All File Changes

v262_preview2 to v262_base (2012-01-17 to 2012-01-24) v262

• python/lib/ucscgenomics/qa.py
  • lines changed 24, context: html, text, full: html, text
    made it so that certain tests skip non-positional tables
• python/lib/ucscgenomics/ra.py
  • lines changed 29, context: html, text, full: html, text
    Willy draft 2 for trackDb print option in ra.py
  • lines changed 11, context: html, text, full: html, text
    fixed a bug where the 'parent' or 'subTrack' key will be treated as such even with things like >>>>> in front of it
• src/hg/encode/encodeMkFilesList/encodeMkFilesList
  • lines changed 18, context: html, text, full: html, text
    changed it so that the md5sum collision check is aware of revoked status
• src/hg/encode/encodeQaInit/encodeQaInit
  • lines changed 7, context: html, text, full: html, text
    changed sql output to change depending on whether it's a release 1 or N
  • lines changed 1, context: html, text, full: html, text
    introduced a random colon in other commit
  • lines changed 0, context: html, text, full: html, text
    fixed whitespace issues
  • lines changed 1, context: html, text, full: html, text
    changing claim mail name
• src/hg/encode/encodeQaPrepareRelease/encodeQaPrepareRelease
  • lines changed 5, context: html, text, full: html, text
    changed it to not put any tag if it's a stage to public
• src/hg/encode/encodeReport/doNhgriReport.csh
  • lines changed 17, context: html, text, full: html, text
    Reformat to NHGRI format for quarterly report
  • lines changed 4, context: html, text, full: html, text
    Add end-date arg. This will prune out any experiments submitted after cut-off date
• src/hg/encode/encodeReport/encodeReport.pl
  • lines changed 23, context: html, text, full: html, text
    Change date reporting -- always use earliest submitted date
  • lines changed 20, context: html, text, full: html, text
    Add fields for Date Unrestricted and Tissue
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 1, context: html, text, full: html, text
    moved mouse data version over to encode.pm
• src/hg/encode/qaUpdateMetadata/qaUpdateMetadata
  • lines changed 1, context: html, text, full: html, text
    fixed broken english
• src/hg/hgGene/info.c
  • lines changed 8, context: html, text, full: html, text
    Changing the wording around RNA accession, addressing Redmine #5983
• src/hg/hgTracks/cutterTrack.c
  • lines changed 1, context: html, text, full: html, text
    fix canPack (see redmine #6632)
• src/hg/hgTracks/hgTracks.c
  • lines changed 5, context: html, text, full: html, text
    fix problem which turned off canPack for hgUserPsl and oligoMatch (trackDb->canPack is now used instead of track->canPack) - see redmine #6632; also modified ajaxWarnHandler to use jsonForClient (fixes problem with warnings vs. errors)
  • lines changed 4, context: html, text, full: html, text
    ParentChildCartCleanupwas tripping on supertracks with downloadsOnly children.
• src/hg/hgTracks/wikiTrack.c
  • lines changed 1, context: html, text, full: html, text
    fix canPack (see redmine #6632)
• src/hg/hgc/t2g.c
  • lines changed 1, context: html, text, full: html, text
    changed two strings based on rachel s comments
  • lines changed 24, context: html, text, full: html, text
    crazy workaround for firefox bug not breaking long words in tables, rachel feedback
• src/hg/htdocs/ENCODE/contacts.html
  • lines changed 4, context: html, text, full: html, text
    made changes according to Katrina's code review: Redmine# 6605
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 2, context: html, text, full: html, text
    added wallaby assembly
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 53, context: html, text, full: html, text
    added wallaby credits
  • lines changed 1, context: html, text, full: html, text
    fixed spelling for Australian
  • lines changed 1, context: html, text, full: html, text
    removed Donna's name from credits
  • lines changed 2, context: html, text, full: html, text
    minor correction to Baylor HGSC link
  • lines changed 2, context: html, text, full: html, text
    corrected spacing
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 48, context: html, text, full: html, text
    added bosTau6 announcement
  • lines changed 2, context: html, text, full: html, text
    added missing line and fixed credits link
• src/hg/htdocs/images/Macropus_eugenii.jpg
  • lines changed 0, context: html, text, full: html, text
    Shrink image of sheep, gibbon and wallby
• src/hg/htdocs/images/Nomascus_leucogenys.jpg
  • lines changed 0, context: html, text, full: html, text
    Shrink image of sheep, gibbon and wallby
• src/hg/htdocs/images/Ovis_aries.jpg
  • lines changed 0, context: html, text, full: html, text
    Shrink image of sheep, gibbon and wallby
• src/hg/htdocs/indexNews.html
