All File Changes

v294_preview2 to v294_base (2014-01-06 to 2014-01-13) v294

• src/hg/encode/getTrackReferences/getTrackReferences
  • lines changed 13, context: html, text, full: html, text
    Fix for sometimes reporting no original paper link when really NCBI's page didn't serve up properly
• src/hg/encode3/encodeDataWarehouse/edwWebXSendFile/edwWebXSendFile.c
  • lines changed 28, context: html, text, full: html, text
    Changes made per Jim's feedback inhttp://redmine.soe.ucsc.edu/issues/12422#note-2
    
• src/hg/encode3/encodeDataWarehouse/makefile
  • lines changed 7, context: html, text, full: html, text
    Taking edwFinishAnalysis out of UTIL_DIRS if we're on a Mac because XCode doesn't come with -luuid;it has to be obtained separately by using homebrew or macports etc. Also, Jim confirms that Mac
    users are extremely unlikely to need encodeDataWarehouse programs.
    
• src/hg/hgTracks/gencodeTracks.c
  • lines changed 0, context: html, text, full: html, text
    GENCODE V19 import
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 1, context: html, text, full: html, text
    code review corrections, refs #12418
• src/hg/htdocs/goldenPath/help/blatSpec.html
  • lines changed 4, context: html, text, full: html, text
    Trying to fix disappearing menubar. Works on dev but not beta. RM #12382.
• src/hg/htdocs/goldenPath/help/hgRegMotifHelp.html
  • lines changed 1, context: html, text, full: html, text
    Removing a confusing text line, code review refs #12429
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 7, context: html, text, full: html, text
    Fixed up format of Raney et al., per Matt code review.
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 5, context: html, text, full: html, text
    code review corrections, refs #12418
• src/hg/htdocs/goldenPath/help/trackDb/README.txt
  • lines changed 3, context: html, text, full: html, text
    adding trackDb documentation for the iframeUrl and iframeOptions trackDbstatements. Also adding an HTML helper page that is required for dynamic
    resizing of iframed pages. Sample HTML code is in the iframeOptions
    doc. (The dynamic resizing option is probably overkill, I guess very few
    users will need it. I got carried away and Mark asked for it a few
    months ago). Also adding a tiny README file for trackDbDoc editing,
    as I keep forgetting how the doc files are structured.
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 6, context: html, text, full: html, text
    adding trackDb documentation for the iframeUrl and iframeOptions trackDbstatements. Also adding an HTML helper page that is required for dynamic
    resizing of iframed pages. Sample HTML code is in the iframeOptions
    doc. (The dynamic resizing option is probably overkill, I guess very few
    users will need it. I got carried away and Mark asked for it a few
    months ago). Also adding a tiny README file for trackDbDoc editing,
    as I keep forgetting how the doc files are structured.
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html
  • lines changed 6, context: html, text, full: html, text
    adding trackDb documentation for the iframeUrl and iframeOptions trackDbstatements. Also adding an HTML helper page that is required for dynamic
    resizing of iframed pages. Sample HTML code is in the iframeOptions
    doc. (The dynamic resizing option is probably overkill, I guess very few
    users will need it. I got carried away and Mark asked for it a few
    months ago). Also adding a tiny README file for trackDbDoc editing,
    as I keep forgetting how the doc files are structured.
    
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 66, context: html, text, full: html, text
    adding trackDb documentation for the iframeUrl and iframeOptions trackDbstatements. Also adding an HTML helper page that is required for dynamic
    resizing of iframed pages. Sample HTML code is in the iframeOptions
    doc. (The dynamic resizing option is probably overkill, I guess very few
    users will need it. I got carried away and Mark asked for it a few
    months ago). Also adding a tiny README file for trackDbDoc editing,
    as I keep forgetting how the doc files are structured.
    
