All File Changes

v276_preview to v276_preview2 (2012-11-06 to 2012-11-13) v276

• src/hg/hgGateway/hgGateway.c
  • lines changed 1, context: html, text, full: html, text
    changing clade to group
• src/hg/hgGene/hgGeneData/Mouse/mm10/otherOrgs.ra
  • lines changed 11, context: html, text, full: html, text
    use rn4 and ce6 for the links to orthologous proteins (#7045)
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 1, context: html, text, full: html, text
    softened the 'not responsible' statement a bit
• src/hg/hgTracks/vcfTrack.c
  • lines changed 4, context: html, text, full: html, text
    Problem: when we have a BAM or VCF track with per-chromosome files,and then view a chromosome for which there is no file (e.g. a random
    or hap), hgTracks was hitting an early errAbort that is more appropriate
    for a single-big-file track that is missing its filename. Fix: allow
    bbiNameFromTableChrom to return NULL if there is a seqName column and
    there simply isn't a file for that seqName.
    
• src/hg/hgc/hgc.c
  • lines changed 133, context: html, text, full: html, text
    Pull doNumtS out from hgc.c and put it in numtsClick.c, in preparation for redmine #8533 NumtS tracks for 10 more organism.
• src/hg/hgc/makefile
  • lines changed 1, context: html, text, full: html, text
    Pull doNumtS out from hgc.c and put it in numtsClick.c, in preparation for redmine #8533 NumtS tracks for 10 more organism.
• src/hg/hgc/numtsClick.c
  • lines changed 138, context: html, text, full: html, text
    Pull doNumtS out from hgc.c and put it in numtsClick.c, in preparation for redmine #8533 NumtS tracks for 10 more organism.
• src/hg/hgc/numtsClick.h
  • lines changed 8, context: html, text, full: html, text
    Pull doNumtS out from hgc.c and put it in numtsClick.c, in preparation for redmine #8533 NumtS tracks for 10 more organism.
• src/hg/hgc/vcfClick.c
  • lines changed 1, context: html, text, full: html, text
    Problem: when we have a BAM or VCF track with per-chromosome files,and then view a chromosome for which there is no file (e.g. a random
    or hap), hgTracks was hitting an early errAbort that is more appropriate
    for a single-big-file track that is missing its filename. Fix: allow
    bbiNameFromTableChrom to return NULL if there is a seqName column and
    there simply isn't a file for that seqName.
    
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 19, context: html, text, full: html, text
    Updated GFF2 spec info and added note about GFF3 (redmine #7661)
  • lines changed 9, context: html, text, full: html, text
    Made some changes based on miswording in the redmine ticket (redmine #7661)
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 42, context: html, text, full: html, text
    Added entries for 10 species (first batch of 28). Fixed a few inconsistencies. Added a mammals group to reflect current clade groupings on RR.
  • lines changed 11, context: html, text, full: html, text
    Fixed archive status of a few entries in assembly table.
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken link to NIAID.
  • lines changed 401, context: html, text, full: html, text
    Added hedgehog, sloth, mouse lemur, and kangaroo rat. Also updated text + links in several places (lots more to do).
  • lines changed 666, context: html, text, full: html, text
    Added squirrel, squirrel monkey, and manatee. Made several more updates to info and links. More to come.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html
  • lines changed 4, context: html, text, full: html, text
    Venkat noticed broken link references to settings not supported for hubs. Redmine maillist #9525.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 9, context: html, text, full: html, text
    And Ann noticed that the bam example still referred to the four not for hub settings. Redmine 9525.
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 53, context: html, text, full: html, text
    Added a new pub. Updated some entries.
• src/hg/htdocs/images/phylo/petMar2_7way.png
  • lines changed 0, context: html, text, full: html, text
    7-way tree image for Lamprey
• src/hg/htdocs/staff.html
  • lines changed 68, context: html, text, full: html, text
    Updated this page, fixed alphabetical order in last group of names.
• src/hg/inc/hdb.h
  • lines changed 2, context: html, text, full: html, text
    Problem: when we have a BAM or VCF track with per-chromosome files,and then view a chromosome for which there is no file (e.g. a random
    or hap), hgTracks was hitting an early errAbort that is more appropriate
    for a single-big-file track that is missing its filename. Fix: allow
    bbiNameFromTableChrom to return NULL if there is a seqName column and
    there simply isn't a file for that seqName.
    