  • lines changed 72, context: html, text, full: html, text
    added announcement for wallaby release and compressed bosTau6 announcement
  • lines changed 6, context: html, text, full: html, text
    Made a few adjustments to links, etc
  • lines changed 1, context: html, text, full: html, text
    fixed credits link
  • lines changed 1, context: html, text, full: html, text
    fixed usage link
  • lines changed 1, context: html, text, full: html, text
    fixed spelling for Australian
  • lines changed 1, context: html, text, full: html, text
    removed Donna's name from announcement
• src/hg/inc/genbankBlackList.h
  • lines changed 28, context: html, text, full: html, text
    changes wanted by Mark, #6456
  • lines changed 2, context: html, text, full: html, text
    last one I think
• src/hg/inc/hgnc.h
  • lines changed 101, context: html, text, full: html, text
    Updated the HGNC object so that it contains all the fields from the HGNC standard download tables
• src/hg/inc/kgXref.h
  • lines changed 2, context: html, text, full: html, text
    In response to Redmine #6660, which rightly points out that the table descriptors are outdated where they reference SwissProt protein IDs, updated the table descriptors to indicate that those fields are actually UniProt IDs
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v262
• src/hg/js/subCfg.js
  • lines changed 6, context: html, text, full: html, text
    Fix to subtrack vis not getting into the cart when populated via the wrench. 4665
  • lines changed 16, context: html, text, full: html, text
    Allow the unexpected case of a composite of tracks that cannot be packed. HapMap LD Phased is that case. Now if the composite has no dense/squish options then none of the children can. 4665
  • lines changed 5, context: html, text, full: html, text
    Vanessa found an invalid debug assert. It has been removed so that the 100 Genomes cov track is not getting erroneous errors'
  • lines changed 25, context: html, text, full: html, text
    Add resizing of subtrack cfg box based upon the sizes of its contents. This fixes redmine 6655.
• src/hg/lib/genbankBlackList.c
  • lines changed 79, context: html, text, full: html, text
    changes wanted by Mark, #6456
  • lines changed 6, context: html, text, full: html, text
    not sure why these changes didn't get sucked in when I moved this file
• src/hg/lib/hgnc.as
  • lines changed 25, context: html, text, full: html, text
    Updated the HGNC object so that it contains all the fields from the HGNC standard download tables
• src/hg/lib/hgnc.c
  • lines changed 435, context: html, text, full: html, text
    Updated the HGNC object so that it contains all the fields from the HGNC standard download tables
• src/hg/lib/hgnc.sql
  • lines changed 41, context: html, text, full: html, text
    Updated the HGNC object so that it contains all the fields from the HGNC standard download tables
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    fix off-by-one error in tagEncode
  • lines changed 19, context: html, text, full: html, text
    move an input tag to make sure it's inside a td (fixes IE 8 problem; see 4665#note-44)
• src/hg/lib/kgXref.as
  • lines changed 2, context: html, text, full: html, text
    In response to Redmine #6660, which rightly points out that the table descriptors are outdated where they reference SwissProt protein IDs, updated the table descriptors to indicate that those fields are actually UniProt IDs
• src/hg/lib/kgXref.sql
  • lines changed 11, context: html, text, full: html, text
    In response to Redmine #6660, which rightly points out that the table descriptors are outdated where they reference SwissProt protein IDs, updated the table descriptors to indicate that those fields are actually UniProt IDs
• src/hg/lib/knownCanonical.as
  • lines changed 2, context: html, text, full: html, text
    Addressing Redmine bug # 6661 by changing the wording for the chromStart and chromEnd fields to indicate that they correspond to txStart and txEnd respectively for + strand genes, not for all genes
  • lines changed 1, context: html, text, full: html, text
    In response to Redmine #6660, which rightly points out that the table descriptors are outdated where they reference SwissProt protein IDs, updated the table descriptors to indicate that those fields are actually UniProt IDs
• src/hg/lib/knownCanonical.c
  • lines changed 146, context: html, text, full: html, text
    Addressing Redmine bug # 6661 by changing the wording for the chromStart and chromEnd fields to indicate that they correspond to txStart and txEnd respectively for + strand genes, not for all genes
• src/hg/lib/knownCanonical.sql
  • lines changed 6, context: html, text, full: html, text