  • lines changed 1, context: html, text, full: html, text
    little clarification of the parent setting in trackDbDoc
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 14, context: html, text, full: html, text
    Added Braney pub on elephant shark, added PMID to 2013 Brennan citation.
• src/hg/htdocs/inc/iframeHelper.html
  • lines changed 31, context: html, text, full: html, text
    adding trackDb documentation for the iframeUrl and iframeOptions trackDbstatements. Also adding an HTML helper page that is required for dynamic
    resizing of iframed pages. Sample HTML code is in the iframeOptions
    doc. (The dynamic resizing option is probably overkill, I guess very few
    users will need it. I got carried away and Mark asked for it a few
    months ago). Also adding a tiny README file for trackDbDoc editing,
    as I keep forgetting how the doc files are structured.
    
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v294
• src/hg/js/hgTracks.js
  • lines changed 1, context: html, text, full: html, text
    Fixed hgTracks image track sorting bug reported in redmine #12455
• src/hg/js/utils.js
  • lines changed 1, context: html, text, full: html, text
    Fixed hgTracks image track sorting bug reported in redmine #12455
• src/hg/lib/bed.c
  • lines changed 2, context: html, text, full: html, text
    removed condition that always evaulates to false and generates warnings with LLVM cc
• src/hg/lib/pubsBingArticle.sql
  • lines changed 19, context: html, text, full: html, text
    adding field descriptions, rm #12212
• src/hg/lib/pubsBingBlat.sql
  • lines changed 21, context: html, text, full: html, text
    adding field descriptions, rm #12212
• src/hg/lib/pubsBingBlatPsl.sql
  • lines changed 28, context: html, text, full: html, text
    adding field descriptions, rm #12212
• src/hg/lib/pubsBingSequenceAnnot.sql
  • lines changed 15, context: html, text, full: html, text
    adding field descriptions, rm #12212
• src/hg/lib/tableList.sql
  • lines changed 5, context: html, text, full: html, text
    modifying table field names to kent style as suggested by angie, code review rm #12431
  • lines changed 1, context: html, text, full: html, text
    fixing one field name from a previous commit
• src/hg/makeDb/doc/bosTau7.txt
  • lines changed 12, context: html, text, full: html, text
    Starting loading of QTL tracks for 3 farm animals refs #10954
  • lines changed 6, context: html, text, full: html, text
    Adding entries for animal QTL tracks. refs #10954
• src/hg/makeDb/doc/galGal4.txt
  • lines changed 11, context: html, text, full: html, text
    Starting loading of QTL tracks for 3 farm animals refs #10954
  • lines changed 2, context: html, text, full: html, text
    Adding entry to make QTL track appear on chicken refs #10954
  • lines changed 6, context: html, text, full: html, text
    animalQtl reloading refs #10954
  • lines changed 5, context: html, text, full: html, text
    Adding entries for animal QTL tracks. refs #10954
• src/hg/makeDb/doc/hg19.txt
  • lines changed 26, context: html, text, full: html, text
    liftOver to hg38 done refs #11681
  • lines changed 53, context: html, text, full: html, text
    GENCODE V19 import
• src/hg/makeDb/doc/hg38.txt
  • lines changed 688, context: html, text, full: html, text
    up to date repeat masker procedures, trf simple repeats and genscan refs #11681
  • lines changed 9, context: html, text, full: html, text
    Adding entry for liftover of temporary cytoband data from hg19.
  • lines changed 83, context: html, text, full: html, text
    rerunning repeat masking refs #11682
  • lines changed 59, context: html, text, full: html, text
    adding par and centromere tracks refs #11681
  • lines changed 159, context: html, text, full: html, text
    the alternate/haplotype sequence lastz chain net psl track refs #11681
  • lines changed 90, context: html, text, full: html, text
    done with rmskHmmer and added hg38.contigs.2bit build refs #11681
  • lines changed 56, context: html, text, full: html, text
    add repeat masker analysis refs #11681
  • lines changed 98, context: html, text, full: html, text
    fixup gc5BaseBw bbi directory path, and running cpgIslands on contig sequence refs #11681
• src/hg/makeDb/doc/susScr3.txt
  • lines changed 11, context: html, text, full: html, text
