All File Changes

v269_preview to v269_preview2 (2012-06-12 to 2012-06-19) v269

• src/hg/encode/DAFs/3.0/mm9/wgEncodeCshlLongRnaSeq.daf
  • lines changed 14, context: html, text, full: html, text
    Added 2 new views to be requried: ExonDeNovo and GeneDeNovo. Redmine #7089.
• src/hg/encode/encodeQaCheckHgdownloadFiles/encodeQaCheckHgdownloadFiles
  • lines changed 2, context: html, text, full: html, text
    updated usage
• src/hg/encode/getTrackReferences/getTrackReferences
  • lines changed 1, context: html, text, full: html, text
    fixing errors inherent in pubmed's date string
• src/hg/featureBits/makefile
  • lines changed 2, context: html, text, full: html, text
    addig featureBits to the userApps delivery
• src/hg/hgLogin/gbMembers.as
  • lines changed 17, context: html, text, full: html, text
    Move gbMembers.as and gbMembers.sql to kent/src/hg/lib from kent/src/hg/hgLogin.
• src/hg/hgLogin/gbMembers.sql
  • lines changed 29, context: html, text, full: html, text
    Move gbMembers.as and gbMembers.sql to kent/src/hg/lib from kent/src/hg/hgLogin.
• src/hg/hgLogin/hgLogin.c
  • lines changed 41, context: html, text, full: html, text
    Soft code the domain value in cookies, use central.domain or domain in returnTo URL.
  • lines changed 1, context: html, text, full: html, text
    Fixed hgLogin.c:1054: warning: function returns address of local variable.
  • lines changed 2, context: html, text, full: html, text
    Yet another warning fix.
  • lines changed 15, context: html, text, full: html, text
    Finish soft code domain name.
• src/hg/hgLogin/hgLogin.h
  • lines changed 6, context: html, text, full: html, text
    Soft code the domain value in cookies, use central.domain or domain in returnTo URL.
• src/hg/htdocs/ENCODE/qualityMetrics.html
  • lines changed 1, context: html, text, full: html, text
    Tweak display width to accomodate Revoke flag field
  • lines changed 4, context: html, text, full: html, text
    A change for clarity
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 32, context: html, text, full: html, text
    Took out a bunch of redundant <TT> tags within <PRE> tags.
  • lines changed 157, context: html, text, full: html, text
    Fixed all sorts of html errors.
  • lines changed 4, context: html, text, full: html, text
    Fix an issue where code in a pre tag was not wrapping and thus forcing the tables to be wider than the browser window.
• src/hg/htdocs/images/Latimeria_chalumnae.png
  • lines changed 0, context: html, text, full: html, text
    public domain drawing from Robbie Cada
• src/hg/htdocs/images/Oreochromis_niloticus.gif
  • lines changed 0, context: html, text, full: html, text
    public commons from Robbie Cada
• src/hg/htdocs/inc/FAQ.topbar.html
  • lines changed 3, context: html, text, full: html, text
    Fixed a couple html errors.
  • lines changed 1, context: html, text, full: html, text
    Fixed a couple html errors, MK II.
  • lines changed 1, context: html, text, full: html, text
    Oops, had to add a height back in, since it wasn't included in the class=topbar as I thought.
• src/hg/lib/gbMembers.as
  • lines changed 17, context: html, text, full: html, text
    Move gbMembers.as and gbMembers.sql to kent/src/hg/lib from kent/src/hg/hgLogin.
• src/hg/lib/gbMembers.sql
  • lines changed 28, context: html, text, full: html, text
    Move gbMembers.as and gbMembers.sql to kent/src/hg/lib from kent/src/hg/hgLogin.
• src/hg/lib/web.c
  • lines changed 2, context: html, text, full: html, text
    break up the genomewiki URL to avoid detection via google robots
• src/hg/makeDb/doc/bosTau7.txt
  • lines changed 28, context: html, text, full: html, text
    Tiuch up bosTau7's description.html.
• src/hg/makeDb/doc/encodeDccHg19/gencodeV11.txt
  • lines changed 41, context: html, text, full: html, text
    Updated CCDS import to reflect changes in the schema.
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeGencodeV11.release1.notes
  • lines changed 10, context: html, text, full: html, text
    Adding the Other files
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeGencodeV12.release1.notes
  • lines changed 82, context: html, text, full: html, text
    Adding notes file
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeGisRnaPet.release2.notes
  • lines changed 783, context: html, text, full: html, text
    First draft of notes file
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeMapability.release1.notes
  • lines changed 56, context: html, text, full: html, text
    fixing some metaData
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeSydhRnaSeq.release1.notes
  • lines changed 114, context: html, text, full: html, text
    creating the notes file
• src/hg/makeDb/doc/hg19.txt
  • lines changed 20, context: html, text, full: html, text
    Updated dgvBeta (DGV has a beta site that they plan to make public~Aug.), and added trackDb entry for testing on hgwdev w/item url
    that points to their beta server for now. We might end up using
    dbVar ID as name instead of DGV's numeric ID -- waiting for updates
    on data formats and item url that supports dbVar accession.