    Addressing Redmine bug # 6661 by changing the wording for the chromStart and chromEnd fields to indicate that they correspond to txStart and txEnd respectively for + strand genes, not for all genes
  • lines changed 1, context: html, text, full: html, text
    In response to Redmine #6660, which rightly points out that the table descriptors are outdated where they reference SwissProt protein IDs, updated the table descriptors to indicate that those fields are actually UniProt IDs
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    changes wanted by Mark, #6456
• src/hg/makeDb/doc/bosTau7.txt
  • lines changed 9, context: html, text, full: html, text
    Finished ctgPos2 for bosTau7
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibTfbs.release2.notes
  • lines changed 4421, context: html, text, full: html, text
    notes for haib tfbs release 2, initial draft, not yet ready
• src/hg/makeDb/doc/fr3.txt
  • lines changed 116, context: html, text, full: html, text
    done with lastz for Atlantic Cod and Coelacanth
• src/hg/makeDb/doc/hg19.txt
  • lines changed 13, context: html, text, full: html, text
    Added commands to download the HGNC data and load it into the hg19 database
• src/hg/makeDb/doc/macEug2.txt
  • lines changed 8, context: html, text, full: html, text
    relink the macEug2.2bit to the masked 2bit file
• src/hg/makeDb/doc/rheMac3.txt
  • lines changed 182, context: html, text, full: html, text
    Finished CpG Islands track for rheMac3
• src/hg/makeDb/doc/tRNAsTrack.txt
  • lines changed 4, context: html, text, full: html, text
    Add new images, and move all images to /hive/data/genomes//bed/tRNAs/gif
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
  • lines changed 1, context: html, text, full: html, text
    a joiner check error revealed that the bioCyc tables had been built with the wrong version of the knownGenes table. They'd been built against the version on hgwdev rather than the version being built in the tempDb. Fixed that.
  • lines changed 33, context: html, text, full: html, text
    In response to Redmine #5180, in all cases where a knownTo* table was not built by hgMapToGene (as most are), added a mysql delete statement to remove antibody parts from the knownTo* table after the table gets loaded
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 1, context: html, text, full: html, text
    added macEug2
• src/hg/makeDb/genbank/src/dbload/gbGeneTbl.c
  • lines changed 2, context: html, text, full: html, text
    only collapse gaps in refSeq PSL's if they're a multiple of three when in CDS, #6565
• src/hg/makeDb/genbank/src/process/gbProcess.c
  • lines changed 1, context: html, text, full: html, text
    changes wanted by Mark, #6456
  • lines changed 2, context: html, text, full: html, text
    sigh... more code review changes
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • lines changed 18, context: html, text, full: html, text
    expand usage message to include meaning of all arguments
• src/hg/makeDb/hgTrackDb/makefile
  • lines changed 9, context: html, text, full: html, text
    adding compile target and a little clean up
• src/hg/makeDb/schema/all.joiner
  • lines changed 2, context: html, text, full: html, text
    Add rheMac3 and bosTau7
• src/hg/makeDb/trackDb/apis/apiMel2/description.html
  • lines changed 3, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/cat/felCat3/multiz4way.html
  • lines changed 10, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/cat/felCat4/cons6way.html
  • lines changed 10, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/cat/felCat4/description.html
  • lines changed 3, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/chicken/galGal3/description.html
  • lines changed 6, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/chicken/galGal3/multiz7way.html
  • lines changed 10, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/chimp/panTro2/description.html
  • lines changed 3, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/chimp/panTro2/multiz8way.html
  • lines changed 10, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/chimp/panTro3/cons12way.html
  • lines changed 10, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/chimp/panTro3/description.html
  • lines changed 4, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/cow/bosTau3/description.html
  • lines changed 3, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/cow/bosTau4/description.html
  • lines changed 3, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/cow/bosTau4/multiz5way.html
  • lines changed 10, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/cow/bosTau6/description.html
  • lines changed 3, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/cow/bosTau7/ctgPos2.html
  • lines changed 15, context: html, text, full: html, text
    Finished ctgPos2 for bosTau7
• src/hg/makeDb/trackDb/cow/bosTau7/trackDb.ra
  • lines changed 17, context: html, text, full: html, text