• src/hg/lib/hdb.c
  • lines changed 12, context: html, text, full: html, text
    Problem: when we have a BAM or VCF track with per-chromosome files,and then view a chromosome for which there is no file (e.g. a random
    or hap), hgTracks was hitting an early errAbort that is more appropriate
    for a single-big-file track that is missing its filename. Fix: allow
    bbiNameFromTableChrom to return NULL if there is a seqName column and
    there simply isn't a file for that seqName.
    
• src/hg/lib/trackDbCustom.c
  • lines changed 2, context: html, text, full: html, text
    add bedTail to the allowed composite configuration options, same as bed types
• src/hg/lib/vcfUi.c
  • lines changed 8, context: html, text, full: html, text
    Problem: when we have a BAM or VCF track with per-chromosome files,and then view a chromosome for which there is no file (e.g. a random
    or hap), hgTracks was hitting an early errAbort that is more appropriate
    for a single-big-file track that is missing its filename. Fix: allow
    bbiNameFromTableChrom to return NULL if there is a seqName column and
    there simply isn't a file for that seqName.
    
• src/hg/makeDb/doc/braFlo2.txt
  • lines changed 2, context: html, text, full: html, text
    add note about Nature paper and 11.5X coverage
• src/hg/makeDb/doc/equCab2.txt
  • lines changed 54, context: html, text, full: html, text
    running white rhino lastz
• src/hg/makeDb/doc/hg19.txt
  • lines changed 45, context: html, text, full: html, text
    COSMIC v61 update done redmine 9386, and liftOver to hg17, redmine 9571
  • lines changed 105, context: html, text, full: html, text
    Track #8360 (snp137): Reloaded snp137 tables affected by dbSNPcorrections to indel coordinates (b137_SNPContigLoc) and functional
    effect predictions (b137_SNPContigLocusId) in Sep, Oct and Nov.
    