    
• src/hg/makeDb/doc/latCha1.txt
  • lines changed 20, context: html, text, full: html, text
    indicate photo pickup procedure
• src/hg/makeDb/doc/mm10.txt
  • lines changed 225, context: html, text, full: html, text
    add gap annotation and phyloFit tree model estimate for 60-way
  • lines changed 1036, context: html, text, full: html, text
    beginning the phastCons/phyloP runs
• src/hg/makeDb/doc/ochPri2.txt
  • lines changed 90, context: html, text, full: html, text
    done with genbank business
• src/hg/makeDb/doc/sarHar1.txt
  • lines changed 25, context: html, text, full: html, text
    Generate new format sarHar1's description.html.
• src/hg/makeDb/doc/sorAra1.txt
  • lines changed 89, context: html, text, full: html, text
    finished with genbank business
• src/hg/makeDb/doc/tupBel1.txt
  • lines changed 165, context: html, text, full: html, text
    done with genbank business
• src/hg/makeDb/doc/turTru2.txt
  • lines changed 91, context: html, text, full: html, text
    genbank business done
• src/hg/makeDb/genbank/doc/config.html
  • lines changed 9, context: html, text, full: html, text
    Modified alignment process to create fewer temporary, intermediate files:- Allow bundling more scaffolds in a single job. The previous
    implementation used an approach that some arbitrarily and unintuitively
    capped the number of scaffolds that were batched.
    - Eliminate the flag files that were created per-partation, which
    we required during migration. Instead create one file that
    lists the partations that needed to aligned or migrated.
    
• src/hg/makeDb/genbank/etc/align-genbank
  • lines changed 3, context: html, text, full: html, text
    use less error prone shell syntax
  • lines changed 1, context: html, text, full: html, text
    reduced number of parallel genbank alignments in an attempt to reduce GPFS impact
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added tupBel1.
  • lines changed 1, context: html, text, full: html, text
    Added sorAra1.
  • lines changed 1, context: html, text, full: html, text
    Added turTru2.
• src/hg/makeDb/genbank/etc/build-genbank
  • lines changed 2, context: html, text, full: html, text
    use less error prone shell syntax
• src/hg/makeDb/genbank/etc/ccds-import
  • lines changed 1, context: html, text, full: html, text
    use less error prone shell syntax
• src/hg/makeDb/genbank/etc/dbload
  • lines changed 4, context: html, text, full: html, text
    use less error prone shell syntax
• src/hg/makeDb/genbank/etc/euronode-copy
  • lines changed 2, context: html, text, full: html, text
    use less error prone shell syntax
• src/hg/makeDb/genbank/etc/euronode.crontab
  • lines changed 1, context: html, text, full: html, text
    remove explictly MAILTO to work around SOE google move
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 1, context: html, text, full: html, text
    changed ensGene to refGene since ensGene doesn't exist on canFam3
  • lines changed 3, context: html, text, full: html, text
    Modified alignment process to create fewer temporary, intermediate files:- Allow bundling more scaffolds in a single job. The previous
    implementation used an approach that some arbitrarily and unintuitively
    capped the number of scaffolds that were batched.
    - Eliminate the flag files that were created per-partation, which
    we required during migration. Instead create one file that
    lists the partations that needed to aligned or migrated.
    
• src/hg/makeDb/genbank/etc/hgdownload-copy
  • lines changed 1, context: html, text, full: html, text
    use less error prone shell syntax
• src/hg/makeDb/genbank/etc/hgnfs1-copy
  • lines changed 2, context: html, text, full: html, text
    use less error prone shell syntax
• src/hg/makeDb/genbank/etc/hgnfs1.crontab
  • lines changed 1, context: html, text, full: html, text
    remove explictly MAILTO to work around SOE google move
• src/hg/makeDb/genbank/etc/hgwbeta-dbload
  • lines changed 1, context: html, text, full: html, text
    use less error prone shell syntax
• src/hg/makeDb/genbank/etc/hgwbeta.crontab
  • lines changed 1, context: html, text, full: html, text
    remove explictly MAILTO to work around SOE google move
• src/hg/makeDb/genbank/etc/hgwdev-dbload
  • lines changed 1, context: html, text, full: html, text
    use less error prone shell syntax
• src/hg/makeDb/genbank/etc/hgwdev.crontab
  • lines changed 1, context: html, text, full: html, text
    remove explictly MAILTO to work around SOE google move
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added tupBel1.
  • lines changed 1, context: html, text, full: html, text
    Added sorAra1.
  • lines changed 1, context: html, text, full: html, text
    Added turTru2.
• src/hg/makeDb/genbank/etc/mkdownload
  • lines changed 3, context: html, text, full: html, text
    use less error prone shell syntax
• src/hg/makeDb/genbank/etc/rr-dbload
  • lines changed 1, context: html, text, full: html, text
    use less error prone shell syntax
• src/hg/makeDb/genbank/src/align/gbAlignFinish
  • lines changed 197, context: html, text, full: html, text
    Modified alignment process to create fewer temporary, intermediate files:- Allow bundling more scaffolds in a single job. The previous
    implementation used an approach that some arbitrarily and unintuitively
    capped the number of scaffolds that were batched.