    Starting loading of QTL tracks for 3 farm animals refs #10954
  • lines changed 5, context: html, text, full: html, text
    Adding entries for animal QTL tracks. refs #10954
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 25, context: html, text, full: html, text
    preparing for GRCh38/hg38 genbank run refs #11681
  • lines changed 1, context: html, text, full: html, text
    comment out ccds build for hg38
• src/hg/makeDb/genbank/src/ccds/createKeys.sql
  • lines changed 1, context: html, text, full: html, text
    CCDS added a new table
• src/hg/makeDb/genbank/src/ccds/createTables.sql
  • lines changed 14, context: html, text, full: html, text
    CCDS added a new table
  • lines changed 1, context: html, text, full: html, text
    oops, fix a syntax error
• src/hg/makeDb/genbank/src/ccds/ncbiSql/createKeys.sql
  • lines changed 10, context: html, text, full: html, text
    CCDS added a new table
• src/hg/makeDb/genbank/src/ccds/ncbiSql/createTables.sql
  • lines changed 13, context: html, text, full: html, text
    CCDS added a new table
• src/hg/makeDb/hgLoadOut/hgLoadOut.c
  • lines changed 7, context: html, text, full: html, text
    ignore the noSplit arguments to make it become the default refs #11681
• src/hg/makeDb/schema/all.joiner
  • lines changed 80, context: html, text, full: html, text
    GENCODE V19 import
• src/hg/makeDb/trackDb/animalQtl.html
  • lines changed 80, context: html, text, full: html, text
    Adding description page for QTL tracks. refs#10954
• src/hg/makeDb/trackDb/chicken/galGal4/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    Adding entries for animal QTL tracks. refs #10954
• src/hg/makeDb/trackDb/cow/bosTau7/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    Adding entries for animal QTL tracks. refs #10954
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 14, context: html, text, full: html, text
    Moved 5 repeats tracks to new repeats group. refs #12284
  • lines changed 4, context: html, text, full: html, text
    Resetting priorities to move pubs to top and impose alpha order for rest of tracks. refs #12362
  • lines changed 5, context: html, text, full: html, text
    Putting settings for new combined phen+lit group down at assembly level - see note 11 refs #12362
  • lines changed 3, context: html, text, full: html, text
    Removing unneccesary lines. refs #12425
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    GENCODE V19 import
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
  • lines changed 71, context: html, text, full: html, text
    GENCODE V19 import
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV18.ra
  • lines changed 17, context: html, text, full: html, text
    GENCODE V19 import
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV19.html
  • lines changed 342, context: html, text, full: html, text
    GENCODE V19 import
  • lines changed 1, context: html, text, full: html, text
    Changing PI foreign character name to fix display in GENCODE V19 html refs #12452
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV19.ra
  • lines changed 263, context: html, text, full: html, text
    GENCODE V19 import
• src/hg/makeDb/trackDb/human/hg38/altSequences.ra
  • lines changed 91, context: html, text, full: html, text
    adding alternate haplotype sequences chain net psl locations track refs #11681
• src/hg/makeDb/trackDb/human/hg38/centromeres.html
  • lines changed 6, context: html, text, full: html, text
    documentation for the centromere track refs #11681
• src/hg/makeDb/trackDb/human/hg38/rmskBlastn.html
  • lines changed 26, context: html, text, full: html, text
    update the featureBits and add the class summary refs #11681
• src/hg/makeDb/trackDb/human/hg38/rmskCM.html
  • lines changed 105, context: html, text, full: html, text
    adding RepeatMasker cross-match documentation refs #11681
  • lines changed 25, context: html, text, full: html, text
    add the class summary refs #11681
  • lines changed 0, context: html, text, full: html, text
    adding HMMER rmsk documentation refs #11681
• src/hg/makeDb/trackDb/human/hg38/rmskGenbank.html
  • lines changed 25, context: html, text, full: html, text
    add the class summary refs #11681
• src/hg/makeDb/trackDb/human/hg38/rmskHmmer.html
  • lines changed 127, context: html, text, full: html, text
    adding HMMER rmsk documentation refs #11681