• src/hg/makeDb/doc/mm10Strains1.txt
  • lines changed 90, context: html, text, full: html, text
    completed lastz alignment to mm10
  • lines changed 4, context: html, text, full: html, text
    change table name from mm10Strains1LiftOverPsl to altSeqLiftOverPslStrains1 to help hgc display the sequence
• src/hg/makeDb/doc/petMar2.txt
  • lines changed 203, context: html, text, full: html, text
    download files constructed for the 7-way alignment
• src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes13.csh
  • lines changed 15, context: html, text, full: html, text
    change blastTabs to use ce6 instead of ce10, and rn4 instead of rn5 (#7045)
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 4, context: html, text, full: html, text
    Added choHof1, dipOrd1, eriEur1 and micMur1
  • lines changed 3, context: html, text, full: html, text
    Added saiBol1, speTri2 and triMan1 (redmine #6350, #7319, #6722)
• src/hg/makeDb/trackDb/anopheles/anoGam1/anoEstNcl.html
  • lines changed 30, context: html, text, full: html, text
    Fixed broken links and made other corrections
• src/hg/makeDb/trackDb/anopheles/anoGam1/anoEstTcl.html
  • lines changed 29, context: html, text, full: html, text
    Fixed broken links and made other corrections
• src/hg/makeDb/trackDb/chainNetPetMar1.ra
  • lines changed 50, context: html, text, full: html, text
    separate petMar chain net for petMar1 and petMar2 different releases
• src/hg/makeDb/trackDb/chainNetPetMar2.ra
  • lines changed 50, context: html, text, full: html, text
    separate petMar chain net for petMar1 and petMar2 different releases
• src/hg/makeDb/trackDb/dog/canFam1/description.html
  • lines changed 1, context: html, text, full: html, text
    Updated photo links
• src/hg/makeDb/trackDb/dog/canFam2/description.html
  • lines changed 1, context: html, text, full: html, text
    Updated photo links
• src/hg/makeDb/trackDb/dog/canFam3/description.html
  • lines changed 1, context: html, text, full: html, text
    Updated photo links
• src/hg/makeDb/trackDb/gadMor/gadMor1/description.html
  • lines changed 1, context: html, text, full: html, text
    remove extra . following May.
• src/hg/makeDb/trackDb/horse/equCab1/description.html
  • lines changed 1, context: html, text, full: html, text
    Updated photo links
• src/hg/makeDb/trackDb/horse/equCab2/description.html
  • lines changed 1, context: html, text, full: html, text
    Updated photo links
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 89, context: html, text, full: html, text
    removed accessions from objStatus stanzas where the accession was in conflict with the newer accessions, ticket 9564
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeDukeAffyExon.ra
  • lines changed 68, context: html, text, full: html, text
    removed accessions from objStatus stanzas where the accession was in conflict with the newer accessions, ticket 9564
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 25, context: html, text, full: html, text
    removed accessions from objStatus stanzas where the accession was in conflict with the newer accessions, ticket 9564
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 15, context: html, text, full: html, text
    removed accessions from objStatus stanzas where the accession was in conflict with the newer accessions, ticket 9564
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 11, context: html, text, full: html, text
    removed accessions from objStatus stanzas where the accession was in conflict with the newer accessions, ticket 9564
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 41, context: html, text, full: html, text
    removed accessions from objStatus stanzas where the accession was in conflict with the newer accessions, ticket 9564
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 70, context: html, text, full: html, text
    Converting ISCA composite to multi-view at Bob's request. Redmine 7550.
• src/hg/makeDb/trackDb/kangarooRat/dipOrd1/description.html
  • lines changed 1, context: html, text, full: html, text
    credit BCM with Broad
  • lines changed 1, context: html, text, full: html, text
    add BCM to NCBI assembly information
• src/hg/makeDb/trackDb/makefile
  • lines changed 2, context: html, text, full: html, text
    papAnu2 is the same identity as papHam1
• src/hg/makeDb/trackDb/medaka/trackDb.chainNet.ra
  • lines changed 1, context: html, text, full: html, text
    add release tag to override block in medaka petMar1
• src/hg/makeDb/trackDb/miRNA.html
  • lines changed 47, context: html, text, full: html, text
    Updated Reference sections
• src/hg/makeDb/trackDb/mouse/mm10/chain.petMar1.ra
  • lines changed 7, context: html, text, full: html, text
    separate petMar chain net for petMar1 and petMar2 different releases
• src/hg/makeDb/trackDb/mouse/mm10/chain.petMar2.ra
  • lines changed 7, context: html, text, full: html, text
    separate petMar chain net for petMar1 and petMar2 different releases
• src/hg/makeDb/trackDb/mouse/mm10/mm10Strains1Composite.ra
  • lines changed 93, context: html, text, full: html, text
    the alternate strains mapping to the reference, redmine 7341
• src/hg/makeDb/trackDb/mouse/mm10/net.petMar1.ra
  • lines changed 7, context: html, text, full: html, text
    separate petMar chain net for petMar1 and petMar2 different releases
• src/hg/makeDb/trackDb/mouse/mm10/net.petMar2.ra
  • lines changed 7, context: html, text, full: html, text
    separate petMar chain net for petMar1 and petMar2 different releases
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    adding the strains composite track to mm10 and the mm10Locations track to mm10Strains1
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.vertebrateChainNet.ra
  • lines changed 14, context: html, text, full: html, text
    separate petMar chain net for petMar1 and petMar2 different releases
• src/hg/makeDb/trackDb/mouse/mm10Strains1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    adding the strains composite track to mm10 and the mm10Locations track to mm10Strains1
• src/hg/makeDb/trackDb/mouse/mm8/miRNA.html
  • lines changed 42, context: html, text, full: html, text
    Updated Reference sections
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
  • lines changed 4, context: html, text, full: html, text
    removed accessions from objStatus stanzas where the accession was in conflict with the newer accessions, ticket 9564
• src/hg/makeDb/trackDb/mouse/mm9/miRNA.html
  • lines changed 42, context: html, text, full: html, text
    Updated Reference sections
• src/hg/makeDb/trackDb/orangutan/ponAbe1/description.html
  • lines changed 1, context: html, text, full: html, text
    Updated photo links
• src/hg/makeDb/trackDb/sacCer/sacCer1/description.html
  • lines changed 4, context: html, text, full: html, text
    Fixed broken links
• src/hg/makeDb/trackDb/sacCer/sacCer2/description.html
  • lines changed 4, context: html, text, full: html, text
    Fixed broken links
• src/hg/makeDb/trackDb/sacCer/sacCer3/description.html
  • lines changed 4, context: html, text, full: html, text
    Fixed broken links
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    add bedTail to the allowed composite configuration options, same as bed types
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 100, context: html, text, full: html, text
    separate petMar chain net for petMar1 and petMar2 different releases
  • lines changed 1, context: html, text, full: html, text
    add release tag to override block in medaka petMar1
• src/hg/makeDb/trackDb/wallaby/macEug2/description.html
  • lines changed 1, context: html, text, full: html, text
    Updated photo links
• src/hg/utils/automation/doBlastzChainNet.pl
  • lines changed 8, context: html, text, full: html, text
    better line wrap in the README files, redmine 8887 note 94
• src/hg/utils/automation/makeDownloads.pl
  • lines changed 10, context: html, text, full: html, text
    better line wrap in the README files, redmine 8887 note 94
• src/hg/utils/automation/makeGenomeDb.pl
  • lines changed 1, context: html, text, full: html, text
    redmine issue 8707 HTML now reads HTTP
• src/lib/linefile.c
  • lines changed 2, context: html, text, full: html, text
    Problem: when we have a BAM or VCF track with per-chromosome files,and then view a chromosome for which there is no file (e.g. a random
    or hap), hgTracks was hitting an early errAbort that is more appropriate
    for a single-big-file track that is missing its filename. Fix: allow
    bbiNameFromTableChrom to return NULL if there is a seqName column and
    there simply isn't a file for that seqName.
    