    - Eliminate the flag files that were created per-partation, which
    we required during migration. Instead create one file that
    lists the partations that needed to aligned or migrated.
    
• src/hg/makeDb/genbank/src/align/gbAlignGet.c
  • lines changed 30, context: html, text, full: html, text
    Modified alignment process to create fewer temporary, intermediate files:- Allow bundling more scaffolds in a single job. The previous
    implementation used an approach that some arbitrarily and unintuitively
    capped the number of scaffolds that were batched.
    - Eliminate the flag files that were created per-partation, which
    we required during migration. Instead create one file that
    lists the partations that needed to aligned or migrated.
    
• src/hg/makeDb/genbank/src/align/gbAlignSetup
  • lines changed 73, context: html, text, full: html, text
    Modified alignment process to create fewer temporary, intermediate files:- Allow bundling more scaffolds in a single job. The previous
    implementation used an approach that some arbitrarily and unintuitively
    capped the number of scaffolds that were batched.
    - Eliminate the flag files that were created per-partation, which
    we required during migration. Instead create one file that
    lists the partations that needed to aligned or migrated.
    
• src/hg/makeDb/genbank/src/ccds/createKeys.sql
  • lines changed 2, context: html, text, full: html, text
    Updated CCDS import to reflect changes in the schema.
• src/hg/makeDb/genbank/src/ccds/createTables.sql
  • lines changed 10, context: html, text, full: html, text
    Updated CCDS import to reflect changes in the schema.
• src/hg/makeDb/genbank/src/ccds/ncbiSql/createKeys.sql
  • lines changed 37, context: html, text, full: html, text
    Updated CCDS import to reflect changes in the schema.
• src/hg/makeDb/genbank/src/ccds/ncbiSql/createTables.sql
  • lines changed 10, context: html, text, full: html, text
    Updated CCDS import to reflect changes in the schema.
• src/hg/makeDb/genbank/src/inc/gbDefs.h
  • lines changed 6, context: html, text, full: html, text
    Modified alignment process to create fewer temporary, intermediate files:- Allow bundling more scaffolds in a single job. The previous
    implementation used an approach that some arbitrarily and unintuitively
    capped the number of scaffolds that were batched.
    - Eliminate the flag files that were created per-partation, which
    we required during migration. Instead create one file that
    lists the partations that needed to aligned or migrated.
    
• src/hg/makeDb/genbank/src/lib/gbCommon.pm
  • lines changed 3, context: html, text, full: html, text
    Modified alignment process to create fewer temporary, intermediate files:- Allow bundling more scaffolds in a single job. The previous
    implementation used an approach that some arbitrarily and unintuitively
    capped the number of scaffolds that were batched.
    - Eliminate the flag files that were created per-partation, which
    we required during migration. Instead create one file that
    lists the partations that needed to aligned or migrated.
    
• src/hg/makeDb/genbank/src/lib/gbDefs.c
  • lines changed 23, context: html, text, full: html, text
    Modified alignment process to create fewer temporary, intermediate files:- Allow bundling more scaffolds in a single job. The previous
    implementation used an approach that some arbitrarily and unintuitively
    capped the number of scaffolds that were batched.
    - Eliminate the flag files that were created per-partation, which
    we required during migration. Instead create one file that
    lists the partations that needed to aligned or migrated.
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 80, context: html, text, full: html, text
    adding in Gencode V12
• src/hg/makeDb/trackDb/apis/apiMel1/description.html
  • lines changed 5, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/apis/apiMel2/description.html
  • lines changed 3, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/apis/apiMel2/gold.html
  • lines changed 4, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/apis/apiMel2/scaffolds.html
  • lines changed 1, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/cow/bosTau1/description.html
  • lines changed 3, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/cow/bosTau2/contigOrient.html
  • lines changed 1, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/cow/bosTau2/description.html
  • lines changed 3, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/cow/bosTau3/description.html
  • lines changed 4, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/cow/bosTau3/scaffold.html
  • lines changed 2, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/cow/bosTau4/description.html
  • lines changed 4, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/cow/bosTau5/description.html
  • lines changed 4, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/cow/bosTau6/description.html
  • lines changed 1, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/cow/bosTau7/description.html
  • lines changed 2, context: html, text, full: html, text
    Tiuch up bosTau7's description.html.
  • lines changed 1, context: html, text, full: html, text
    Fixed capitalization error
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 1, context: html, text, full: html, text
    Shortned term for Spleen so that table limit wouldn't be hit. Redmine #7501.
  • lines changed 5, context: html, text, full: html, text
    Fixing a couple of BioChain links in CV
  • lines changed 1, context: html, text, full: html, text
    I have no idea waht displayName is or why is was there
  • lines changed 3, context: html, text, full: html, text
    Fixed typo in age to be EO instead of E0.