    Finished ctgPos2 for bosTau7
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 1, context: html, text, full: html, text
    Removing PROVISIONAL tag from SK-N-SH
  • lines changed 12, context: html, text, full: html, text
    Updating Peggys webpage to USC
  • lines changed 1, context: html, text, full: html, text
    Fixing TRIM28 gene card ref
  • lines changed 15, context: html, text, full: html, text
    Improving assay descriptions and labels
  • lines changed 1, context: html, text, full: html, text
    Adding Crawford to Hypoxia description
  • lines changed 1, context: html, text, full: html, text
    changing E2F6's tag to be like normal convention
  • lines changed 1, context: html, text, full: html, text
    Revert "changing E2F6's tag to be like normal convention" This reverts commit 0d8dec27181aaaa6bee914bc1f5b1954b06d7ab3.
  • lines changed 1, context: html, text, full: html, text
    Change lab entry for CRG-Guigo so it belongs to a registered grant (Gingeras)
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 37, context: html, text, full: html, text
    Copying alpha cv to beta
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 324, context: html, text, full: html, text
    Moved over approved stanzas and changes from beta to publc. Redmine #6592.
• src/hg/makeDb/trackDb/dog/canFam2/description.html
  • lines changed 3, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/drosophila/dm2/multiz15way.html
  • lines changed 10, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/drosophila/dm3/description.html
  • lines changed 4, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/drosophila/dm3/multiz15way.html
  • lines changed 10, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/elephant/loxAfr3/description.html
  • lines changed 3, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/fugu/fr2/multiz5way.html
  • lines changed 10, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/gibbon/nomLeu1/description.html
  • lines changed 4, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/gorilla/gorGor3/cons11way.html
  • lines changed 1, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/gorilla/gorGor3/description.html
  • lines changed 4, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/horse/equCab2/description.html
  • lines changed 3, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/horse/equCab2/multiz6way.html
  • lines changed 10, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/human/hg16/description.html
  • lines changed 4, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/human/hg17/description.html
  • lines changed 4, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/human/hg17/multiz17way.html
  • lines changed 9, context: html, text, full: html, text
    Made some formatting corrections
  • lines changed 1, context: html, text, full: html, text
    Corrected name of drop-down menu
• src/hg/makeDb/trackDb/human/hg18/cons44way.html
  • lines changed 10, context: html, text, full: html, text
    Made some formatting corrections
  • lines changed 1, context: html, text, full: html, text
    Corrected name of drop-down menu
• src/hg/makeDb/trackDb/human/hg18/description.html
  • lines changed 4, context: html, text, full: html, text
    Added link to NCBI Assemblies database
  • lines changed 2, context: html, text, full: html, text
    Edited sentence linking to NCBI Assembly database
• src/hg/makeDb/trackDb/human/hg19/cons46way.html
  • lines changed 10, context: html, text, full: html, text
    Made some formatting corrections
  • lines changed 1, context: html, text, full: html, text
    Corrected name of drop-down menu
• src/hg/makeDb/trackDb/human/hg19/description.html
  • lines changed 4, context: html, text, full: html, text
    Added link to NCBI Assemblies database
  • lines changed 2, context: html, text, full: html, text
    Edited sentence linking to NCBI Assembly database
  • lines changed 1, context: html, text, full: html, text
    Edited sentence linking to NCBI Assembly database
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibGenotype.ra
  • lines changed 7, context: html, text, full: html, text
    changed dataVersion date
  • lines changed 2, context: html, text, full: html, text
    udpated md5sum
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 1642, context: html, text, full: html, text
    massive metadata update and fixes
  • lines changed 231, context: html, text, full: html, text
    fixed E2F6 cv issue
  • lines changed 353, context: html, text, full: html, text
    added in replacement tracks for haib tfbs
  • lines changed 353, context: html, text, full: html, text
    Error in last submission. Not all tracks should be a V2. Revert "added in replacement tracks for haib tfbs" This reverts commit 8348cae9f1eb51ce89b59195d4d7aaad5b685f1b.
