All File Changes

v277_preview2 to v277_base (2012-12-11 to 2012-12-18) v277

• confs/hgwbeta.hg.conf
  • lines changed 113, context: html, text, full: html, text
    added hgwbeta's hg.conf to kent tree #8303
• confs/hgwdev.hg.conf
  • lines changed 269, context: html, text, full: html, text
    add hgwdev hg.conf to kent tree. #8383
• src/hg/hgc/gencodeClick.c
  • lines changed 2, context: html, text, full: html, text
    APPRIS gene and transcript links were reversed
• src/hg/htdocs/FAQ/FAQtracks.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken links reported by static page link checker.
• src/hg/htdocs/cite.html
  • lines changed 17, context: html, text, full: html, text
    replaced previous years NAR papers with next years (GB and ENCODE)
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 38, context: html, text, full: html, text
    Fixed broken links reported by static page link checker.
• src/hg/htdocs/goldenPath/help/customTrackManage.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken links reported by static page link checker.
• src/hg/htdocs/goldenPath/help/cutters.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken links reported by static page link checker.
• src/hg/htdocs/goldenPath/help/hgTablesHelp.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken links reported by static page link checker.
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken links reported by static page link checker.
• src/hg/htdocs/goldenPath/help/index.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken links reported by static page link checker.
• src/hg/htdocs/goldenPath/help/oligoMatch.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken links reported by static page link checker.
• src/hg/htdocs/goldenPath/labs.html
  • lines changed 5, context: html, text, full: html, text
    Fixed broken links reported by static page link checker.
• src/hg/htdocs/goldenPath/mapPlots/arch.html
  • lines changed 133, context: html, text, full: html, text
    Converted these files into redirects to the real files on genome-archive.
• src/hg/htdocs/goldenPath/mapPlots/cytoguide.html
  • lines changed 89, context: html, text, full: html, text
    Converted these files into redirects to the real files on genome-archive.
• src/hg/htdocs/goldenPath/mapPlots/cytoprogram.html
  • lines changed 74, context: html, text, full: html, text
    Converted these files into redirects to the real files on genome-archive.
• src/hg/htdocs/goldenPath/mapPlots/index.html
  • lines changed 125, context: html, text, full: html, text
    Converted these files into redirects to the real files on genome-archive.
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 15, context: html, text, full: html, text
    added news about campus curtailment
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 2, context: html, text, full: html, text
    Fixed broken links reported by static page link checker.
• src/hg/htdocs/indexNews.html
  • lines changed 15, context: html, text, full: html, text
    added news about campus curtailment
• src/hg/inc/annoGrateWig.h
  • lines changed 11, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): added annoStreamBigWigand moved up annoGrateWig from hg/lib to lib. Tested with comparison
    to hgTables intersection, bitwise. Output is not identical because
    hgTables merges adjacent bases and splits on value changes, while
    annoGrator prints original item and comma-sep list of per-base values.
    
• src/hg/inc/annoGrateWigDb.h
  • lines changed 11, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): added annoStreamBigWigand moved up annoGrateWig from hg/lib to lib. Tested with comparison
    to hgTables intersection, bitwise. Output is not identical because
    hgTables merges adjacent bases and splits on value changes, while
    annoGrator prints original item and comma-sep list of per-base values.
    
• src/hg/inc/exonJunctionPrimers.h
  • lines changed 70, context: html, text, full: html, text
    Track #9269 ExonJunction Primers displayed as a bedDetail track.
• src/hg/inc/hubConnect.h
  • lines changed 3, context: html, text, full: html, text
    re-try a hub with an error message after a hg.conf configurable amount of time has passed (#9666)
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v277
• src/hg/lib/annoGrateWig.c
  • lines changed 79, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): added annoStreamBigWigand moved up annoGrateWig from hg/lib to lib. Tested with comparison
    to hgTables intersection, bitwise. Output is not identical because
    hgTables merges adjacent bases and splits on value changes, while
    annoGrator prints original item and comma-sep list of per-base values.
    
• src/hg/lib/annoGrateWigDb.c
  • lines changed 12, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): added annoStreamBigWigand moved up annoGrateWig from hg/lib to lib. Tested with comparison
    to hgTables intersection, bitwise. Output is not identical because
    hgTables merges adjacent bases and splits on value changes, while
    annoGrator prints original item and comma-sep list of per-base values.
    