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 43, context: html, text, full: html, text
    Copying alpha CV to beta
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 227, context: html, text, full: html, text
    Moved approved changes from beta/cv.ra to public/cv.ra. Redmine #8181.
• src/hg/makeDb/trackDb/dog/canFam3/description.html
  • lines changed 1, context: html, text, full: html, text
    Changed NCBI link to point to most recent assembly
  • lines changed 1, context: html, text, full: html, text
    Minor correction to NCBI link
• src/hg/makeDb/trackDb/dog/canFam3/gap.html
  • lines changed 45, context: html, text, full: html, text
    cleaned up for release
• src/hg/makeDb/trackDb/dog/canFam3/gold.html
  • lines changed 7, context: html, text, full: html, text
    cleaned up for release
• src/hg/makeDb/trackDb/drosophila/dm1/axtNetDp1.html
  • lines changed 1, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/drosophila/dm1/netDp1.html
  • lines changed 1, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/drosophila/dp2/description.html
  • lines changed 2, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/drosophila/netDp2.html
  • lines changed 1, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/gibbon/nomLeu1/description.html
  • lines changed 1, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/gibbon/nomLeu1/gap.html
  • lines changed 1, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/gibbon/nomLeu1/gold.html
  • lines changed 1, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/human/evofold.html
  • lines changed 2, context: html, text, full: html, text
    added bolding so you can find the species involved in the analysis
• src/hg/makeDb/trackDb/human/hg13/syntenyRat.html
  • lines changed 1, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/human/hg15/syntenyRat.html
  • lines changed 1, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/human/hg16/syntenyRn3.html
  • lines changed 1, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/human/hg17/ensRatMusHom.html
  • lines changed 1, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/human/hg17/syntenyRn3.html
  • lines changed 1, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeAffyRnaChip.ra
  • lines changed 110, context: html, text, full: html, text
    releasing expIds and composite objects and for BU removing errant cell line
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeBuOrchid.ra
  • lines changed 12, context: html, text, full: html, text
    releasing expIds and composite objects and for BU removing errant cell line
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeGisDnaPet.ra
  • lines changed 40, context: html, text, full: html, text
    releasing expIds and composite objects and for BU removing errant cell line
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeUwDGF.ra
  • lines changed 34, context: html, text, full: html, text
    releasing expIds and composite objects and for BU removing errant cell line
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeAffyRnaChip.ra
  • lines changed 110, context: html, text, full: html, text
    releasing expIds and composite objects and for BU removing errant cell line
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeBuOrchid.ra
  • lines changed 12, context: html, text, full: html, text
    releasing expIds and composite objects and for BU removing errant cell line
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeGisDnaPet.ra
  • lines changed 40, context: html, text, full: html, text
    releasing expIds and composite objects and for BU removing errant cell line
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeUwDGF.ra
  • lines changed 34, context: html, text, full: html, text
    releasing expIds and composite objects and for BU removing errant cell line
• src/hg/makeDb/trackDb/human/hg18/nestedRepeats.html
  • lines changed 107, context: html, text, full: html, text
    Created new files specific to hg18 and added a note that the tracks in hg18 are based upon the original RepeatMasker and Interruped Repeats tracks and not upon the newer 3.2.7 versions of those tracks (redmine #7175)
• src/hg/makeDb/trackDb/human/hg18/rmsk.html
  • lines changed 113, context: html, text, full: html, text
    Created new files specific to hg18 and added a note that the tracks in hg18 are based upon the original RepeatMasker and Interruped Repeats tracks and not upon the newer 3.2.7 versions of those tracks (redmine #7175)
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
  • lines changed 1, context: html, text, full: html, text
    adding in Gencode V12
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHmm.ra
  • lines changed 11, context: html, text, full: html, text
    added GEO accessions to metadata for new hg19 submissions
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 13, context: html, text, full: html, text
    Changing the date format
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV12.ra
  • lines changed 278, context: html, text, full: html, text
    adding in Gencode V12
  • lines changed 18, context: html, text, full: html, text
    Adding md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
  • lines changed 631, context: html, text, full: html, text
    Adding missing data, long and short labels, removing commented out tracks, sorting out V2's, changing to filter composites
  • lines changed 24, context: html, text, full: html, text
    Trying to work out the issue with GM12878 Cytosol. See ticket 5942
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyRipSeq.ra
  • lines changed 39, context: html, text, full: html, text
    added GEO accessions to metadata for new hg19 submissions
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 26, context: html, text, full: html, text
    added GEO accessions to metadata for new hg19 submissions
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 1486, context: html, text, full: html, text
    added GEO accessions to metadata for new hg19 submissions
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 934, context: html, text, full: html, text