• src/makefile
  • lines changed 5, context: html, text, full: html, text
    Bug #9548 hg/makeDb/hgWiggle: No such file or directory during makeUserApp.csh called by ./doHgDownloadUtils.csh.
• src/parasol/parasol/parasol.c
  • lines changed 2, context: html, text, full: html, text
    minor fix to make informational message go to stdout instead of stderr
• src/product/README.QuickStart
  • lines changed 1, context: html, text, full: html, text
    Removing misleading line about when the file was last updated since people are not maintaining it.
• src/product/README.building.source
  • lines changed 1, context: html, text, full: html, text
    Removing misleading line about when the file was last updated since people are not maintaining it.
• src/product/README.customTracks.dataBase
  • lines changed 1, context: html, text, full: html, text
    Removing misleading line about when the file was last updated since people are not maintaining it.
• src/product/README.install
  • lines changed 1, context: html, text, full: html, text
    Removing misleading line about when the file was last updated since people are not maintaining it.
• src/product/README.mysql.setup
  • lines changed 3, context: html, text, full: html, text
    add note about LOCK TABLES for MySQL 5.5, redmine 9553
  • lines changed 2, context: html, text, full: html, text
    removing date that is out of date
  • lines changed 1, context: html, text, full: html, text
    INSERT privilege is not needed by readonly user
  • lines changed 4, context: html, text, full: html, text
    added version-specific explanation of temp table privileges required
• src/product/README.trackDb
  • lines changed 1, context: html, text, full: html, text
    Removing misleading line about when the file was last updated since people are not maintaining it.
• src/product/ex.MySQLUserPerms.sh
  • lines changed 4, context: html, text, full: html, text
    add note about LOCK TABLES for MySQL 5.5, redmine 9553
• src/utils/gitTools/gitu
  • lines changed 7, context: html, text, full: html, text
    adding gitu to tools
• src/utils/gitTools/makefile
  • lines changed 1, context: html, text, full: html, text
    adding gitu to tools
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v276 preview2

• lines changed: 3072
• files changed: 95