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    move the rmsk experments to experimental track group refs #11681
  • lines changed 20, context: html, text, full: html, text
    adding alternate haplotype sequences chain net psl locations track refs #11681
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 14, context: html, text, full: html, text
    Resetting priorities to move pubs to top and impose alpha order for rest of tracks. refs #12362
• src/hg/makeDb/trackDb/pig/susScr3/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    Adding entries for animal QTL tracks. refs #10954
• src/hg/makeDb/trackDb/pubsBingBlat.html
  • lines changed 1, context: html, text, full: html, text
    Removing odd line break in the middle of the Display Convention and Configuration section
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Folding pubs track into combined phen+lit group. refs #12362
  • lines changed 1, context: html, text, full: html, text
    Resetting priorities to move pubs to top and impose alpha order for rest of tracks. refs #12362
  • lines changed 2, context: html, text, full: html, text
    Putting settings for new combined phen+lit group down at assembly level - see note 11 refs #12362
  • lines changed 10, context: html, text, full: html, text
    Adding entry to make QTL track appear on chicken refs #10954
  • lines changed 4, context: html, text, full: html, text
    add url to animalQtl refs #10954
  • lines changed 2, context: html, text, full: html, text
    Adding entries for animal QTL tracks. refs #10954
  • lines changed 3, context: html, text, full: html, text
    Updating coloring for animal QTL tracks, removing lines moved to lower level. refs #10954
  • lines changed 2, context: html, text, full: html, text
    moved animalQtl track to expression and regulation group and expanded longLabel to spell out QTL. refs 10954
  • lines changed 1, context: html, text, full: html, text
    moved animalQtl back to map group. refs #10954
• src/hg/utils/automation/doRepeatMasker.pl
  • lines changed 2, context: html, text, full: html, text
    need to use 32Gb and 4 CPU limits on HMMER refs #11681
• src/hg/utils/automation/makeGenomeDb.pl
  • lines changed 8, context: html, text, full: html, text
    new convention for location of bbi files, in bbi/tableName/... refs #11681
• src/hg/utils/makeTableList/makeTableList.c
  • lines changed 4, context: html, text, full: html, text
    modifying table field names to kent style as suggested by angie, code review rm #12431
  • lines changed 1, context: html, text, full: html, text
    fixing one field name from a previous commit
• src/hg/utils/phyloTrees/dbCommonScientificCladeOrderkey.tab
  • lines changed 14, context: html, text, full: html, text
    adding other genomes found on the RR for completeness refs #10272
• src/lib/bamFile.c
  • lines changed 1, context: html, text, full: html, text
    Changing warn to errAbort as suggested by Jonathan (since that is more consistent with how bamFileAndIndexMustExist works).refs #12401
    
• src/lib/vcf.c
  • lines changed 1, context: html, text, full: html, text
    Tolerate missing '=' in metadata line for VCF3 because as Jonathan pointed out, the spec didn't demand key=val in 3.3.refs #12412
    
  • lines changed 2, context: html, text, full: html, text
    Oops, as Jonathan pointed out, VCF 4.0 can still have meta-information lineswithout '='. fixes #12417
    
• src/parasol/parasol/parasol.c
  • lines changed 1, context: html, text, full: html, text
    oops, Jim accidentally removed the -dir option.
• src/product/scripts/kentSrcUpdate.sh
  • lines changed 15, context: html, text, full: html, text
    add directory safety checks as it starts refs #9104
• src/utils/bigWigCat/bigWigCat.c
  • lines changed 3, context: html, text, full: html, text
    Fixing usage message. Daniel was supposed to have already fixed this. Originally the utility was called mergeBigWig instead of bigWigCat. Also fixed capitalization problem for one function name that neede to start with lower-case letter.
  • lines changed 2, context: html, text, full: html, text
    bigWigCat - adding helpful information to the usage statement about creating the right input files.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v294 final build refs #12191

• lines changed: 3161
• files changed: 101