    added GEO accessions to metadata for new hg19 submissions
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    Staging GENCODE V12 (Release 1) on beta, redmine# 8137
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeAffyRnaChip.ra
  • lines changed 53, context: html, text, full: html, text
    pushing md5sums, geo accessions, bai file names and removing rip target proteinand for RIKEN, correcting signals from Raw Signals to Signals
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeBroadHmm.ra
  • lines changed 11, context: html, text, full: html, text
    pushing md5sums, geo accessions, bai file names and removing rip target proteinand for RIKEN, correcting signals from Raw Signals to Signals
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeBuOrchid.ra
  • lines changed 2, context: html, text, full: html, text
    pushing md5sums, geo accessions, bai file names and removing rip target proteinand for RIKEN, correcting signals from Raw Signals to Signals
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeGencodeV12.ra
  • lines changed 295, context: html, text, full: html, text
    Staging GENCODE V12 (Release 1) on beta, redmine# 8137
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeGencodeV4.ra
  • lines changed 122, context: html, text, full: html, text
    pushing md5sums, geo accessions, bai file names and removing rip target proteinand for RIKEN, correcting signals from Raw Signals to Signals
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeGencodeV7.ra
  • lines changed 16, context: html, text, full: html, text
    pushing md5sums, geo accessions, bai file names and removing rip target proteinand for RIKEN, correcting signals from Raw Signals to Signals
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeGisDnaPet.ra
  • lines changed 41, context: html, text, full: html, text
    pushing md5sums, geo accessions, bai file names and removing rip target proteinand for RIKEN, correcting signals from Raw Signals to Signals
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeGisRnaSeq.ra
  • lines changed 23, context: html, text, full: html, text
    pushing md5sums, geo accessions, bai file names and removing rip target proteinand for RIKEN, correcting signals from Raw Signals to Signals
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeRikenCage.ra
  • lines changed 369, context: html, text, full: html, text
    pushing md5sums, geo accessions, bai file names and removing rip target proteinand for RIKEN, correcting signals from Raw Signals to Signals
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSunyAlbanyTiling.ra
  • lines changed 17, context: html, text, full: html, text
    pushing md5sums, geo accessions, bai file names and removing rip target proteinand for RIKEN, correcting signals from Raw Signals to Signals
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSunyRipSeq.ra
  • lines changed 72, context: html, text, full: html, text
    pushing md5sums, geo accessions, bai file names and removing rip target proteinand for RIKEN, correcting signals from Raw Signals to Signals
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSunySwitchgear.ra
  • lines changed 3, context: html, text, full: html, text
    pushing md5sums, geo accessions, bai file names and removing rip target proteinand for RIKEN, correcting signals from Raw Signals to Signals
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSydhHistone.ra
  • lines changed 26, context: html, text, full: html, text
    Adding updated metaDb to hgwbeta so everything is updated for this final release of SYDH Histone (Release 3), redmine# 7510
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSydhNsome.ra
  • lines changed 44, context: html, text, full: html, text
    pushing md5sums, geo accessions, bai file names and removing rip target proteinand for RIKEN, correcting signals from Raw Signals to Signals
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSydhRnaSeq.ra
  • lines changed 18, context: html, text, full: html, text
    pushing md5sums, geo accessions, bai file names and removing rip target proteinand for RIKEN, correcting signals from Raw Signals to Signals
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwRepliSeq.ra
  • lines changed 257, context: html, text, full: html, text
    pushing md5sums, geo accessions, bai file names and removing rip target proteinand for RIKEN, correcting signals from Raw Signals to Signals
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeAffyRnaChip.ra
  • lines changed 53, context: html, text, full: html, text
    pushing md5sums, geo accessions, bai file names and removing rip target proteinand for RIKEN, correcting signals from Raw Signals to Signals
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeBroadHmm.ra
  • lines changed 11, context: html, text, full: html, text
    pushing md5sums, geo accessions, bai file names and removing rip target proteinand for RIKEN, correcting signals from Raw Signals to Signals
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeBuOrchid.ra
  • lines changed 2, context: html, text, full: html, text
    pushing md5sums, geo accessions, bai file names and removing rip target proteinand for RIKEN, correcting signals from Raw Signals to Signals
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeGencodeV4.ra
  • lines changed 122, context: html, text, full: html, text
    pushing md5sums, geo accessions, bai file names and removing rip target proteinand for RIKEN, correcting signals from Raw Signals to Signals
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeGencodeV7.ra
  • lines changed 16, context: html, text, full: html, text
    pushing md5sums, geo accessions, bai file names and removing rip target proteinand for RIKEN, correcting signals from Raw Signals to Signals
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeGisDnaPet.ra
  • lines changed 41, context: html, text, full: html, text
    pushing md5sums, geo accessions, bai file names and removing rip target proteinand for RIKEN, correcting signals from Raw Signals to Signals
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeGisRnaSeq.ra
  • lines changed 23, context: html, text, full: html, text