• src/hg/lib/exonJunctionPrimers.as
  • lines changed 18, context: html, text, full: html, text
    Track #9269 ExonJunction Primers displayed as a bedDetail track.
• src/hg/lib/exonJunctionPrimers.c
  • lines changed 218, context: html, text, full: html, text
    Track #9269 ExonJunction Primers displayed as a bedDetail track.
• src/hg/lib/exonJunctionPrimers.sql
  • lines changed 24, context: html, text, full: html, text
    Track #9269 ExonJunction Primers displayed as a bedDetail track.
• src/hg/lib/hubConnect.c
  • lines changed 19, context: html, text, full: html, text
    re-try a hub with an error message after a hg.conf configurable amount of time has passed (#9666)
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Track #9269 ExonJunction Primers displayed as a bedDetail track.
  • lines changed 1, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): added annoStreamBigWigand moved up annoGrateWig from hg/lib to lib. Tested with comparison
    to hgTables intersection, bitwise. Output is not identical because
    hgTables merges adjacent bases and splits on value changes, while
    annoGrator prints original item and comma-sep list of per-base values.
    
• src/hg/lib/tests/annoGratorTester.c
  • lines changed 21, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): added annoStreamBigWigand moved up annoGrateWig from hg/lib to lib. Tested with comparison
    to hgTables intersection, bitwise. Output is not identical because
    hgTables merges adjacent bases and splits on value changes, while
    annoGrator prints original item and comma-sep list of per-base values.
    
• src/hg/lib/tests/annoGratorTests.mk
  • lines changed 5, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): added annoStreamBigWigand moved up annoGrateWig from hg/lib to lib. Tested with comparison
    to hgTables intersection, bitwise. Output is not identical because
    hgTables merges adjacent bases and splits on value changes, while
    annoGrator prints original item and comma-sep list of per-base values.
    
• src/hg/lib/tests/expected/annoGrator/snpBigWigToTabOut.txt
  • lines changed 304, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): added annoStreamBigWigand moved up annoGrateWig from hg/lib to lib. Tested with comparison
    to hgTables intersection, bitwise. Output is not identical because
    hgTables merges adjacent bases and splits on value changes, while
    annoGrator prints original item and comma-sep list of per-base values.
    