  • lines changed 41, context: html, text, full: html, text
    added in accessions and expIds
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 1, context: html, text, full: html, text
    revoked old bad bigwig
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
  • lines changed 2, context: html, text, full: html, text
    staging Gencode V10 on beta. #6230
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeGencodeV10.ra
  • lines changed 312, context: html, text, full: html, text
    staging Gencode V10 on beta. #6230
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeHaibGenotype.ra
  • lines changed 57, context: html, text, full: html, text
    staging HAIB Genotype Release 2 on beta, redmine #5699
  • lines changed 7, context: html, text, full: html, text
    changed dataVersion date
  • lines changed 2, context: html, text, full: html, text
    udpated md5sum
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwTfbs.ra
  • lines changed 286, context: html, text, full: html, text
    updating beta metadata with revised freeze date, #4461, #6577
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeCaltechRnaSeq.ra
  • lines changed 11408, context: html, text, full: html, text
    releasing Caltech RNA-seq (Release2), Redmine# 2019
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeHaibGenotype.ra
  • lines changed 57, context: html, text, full: html, text
    preparing to release HAIB Genotype (Release 2), redmine #5699
  • lines changed 8, context: html, text, full: html, text
    updated some records with new freeze date according to redmine #6581 before releasing track, #5699
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwDnase.ra
  • lines changed 66, context: html, text, full: html, text
    releasing dropping of CD14+ monocytes from release 3, redmine 6084
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwTfbs.ra
  • lines changed 10753, context: html, text, full: html, text
    preparing to release ENCODE UW CTCF Binding (release 2), 4461
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Updated tags to be releaseN tag instead of .new. Redmine #2019.
  • lines changed 2, context: html, text, full: html, text
    preparing to release ENCODE UW CTCF Binding (release 2), 4461
  • lines changed 2, context: html, text, full: html, text
    releasing Caltech RNA-seq (Release2), Redmine# 2019
  • lines changed 2, context: html, text, full: html, text
    fixed include statements to set the stage for how uwdnase should have been
  • lines changed 3, context: html, text, full: html, text
    releasing fix to Monocyte CD14+ matrix label, redmine #6290
  • lines changed 2, context: html, text, full: html, text
    releasing dropping of CD14+ monocytes from release 3, redmine 6084
  • lines changed 2, context: html, text, full: html, text
    staging HAIB Genotype Release 2 on beta, redmine #5699
  • lines changed 2, context: html, text, full: html, text
    preparing to release HAIB Genotype (Release 2), redmine #5699
  • lines changed 1, context: html, text, full: html, text
    staging Gencode V10 on beta. #6230
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.html
  • lines changed 189, context: html, text, full: html, text
    Updated tags to be releaseN tag instead of .new, forgot html file. Redmine #2019.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.ra
  • lines changed 1526, context: html, text, full: html, text
    Updated tags to be releaseN tag instead of .new. Redmine #2019.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.release2.html
  • lines changed 189, context: html, text, full: html, text
    Updated tags to be releaseN tag instead of .new, forgot html file. Redmine #2019.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.release2.ra
  • lines changed 1526, context: html, text, full: html, text
    Updated tags to be releaseN tag instead of .new. Redmine #2019.
  • lines changed 1, context: html, text, full: html, text
    Updated tags to be releaseN tag instead of .new, forgot html file. Redmine #2019.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeChromSuper.html
  • lines changed 12, context: html, text, full: html, text
    Fixes from QA
  • lines changed 1, context: html, text, full: html, text
    Changing capitolization
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV10.html
  • lines changed 34, context: html, text, full: html, text
    Adding the verification section and making the fixes found in note 12 ticket 6230.