    pushing md5sums, geo accessions, bai file names and removing rip target proteinand for RIKEN, correcting signals from Raw Signals to Signals
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeRikenCage.ra
  • lines changed 369, context: html, text, full: html, text
    pushing md5sums, geo accessions, bai file names and removing rip target proteinand for RIKEN, correcting signals from Raw Signals to Signals
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeSunyAlbanyTiling.ra
  • lines changed 17, context: html, text, full: html, text
    pushing md5sums, geo accessions, bai file names and removing rip target proteinand for RIKEN, correcting signals from Raw Signals to Signals
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeSunyRipSeq.ra
  • lines changed 72, context: html, text, full: html, text
    pushing md5sums, geo accessions, bai file names and removing rip target proteinand for RIKEN, correcting signals from Raw Signals to Signals
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeSunySwitchgear.ra
  • lines changed 3, context: html, text, full: html, text
    pushing md5sums, geo accessions, bai file names and removing rip target proteinand for RIKEN, correcting signals from Raw Signals to Signals
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeSydhHistone.ra
  • lines changed 1264, context: html, text, full: html, text
    Release SYDH Histone (Release 3) to the RR, remine# 7510
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeSydhNsome.ra
  • lines changed 44, context: html, text, full: html, text
    pushing md5sums, geo accessions, bai file names and removing rip target proteinand for RIKEN, correcting signals from Raw Signals to Signals
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeSydhRnaSeq.ra
  • lines changed 18, context: html, text, full: html, text
    pushing md5sums, geo accessions, bai file names and removing rip target proteinand for RIKEN, correcting signals from Raw Signals to Signals
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwDnase.ra
  • lines changed 3926, context: html, text, full: html, text
    preparing to release UW DNaseI HS (Release 5) Redmine# 6807
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwRepliSeq.ra
  • lines changed 257, context: html, text, full: html, text
    pushing md5sums, geo accessions, bai file names and removing rip target proteinand for RIKEN, correcting signals from Raw Signals to Signals
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 12, context: html, text, full: html, text
    Updated Cow and Mouse entries so bosTau7 and mm10 would replace bosTau6 and mm9, respectively, in the Placental Chain/Net composite track
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    preparing to release UW DNaseI HS (Release 5) Redmine# 6807
  • lines changed 7, context: html, text, full: html, text
    Cleaning up the release2 for MarkD
  • lines changed 2, context: html, text, full: html, text
    Release SYDH Histone (Release 3) to the RR, remine# 7510
  • lines changed 1, context: html, text, full: html, text
    Staging GENCODE V12 (Release 1) on beta, redmine# 8137
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release3.ra
  • lines changed 514, context: html, text, full: html, text
    Long labels
  • lines changed 2, context: html, text, full: html, text
    Lost two lines, restoring them
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
  • lines changed 3, context: html, text, full: html, text
    Updating to explain the most recent release
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV10.ra
  • lines changed 1, context: html, text, full: html, text
    Cleaning up the release2 for MarkD
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV10.release2.ra
  • lines changed 224, context: html, text, full: html, text
    Cleaning up the release2 for MarkD
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV11.ra
  • lines changed 19, context: html, text, full: html, text
    Cleaning up the release2 for MarkD
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV11.release2.ra
  • lines changed 224, context: html, text, full: html, text
    Cleaning up the release2 for MarkD
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV12.html
  • lines changed 7, context: html, text, full: html, text
    added not on Ensembl convergence with GENCODE
  • lines changed 2, context: html, text, full: html, text
    changed the month to the current month and fixed some typos for GENCODE V12, redmine# 8137
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV7.ra
  • lines changed 7, context: html, text, full: html, text
    Cleaning up the release2 for MarkD
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV7.release2.ra
  • lines changed 189, context: html, text, full: html, text
    Cleaning up the release2 for MarkD
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.release2.ra
  • lines changed 2565, context: html, text, full: html, text
    Adding missing data, long and short labels, removing commented out tracks, sorting out V2's, changing to filter composites
  • lines changed 119, context: html, text, full: html, text
    Trying to work out the issue with GM12878 Cytosol. See ticket 5942
  • lines changed 38, context: html, text, full: html, text
    Trying to work out the bedRnaElements
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.release3.html
  • lines changed 2, context: html, text, full: html, text
    added a comma and changed the release date for SYDH Histone (Release 3), redmine# 7510
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release5.html
  • lines changed 1, context: html, text, full: html, text
    Removing Release Notes specifying DEV ONLY, RedMine# 6807
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 15, context: html, text, full: html, text
    Updated dgvBeta (DGV has a beta site that they plan to make public~Aug.), and added trackDb entry for testing on hgwdev w/item url
    that points to their beta server for now. We might end up using
    dbVar ID as name instead of DGV's numeric ID -- waiting for updates
    on data formats and item url that supports dbVar accession.