• src/hg/lib/tests/expected/annoGrator/snpConsDbToTabOutShort.txt
  • lines changed 12, context: html, text, full: html, text
    annoFormatTab: use %g instead of %f for floats, for consistency with bigWig output.
• src/hg/lib/wigAsciiToBinary.c
  • lines changed 1, context: html, text, full: html, text
    improve too much data message during custom track loading
• src/hg/makeDb/doc/hg18.txt
  • lines changed 4, context: html, text, full: html, text
    Track #1656: GWAS Catalog bi-monthly update.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 48, context: html, text, full: html, text
    Track #1656: GWAS Catalog bi-monthly update.
  • lines changed 66, context: html, text, full: html, text
    gencode V14 load
  • lines changed 16, context: html, text, full: html, text
    Initial Track #9269 ExonJunction Primers works for mm10 and hg19.
• src/hg/makeDb/doc/mm10.txt
  • lines changed 22, context: html, text, full: html, text
    Initial Track #9269 ExonJunction Primers works for mm10 and hg19.
• src/hg/makeDb/doc/proteins/121210.txt
  • lines changed 560, context: html, text, full: html, text
    got up to pfam part, pruned a bunch of stuff we don't need to do anymore
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes14.csh
  • lines changed 29, context: html, text, full: html, text
    moving right along (#9783)
• src/hg/makeDb/doc/uniProt/sp121210.txt
  • lines changed 11, context: html, text, full: html, text
    finished this
• src/hg/makeDb/schema/all.joiner
  • lines changed 80, context: html, text, full: html, text
    gencode V14 load
• src/hg/makeDb/trackDb/cv/alpha/.#cv.ra
  • lines changed 1, context: html, text, full: html, text
    Adding affinity purified to CEBPZ, and full manuf website to CELF1 antibody, clean cv.ra project
  • lines changed 1, context: html, text, full: html, text
    Adding details about catalogue to CELF1, lowercasing CBX8 description, adding affinity purfied to CHD1 and COREST CREB1, removing RNA-seq from FLI1
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 2, context: html, text, full: html, text
    Adding affinity purified to CEBPZ, and full manuf website to CELF1 antibody, clean cv.ra project
  • lines changed 6, context: html, text, full: html, text
    Adding details about catalogue to CELF1, lowercasing CBX8 description, adding affinity purfied to CHD1 and COREST CREB1, removing RNA-seq from FLI1
  • lines changed 33, context: html, text, full: html, text
    Changing all MassSpec to IP-MassSpec and Co-occupancy to Correlation for antibody clean up
  • lines changed 6, context: html, text, full: html, text
    Adding purified info for antibodies and for _EBF1_ removing IP-Mass Spec as not in validation document
  • lines changed 10, context: html, text, full: html, text
    Adding antibody information, affinity purified, lot numbers as cleaning up cv.ra
  • lines changed 13, context: html, text, full: html, text
    Adding antibody purification and validation information and lot number
  • lines changed 6, context: html, text, full: html, text
    Adding lot info, purified info, and manuf# to file name for antibodies
  • lines changed 7, context: html, text, full: html, text
    Adding purified and correcting validation methods to western blot matching our pdf documents
  • lines changed 16, context: html, text, full: html, text
    Adding changes to cv.ra for lot# and antibody corrections to coordinate validation document pdf with metaData
  • lines changed 17, context: html, text, full: html, text
    Adding information to antibodies such as affinity purified, full lot# such as ZIJ0107031, and correcting other details, such as adding note about typos in validation documents.
  • lines changed 20, context: html, text, full: html, text
    Adding antibody information from lots to affinity purified and correct validation method
  • lines changed 24, context: html, text, full: html, text
    Adding changes to antibody information from lots to purified method
  • lines changed 39, context: html, text, full: html, text
    Adding antibody information from lots to affinity purificaiton information to correcting validation method (Western_blot vs ChIP-seq) for example
  • lines changed 1, context: html, text, full: html, text
    Adding correct validation information for FLI1
  • lines changed 3, context: html, text, full: html, text
    Adding santra cruz number to antibodies
  • lines changed 1, context: html, text, full: html, text
    Correcting error, wrote lot rather than lots, for field information for PAX5-C20 antibody
  • lines changed 48, context: html, text, full: html, text
    adding heart and liver samples from ENCODE 2 extension data
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 203, context: html, text, full: html, text
    Copying alpha/cv.ra to beta/cv.ra -antibody changes, lot info, validation docucument checks
  • lines changed 1, context: html, text, full: html, text
    Copying alpha/cv.ra to beta/cv.ra: Correcting error, wrote lot rather than lots, for field information for PAX5-C20 antibody
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 96, context: html, text, full: html, text
    moving beta to public after review
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    remove nextItemButton option for retroTrack per markd
  • lines changed 1, context: html, text, full: html, text
    set retroposon track to hide by default
  • lines changed 12, context: html, text, full: html, text
    Initial Track #9269 ExonJunction Primers works for mm10 and hg19.
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    gencode V14 load
  • lines changed 3, context: html, text, full: html, text
    Takeing out the HAIB WGBS track per Flo request and adding back the version 2 of the UChicago page
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV13.html
  • lines changed 2, context: html, text, full: html, text
    gencode V14 load
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV14.html
  • lines changed 343, context: html, text, full: html, text
    gencode V14 load
  • lines changed 7, context: html, text, full: html, text
    disconnect gencode V14 from encode metadata and downloads, its a normal track now
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV14.ra
  • lines changed 222, context: html, text, full: html, text
    gencode V14 load
  • lines changed 1, context: html, text, full: html, text
    disconnect gencode V14 from encode metadata and downloads, its a normal track now
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSuper.release2.ra
  • lines changed 1, context: html, text, full: html, text
    disconnect gencode V14 from encode metadata and downloads, its a normal track now
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 11, context: html, text, full: html, text
    Initial Track #9269 ExonJunction Primers works for mm10 and hg19.
• src/hg/makeDb/trackDb/mouse/mm8/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    remove nextItemButton option for retroTrack per markd
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    remove nextItemButton option for retroTrack per markd
• src/hg/makeDb/trackDb/zebrafish/danRer7/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Per Ann, changed visibility setting of UMass ChIP-Seq track to hide
• src/inc/annoGrateWig.h
  • lines changed 14, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): added annoStreamBigWigand moved up annoGrateWig from hg/lib to lib. Tested with comparison
    to hgTables intersection, bitwise. Output is not identical because
    hgTables merges adjacent bases and splits on value changes, while
    annoGrator prints original item and comma-sep list of per-base values.
    