  • lines changed 3, context: html, text, full: html, text
    GENCODE Validation Notes and Gonzalez see ticket 5234
  • lines changed 1, context: html, text, full: html, text
    pre-qa fix
  • lines changed 20, context: html, text, full: html, text
    editing for consistency and a typo, redmine #6230
  • lines changed 3, context: html, text, full: html, text
    fixing all caps instances of Ensembl, redmine #6230
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV4.html
  • lines changed 12, context: html, text, full: html, text
    GENCODE Validation Notes and Gonzalez see ticket 5234
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV7.html
  • lines changed 13, context: html, text, full: html, text
    GENCODE Validation Notes and Gonzalez see ticket 5234
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV9.html
  • lines changed 13, context: html, text, full: html, text
    GENCODE Validation Notes and Gonzalez see ticket 5234
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.html
  • lines changed 11, context: html, text, full: html, text
    Fixes from Willy
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.release2.html
  • lines changed 6, context: html, text, full: html, text
    qa changes for haib genotype html
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release2.ra
  • lines changed 171, context: html, text, full: html, text
    long label changes
  • lines changed 402, context: html, text, full: html, text
    short labels
  • lines changed 8, context: html, text, full: html, text
    renamed tracks to not have vendor code in antibody name
  • lines changed 48, context: html, text, full: html, text
    added in replacement tracks for haib tfbs
  • lines changed 48, context: html, text, full: html, text
    Error in last submission. Not all tracks should be a V2. Revert "added in replacement tracks for haib tfbs" This reverts commit 8348cae9f1eb51ce89b59195d4d7aaad5b685f1b.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUmassDekker5C.html
  • lines changed 155, context: html, text, full: html, text
    Added trackDescription for track. Based on information found in Encode Wiki. Redmine #225.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.html
  • lines changed 129, context: html, text, full: html, text
    moving to release3 html
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra
  • lines changed 1, context: html, text, full: html, text
    removing html lines because they were pointing at the wrong file name and they are not necessary as long as the .ra and .html have the same names; this will reinstate the description pages
  • lines changed 19, context: html, text, full: html, text
    manual revert of an accidentally leaked revoke, setting up scenario for some qa process tests
  • lines changed 4076, context: html, text, full: html, text
    renaming uwdnase to have the proper track tag
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release3.html
  • lines changed 129, context: html, text, full: html, text
    moving to release3 html
  • lines changed 5, context: html, text, full: html, text
    adding information about the udpate to the release 3 which removes the Monocytes-CD14+ data from the track, redmine 6084
  • lines changed 2, context: html, text, full: html, text
    adding paragaph tags to improve spacing on edit just made, redmine 6084
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release3.patch.ra
  • lines changed 4076, context: html, text, full: html, text
    checking in patch for uw Dnase patch to revoke cd14 rep 1
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release3.ra
  • lines changed 4076, context: html, text, full: html, text
    renaming uwdnase to have the proper track tag
  • lines changed 18, context: html, text, full: html, text
    releasing dropping of CD14+ monocytes from release 3, redmine 6084
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release4.ra
  • lines changed 1, context: html, text, full: html, text
    removing html lines because they were pointing at the wrong file name and they are not necessary as long as the .ra and .html have the same names; this will reinstate the description pages
  • lines changed 1, context: html, text, full: html, text
    adding in correct html line, do need it since make only looks at first section before the '.'
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.patch.ra
  • lines changed 1, context: html, text, full: html, text
    fixing html line since it was refering to a .html that doesn't exist
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release2.ra
  • lines changed 1, context: html, text, full: html, text
    releasing fix to Monocyte CD14+ matrix label, redmine #6290
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release3.ra
  • lines changed 1, context: html, text, full: html, text
    applying correction to release 3
• src/hg/makeDb/trackDb/human/trackDb.nt.ra
  • lines changed 1, context: html, text, full: html, text
    fix "show names" bug on BAM sub-tracks of a composite. #6292
• src/hg/makeDb/trackDb/lamprey/petMar1/multiz6way.html
  • lines changed 10, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/lancelet/braFlo1/multiz5way.html
  • lines changed 10, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/lizard/anoCar2/cons7way.html
  • lines changed 10, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/lizard/anoCar2/description.html
  • lines changed 6, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/loadTracks
  • lines changed 1, context: html, text, full: html, text
    avoid old descriptions being pushed on top of newer descriptions
  • lines changed 3, context: html, text, full: html, text
    MKDIR for encode directory to get it to exist, and the rsync in loadTracks did not actually work
  • lines changed 1, context: html, text, full: html, text
    missing ;
• src/hg/makeDb/trackDb/makefile
  • lines changed 4, context: html, text, full: html, text
    MKDIR for encode directory to get it to exist, and the rsync in loadTracks did not actually work
• src/hg/makeDb/trackDb/marmoset/calJac1/multiz9way.html
  • lines changed 10, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/marmoset/calJac3/cons13way.html
  • lines changed 10, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/marmoset/calJac3/ctgPos2.html
  • lines changed 2, context: html, text, full: html, text
    Fixed broken link. Removed unnecessary period.