    
• src/hg/makeDb/trackDb/latCha/latCha1/description.html
  • lines changed 116, context: html, text, full: html, text
    minimalist page from makeGenomeDb.pl
  • lines changed 1, context: html, text, full: html, text
    it is a png, not a jpg
• src/hg/makeDb/trackDb/marmoset/calJac1/description.html
  • lines changed 1, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/marmoset/calJac3/description.html
  • lines changed 1, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/mouse/mm4/syntenyRn3.html
  • lines changed 1, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/mouse/mm9/mapability.ra
  • lines changed 50, context: html, text, full: html, text
    Pulling mapability into a file so that you can track the alpha,beta,public progress
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/makefile
  • lines changed 1, context: html, text, full: html, text
    adding in mapability metadata
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeFsuRepliChip.ra
  • lines changed 430, context: html, text, full: html, text
    Added last submissions for the track. Redmine #6627.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeHistone.ra
  • lines changed 20477, context: html, text, full: html, text
    update re-submission of spleen datasets whose previous length exceeded length limit
  • lines changed 20477, context: html, text, full: html, text
    this file was accidently created in June 12, just need to delete it
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
  • lines changed 109, context: html, text, full: html, text
    redo update of the resubmission of the two spleen datasets whose length in previous submission exceeded the length limit, it seems that after make, the updates in this file disappearred, but I might be wrong, so I am redoing this
  • lines changed 747, context: html, text, full: html, text
    update with new submission and resubmission of some datasets of previous releases
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
  • lines changed 936, context: html, text, full: html, text
    update with new submissions and resubmission of some datasets of previous release
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeMapability.ra
  • lines changed 96, context: html, text, full: html, text
    adding in mapability metadata
  • lines changed 21, context: html, text, full: html, text
    fixing some metaData
  • lines changed 16, context: html, text, full: html, text
    fixed metadata and dates
  • lines changed 11, context: html, text, full: html, text
    changing datatype to mouse mapability
  • lines changed 21, context: html, text, full: html, text
    Adding accesions and putting uniqueness as a labVersion
  • lines changed 11, context: html, text, full: html, text
    adding in mapability expIDs and accessions
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHist.ra
  • lines changed 293, context: html, text, full: html, text
    update 2 new submissions
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    Staging mouse mm9 Mapability (Final/Release1) on beta (Redmine# 3649)
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeCaltechHist.ra
  • lines changed 47, context: html, text, full: html, text
    releasing geo accessions and rnaExtract for CaltechRnaSeq
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeCaltechRnaSeq.ra
  • lines changed 70, context: html, text, full: html, text
    releasing geo accessions and rnaExtract for CaltechRnaSeq
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeCaltechTfbs.ra
  • lines changed 93, context: html, text, full: html, text
    releasing geo accessions and rnaExtract for CaltechRnaSeq
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeLicrRnaSeq.ra
  • lines changed 89, context: html, text, full: html, text
    releasing geo accessions and rnaExtract for CaltechRnaSeq
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeSydhTfbs.ra
  • lines changed 3586, context: html, text, full: html, text
    Staging Stanford/Yale TFBS (Release 3) on beta (Redmine# 5397)
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeCaltechHist.ra
  • lines changed 47, context: html, text, full: html, text
    releasing geo accessions and rnaExtract for CaltechRnaSeq
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeCaltechRnaSeq.ra
  • lines changed 70, context: html, text, full: html, text
    releasing geo accessions and rnaExtract for CaltechRnaSeq
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeCaltechTfbs.ra
  • lines changed 93, context: html, text, full: html, text
    releasing geo accessions and rnaExtract for CaltechRnaSeq
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeLicrRnaSeq.ra
  • lines changed 89, context: html, text, full: html, text
    releasing geo accessions and rnaExtract for CaltechRnaSeq
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeSydhTfbs.ra
  • lines changed 3586, context: html, text, full: html, text
    preparing to release Stan/Yale SydhTfbs (Release 3) RM#5397
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • lines changed 50, context: html, text, full: html, text
    restoring for beta,public
  • lines changed 6, context: html, text, full: html, text
    moving old mapability to beta,public only
  • lines changed 55, context: html, text, full: html, text
    Pulling mapability into a file so that you can track the alpha,beta,public progress
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    add LicrTfbs.release3
  • lines changed 2, context: html, text, full: html, text
    Staging Stanford/Yale TFBS (Release 3) on beta (Redmine# 5397)
  • lines changed 4, context: html, text, full: html, text
    restoring for beta,public
  • lines changed 2, context: html, text, full: html, text
    alpha release
  • lines changed 2, context: html, text, full: html, text
    preparing to release Stan/Yale SydhTfbs (Release 3) RM#5397
  • lines changed 1, context: html, text, full: html, text
    Pulling mapability into a file so that you can track the alpha,beta,public progress
  • lines changed 1, context: html, text, full: html, text
    Staging mouse mm9 Mapability (Final/Release1) on beta (Redmine# 3649)
  • lines changed 2, context: html, text, full: html, text
    Staging mouse mm9 Mapability (Final/Release1)Resolving Merge Conflict RM# 3649
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeFsuRepliChip.ra
  • lines changed 147, context: html, text, full: html, text
    Added last submissions for the track. Redmine #6627.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release3.ra
  • lines changed 19, context: html, text, full: html, text
    update with new submissions and resubmission of some datasets of previous release
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.release3.html