• src/inc/annoStreamBigBed.h
  • lines changed 1, context: html, text, full: html, text
    typo fix in comment
• src/inc/annoStreamBigWig.h
  • lines changed 11, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): added annoStreamBigWigand moved up annoGrateWig from hg/lib to lib. Tested with comparison
    to hgTables intersection, bitwise. Output is not identical because
    hgTables merges adjacent bases and splits on value changes, while
    annoGrator prints original item and comma-sep list of per-base values.
    
• src/inc/bbiFile.h
  • lines changed 1, context: html, text, full: html, text
    Added #include <localmem.h> in case some earlier-included file hasn't already done so.
• src/inc/common.h
  • lines changed 3, context: html, text, full: html, text
    re-try a hub with an error message after a hg.conf configurable amount of time has passed (#9666)
• src/lib/annoFormatTab.c
  • lines changed 1, context: html, text, full: html, text
    annoFormatTab: use %g instead of %f for floats, for consistency with bigWig output.
• src/lib/annoGrateWig.c
  • lines changed 87, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): added annoStreamBigWigand moved up annoGrateWig from hg/lib to lib. Tested with comparison
    to hgTables intersection, bitwise. Output is not identical because
    hgTables merges adjacent bases and splits on value changes, while
    annoGrator prints original item and comma-sep list of per-base values.
    
• src/lib/annoStreamBigBed.c
  • lines changed 2, context: html, text, full: html, text
    minor: needed to reset one more private variable when region changes.
• src/lib/annoStreamBigWig.c
  • lines changed 133, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): added annoStreamBigWigand moved up annoGrateWig from hg/lib to lib. Tested with comparison
    to hgTables intersection, bitwise. Output is not identical because
    hgTables merges adjacent bases and splits on value changes, while
    annoGrator prints original item and comma-sep list of per-base values.
    
• src/lib/common.c
  • lines changed 8, context: html, text, full: html, text
    re-try a hub with an error message after a hg.conf configurable amount of time has passed (#9666)
• src/lib/makefile
  • lines changed 2, context: html, text, full: html, text
    Feature #6152 (Variant Annotation Integrator): added annoStreamBigWigand moved up annoGrateWig from hg/lib to lib. Tested with comparison
    to hgTables intersection, bitwise. Output is not identical because
    hgTables merges adjacent bases and splits on value changes, while
    annoGrator prints original item and comma-sep list of per-base values.
    
• src/product/ex.hg.conf
  • lines changed 3, context: html, text, full: html, text
    re-try a hub with an error message after a hg.conf configurable amount of time has passed (#9666)
• src/utils/qa/checkAllStaticLinks.csh
  • lines changed 6, context: html, text, full: html, text
    added some logic to get the link name for each url and provision for backup in genecats when running script more than once in a day. still needs some work.
  • lines changed 2, context: html, text, full: html, text
    cleaning up formatting and grammar a bit
  • lines changed 4, context: html, text, full: html, text
    moved some output outside an if-statemenet
• src/utils/qa/checkStaticLinks.csh
  • lines changed 66, context: html, text, full: html, text
    added some logic to get the link name for each url and provision for backup in genecats when running script more than once in a day. still needs some work.
  • lines changed 2, context: html, text, full: html, text
    removed the -q flag from a grep. It was =too= quiet, allowing nothing to get through
  • lines changed 17, context: html, text, full: html, text
    cleaning up formatting and grammar a bit
  • lines changed 4, context: html, text, full: html, text
    cleaned up output logic a bit and added another exception
  • lines changed 1, context: html, text, full: html, text
    removed a line that ignores extra levels of .. (up a dir)
• src/utils/qa/checkTrackUiLinks.csh
  • lines changed 22, context: html, text, full: html, text
    Made changes suggested by Brooke in code review (redmine #9723)
• src/utils/qa/findBigFiles.csh
  • lines changed 22, context: html, text, full: html, text
    changed so it will do current dir as well as whole tree from here down
• src/utils/qa/makefile
  • lines changed 1, context: html, text, full: html, text
    added script for finding last commit on a file
• src/utils/qa/showLastGit.csh
  • lines changed 25, context: html, text, full: html, text
    added script for finding last commit on a file
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v277 final build
• src/utils/qa/whoMadeIt.csh
  • lines changed 46, context: html, text, full: html, text
    added totaling for whole directory

• lines changed: 4201
• files changed: 110