• src/hg/makeDb/trackDb/marmoset/calJac3/description.html
  • lines changed 3, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/medaka/oryLat1/multiz5way.html
  • lines changed 10, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/medaka/oryLat2/multiz5way.html
  • lines changed 10, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/microbat/myoLuc2/description.html
  • lines changed 3, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/mouse/mm7/description.html
  • lines changed 3, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/mouse/mm8/description.html
  • lines changed 3, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/mouse/mm8/multiz17way.html
  • lines changed 10, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/mouse/mm9/cons30way.html
  • lines changed 10, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/mouse/mm9/description.html
  • lines changed 4, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
  • lines changed 2, context: html, text, full: html, text
    Added age as new experimental variable for new data.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrRnaSeq.ra
  • lines changed 2, context: html, text, full: html, text
    Updated md5sum of files. Redmine #6476.
  • lines changed 2, context: html, text, full: html, text
    Added age as new experimental variable for new data.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
  • lines changed 2, context: html, text, full: html, text
    Added age as new experimental variable for new data.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuHistone.ra
  • lines changed 877, context: html, text, full: html, text
    Added dccAccession and expId's and updated controId's to use dccAccession for matching.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
  • lines changed 715, context: html, text, full: html, text
    Added dccAccession and expId's and updated controId's to use dccAccession for matching.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 19, context: html, text, full: html, text
    Updated files for experiment subId 5241. Redmine #3631.
  • lines changed 148, context: html, text, full: html, text
    Revoked Genetial Fat Pad experiment on recomendation from lab. Redmine #3631
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.ra
  • lines changed 10, context: html, text, full: html, text
    Fixed longLabels for track. Redmine #111.
  • lines changed 51, context: html, text, full: html, text
    Set track defaults. Redmine #111.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.ra
  • lines changed 2, context: html, text, full: html, text
    Fixed longLabels for track. Redmine #110.
  • lines changed 22, context: html, text, full: html, text
    Set track defaults. Redmine #110.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDgf.ra
  • lines changed 6, context: html, text, full: html, text
    Updated files for experiment subId 5241. Redmine #3631.