  • lines changed 245, context: html, text, full: html, text
    make new release for some new datasets and V2 submission of some fastq, bam files of previous release
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.release3.ra
  • lines changed 993, context: html, text, full: html, text
    make new release for some new datasets and V2 submission of some fastq, bam files of previous release
  • lines changed 19, context: html, text, full: html, text
    update with new submission and resubmission of previous release datasets
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeMapability.html
  • lines changed 62, context: html, text, full: html, text
    first attempt at html for mapability
  • lines changed 8, context: html, text, full: html, text
    qa fixes
  • lines changed 2, context: html, text, full: html, text
    fixes for qa
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeMapability.ra
  • lines changed 23, context: html, text, full: html, text
    trackDb for mm9 mapability
  • lines changed 6, context: html, text, full: html, text
    fixed longLabels
  • lines changed 2, context: html, text, full: html, text
    fixed stuff for QA
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHist.release2.ra
  • lines changed 36, context: html, text, full: html, text
    update 2 new submissions
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhRnaSeq.html
  • lines changed 39, context: html, text, full: html, text
    update description sent by Zhihai
  • lines changed 19, context: html, text, full: html, text
    add reference
  • lines changed 1, context: html, text, full: html, text
    remove bold
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhRnaSeq.ra
  • lines changed 1, context: html, text, full: html, text
    remove Yale from the title as all these experiments in this track were done at Stanford
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.html
  • lines changed 1, context: html, text, full: html, text
    adding a period to html file in mm9, hgEncodeSydhTfbs (Release3) Redmine#5397
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.release3.html
  • lines changed 1, context: html, text, full: html, text
    minor edit, adding a period. RedMine #5397
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.release3.ra
  • lines changed 1, context: html, text, full: html, text
    change the setting of visibility for Peak from dense to pack
  • lines changed 4, context: html, text, full: html, text
    changed (S) to (SC) in CH12 and added (SC) in MEL using (SC-584)
  • lines changed 0, context: html, text, full: html, text
    correcting a typo
  • lines changed 114, context: html, text, full: html, text
    add SC-584 to represent antibody to the epitome at the N-terminal of P300 in MEL and CH12, remove P and S in short label to make room for SC-584 from all the other subtracks
  • lines changed 1, context: html, text, full: html, text
    fixed short labels
  • lines changed 8, context: html, text, full: html, text
    add anbibody specific informaiton to long labels, add a to MafK in the previous release
• src/hg/makeDb/trackDb/oreNil/oreNil2/description.html
  • lines changed 119, context: html, text, full: html, text
    minimalist page from makeGenomeDb.pl
• src/hg/makeDb/trackDb/rat/bactigPos.html
  • lines changed 1, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/rat/rn1/description.html
  • lines changed 2, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/rat/rn1/ensRatMusHom.html
  • lines changed 1, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/rat/rn2/description.html
  • lines changed 1, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/rat/rn3/description.html
  • lines changed 2, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/rat/rn3/ensRatMusHom.html
  • lines changed 1, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/rat/rn4/description.html
  • lines changed 2, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/rhesus/rheMac1/description.html
  • lines changed 3, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/rhesus/rheMac2/ctgPos.html
  • lines changed 1, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/rhesus/rheMac2/description.html
  • lines changed 2, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/tasmanianDevil/sarHar1/description.html
  • lines changed 117, context: html, text, full: html, text
    Using new format description.html of sarHar1.
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    turning off snp132 by default
• src/hg/makeDb/trackDb/urchin/strPur1/description.html
  • lines changed 3, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/urchin/strPur2/description.html
  • lines changed 4, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/makeDb/trackDb/wallaby/macEug2/description.html
  • lines changed 1, context: html, text, full: html, text
    Updated links to new Baylor URLs
• src/hg/mouseStuff/mafFetch/mafFetch.c
  • lines changed 2, context: html, text, full: html, text
    include maf header in output to prevent downstream programs from crashing on empty mafs
• src/hg/utils/automation/configFiles/bosTau7.config.ra
  • lines changed 2, context: html, text, full: html, text
    Shorten assemblyShortLabel.
• src/hg/utils/automation/configFiles/latCha1.config.ra
  • lines changed 22, context: html, text, full: html, text
    copy from 2012-06-12
• src/hg/utils/automation/configFiles/oreNil2.config.ra
  • lines changed 22, context: html, text, full: html, text
    copy from 2012-06-14
• src/hg/utils/automation/makeDownloads.pl
  • lines changed 139, context: html, text, full: html, text
    now using the db.config.ra file to place assembly information into the README files
• src/hg/utils/automation/makeGenomeDb.pl
  • lines changed 8, context: html, text, full: html, text
    allow png or jpg images for species picture on gateway page
  • lines changed 12, context: html, text, full: html, text
    allow png,jpg,gif species photographs
• src/lib/bamFile.c
  • lines changed 1, context: html, text, full: html, text
    Fixing BAM tag-printing bug reported by Sol: signed 8-bit ints were displayed as unsigned.
• src/makefile
  • lines changed 1, context: html, text, full: html, text
    addig featureBits to the userApps delivery
• src/utils/qa/checkGenomeMysql
  • lines changed 3, context: html, text, full: html, text
    Commented out check of san diego remote mysql as jorge says it is not working.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v269 preview2
• src/utils/qa/weeklybld/buildZip.csh
  • lines changed 1, context: html, text, full: html, text
    Avoid script asking for permission to replace a file

• lines changed: 73737
• files changed: 283