data.
• src/utils/qa/weeklybld/buildEnv.csh
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    v244 preview
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    v244 final build
• src/utils/qa/weeklybld/buildGitReports.csh
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    fix a silly error with else/if bracketing
• src/utils/qa/weeklybld/doNewBranch.csh
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    changed a 9 to a 16
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    adding Kate to announcement of git reports
• src/utils/qa/weeklybld/doNewReview.csh
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    adding Kate to announcement of git reports
• src/utils/qa/weeklybld/doNewReview2.csh
  • lines changed 3, context: html, text, full: html, text
    adding Kate to announcement of git reports

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