  • lines changed 36, context: html, text, full: html, text
    Revoked Genetial Fat Pad experiment on recomendation from lab. Redmine #3631
• src/hg/makeDb/trackDb/opossum/monDom4/multiz7way.html
  • lines changed 10, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/opossum/monDom5/description.html
  • lines changed 3, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/opossum/monDom5/multiz9way.html
  • lines changed 10, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/orangutan/ponAbe2/description.html
  • lines changed 3, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/orangutan/ponAbe2/multiz8way.html
  • lines changed 10, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/panda/ailMel1/description.html
  • lines changed 4, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/pig/susScr2/description.html
  • lines changed 4, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/platypus/ornAna1/description.html
  • lines changed 3, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/platypus/ornAna1/multiz6way.html
  • lines changed 10, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/rabbit/oryCun2/description.html
  • lines changed 4, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/rat/rn4/description.html
  • lines changed 4, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/rat/rn4/multiz9way.html
  • lines changed 10, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/rhesus/rheMac2/description.html
  • lines changed 4, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/sacCer/sacCer3/description.html
  • lines changed 3, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/seaHare/aplCal1/description.html
  • lines changed 3, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/sheep/oviAri1/description.html
  • lines changed 3, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/stickleback/gasAcu1/description.html
  • lines changed 3, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/stickleback/gasAcu1/multiz8way.html
  • lines changed 10, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/t2g.html
  • lines changed 7, context: html, text, full: html, text
    changed two strings based on rachel s comments
• src/hg/makeDb/trackDb/tetraodon/tetNig1/description.html
  • lines changed 3, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/tetraodon/tetNig2/description.html
  • lines changed 3, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    increasing maxItems for t2g to 300
• src/hg/makeDb/trackDb/turkey/melGal1/description.html
  • lines changed 3, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/urchin/strPur2/description.html
  • lines changed 4, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/wallaby/macEug2/description.html
  • lines changed 1, context: html, text, full: html, text
    Fixed a typo
  • lines changed 2, context: html, text, full: html, text
    commented out pseudogene mRNA sample query, redmine #1648
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    removed extra 'and'
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    made some adjustments to acknowledgments
  • lines changed 1, context: html, text, full: html, text
    added missing period
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    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/worm/caePb2/description.html
  • lines changed 3, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/worm/caeRem3/description.html
  • lines changed 3, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/worm/ce10/cons9way.html
  • lines changed 18, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/worm/ce4/multiz5way.html
  • lines changed 15, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/worm/ce6/description.html
  • lines changed 7, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/worm/ce6/multiz6way.html
  • lines changed 16, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/worm/ce9/cons10way.html
  • lines changed 10, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/xenTro/xenTro2/multiz7way.html
  • lines changed 10, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/xenTro/xenTro3/cons9way.html
  • lines changed 1, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/xenTro/xenTro3/description.html
  • lines changed 6, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/zebrafish/danRer3/multiz5way.html
  • lines changed 10, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/zebrafish/danRer4/multiz7way.html
  • lines changed 10, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/zebrafish/danRer5/description.html
  • lines changed 7, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/zebrafish/danRer6/description.html
  • lines changed 5, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/makeDb/trackDb/zebrafish/danRer6/multiz6way.html
  • lines changed 10, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/zebrafish/danRer7/cons8way.html
  • lines changed 10, context: html, text, full: html, text
    Made some formatting corrections
• src/hg/makeDb/trackDb/zebrafish/danRer7/description.html
  • lines changed 3, context: html, text, full: html, text
    Added link to NCBI Assembly database
• src/hg/pslCDnaFilter/makefile
  • lines changed 1, context: html, text, full: html, text
    oops, left this out in earlier commit for Code review changes
• src/hg/pslCDnaFilter/pslCDnaFilter.c
  • lines changed 1, context: html, text, full: html, text
    changes wanted by Mark, #6456
  • lines changed 2, context: html, text, full: html, text
    omg... this is taking me forever.
• src/hg/txGene/txGeneXref/txGeneXref.c
  • lines changed 5, context: html, text, full: html, text
    Cleaning up the code in response to some excellent code review feedback from Angie
• src/hg/utils/automation/Encode.pm
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    moved mouse data version over to encode.pm
• src/hg/utils/phyloTrees/60way.nh
  • lines changed 25, context: html, text, full: html, text
    with distances very similar to the 46way
• src/hg/utils/phyloTrees/placentals.txt
  • lines changed 15, context: html, text, full: html, text
    adding new species, plus new nomenclature from NCBI taxonomy viewer
• src/hg/utils/phyloTrees/primates.txt
  • lines changed 2, context: html, text, full: html, text
    adding new species, plus new nomenclature from NCBI taxonomy viewer
• src/hg/utils/phyloTrees/vertebrates.txt
  • lines changed 51, context: html, text, full: html, text
    adding new species, plus new nomenclature from NCBI taxonomy viewer
• src/inc/blackList.h
  • lines changed 28, context: html, text, full: html, text
    changes wanted by Mark, #6456
• src/lib/blackList.c
  • lines changed 79, context: html, text, full: html, text
    changes wanted by Mark, #6456
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    changes wanted by Mark, #6456
• src/product/README.trackDb
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    clarify the operations of hgTrackDb operations
• src/utils/qa/weeklybld/buildEnv.csh
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    v262 final build

• lines changed: 51877
• files changed: 292