All File Changes

v305_base to v306_preview (2014-09-02 to 2014-09-08) v306

• src/hg/htdocs/ENCODE/dataMatrix/encodeChipMatrixHg18.html
  • lines changed 1, context: html, text, full: html, text
    Simplify and style ENCODE2 dates on DataMatrix pages. refs #13616
• src/hg/htdocs/ENCODE/dataMatrix/encodeChipMatrixHuman.html
  • lines changed 1, context: html, text, full: html, text
    Simplify and style ENCODE2 dates on DataMatrix pages. refs #13616
• src/hg/htdocs/ENCODE/dataMatrix/encodeChipMatrixInclude.html
  • lines changed 2, context: html, text, full: html, text
    Simplify and style ENCODE2 dates on DataMatrix pages. refs #13616
• src/hg/htdocs/ENCODE/dataMatrix/encodeChipMatrixMouse.html
  • lines changed 1, context: html, text, full: html, text
    Simplify and style ENCODE2 dates on DataMatrix pages. refs #13616
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixHg18.html
  • lines changed 3, context: html, text, full: html, text
    Simplify and style ENCODE2 dates on DataMatrix pages. refs #13616
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixHuman.html
  • lines changed 3, context: html, text, full: html, text
    Simplify and style ENCODE2 dates on DataMatrix pages. refs #13616
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixInclude.html
  • lines changed 2, context: html, text, full: html, text
    Simplify and style ENCODE2 dates on DataMatrix pages. refs #13616
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixMouse.html
  • lines changed 3, context: html, text, full: html, text
    Simplify and style ENCODE2 dates on DataMatrix pages. refs #13616
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataSummaryHuman.html
  • lines changed 1, context: html, text, full: html, text
    Simplify and style ENCODE2 dates on DataMatrix pages. refs #13616
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataSummaryInclude.html
  • lines changed 2, context: html, text, full: html, text
    Simplify and style ENCODE2 dates on DataMatrix pages. refs #13616
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataSummaryMouse.html
  • lines changed 1, context: html, text, full: html, text
    Simplify and style ENCODE2 dates on DataMatrix pages. refs #13616
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 23, context: html, text, full: html, text
    Making small corrections to Maxs additions. Also added links to gb store and gbib license. refs #12843
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 19, context: html, text, full: html, text
    Adding a new quick start guide for hubs to show groupings via multiWig, composite, and superTrack
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 4, context: html, text, full: html, text
    Adding a new quick start guide for hubs to show groupings via multiWig, composite, and superTrack
• src/hg/htdocs/goldenPath/help/hubQuickStart.html
  • lines changed 11, context: html, text, full: html, text
    Adding a new quick start guide for hubs to show groupings via multiWig, composite, and superTrack
  • lines changed 4, context: html, text, full: html, text
    Removing uneeded html markup from quick start hub pages per code review refs #13914
• src/hg/htdocs/goldenPath/help/hubQuickStartGroups.html
  • lines changed 233, context: html, text, full: html, text
    Adding a new quick start guide for hubs to show groupings via multiWig, composite, and superTrack
  • lines changed 4, context: html, text, full: html, text
    Removing uneeded html markup from quick start hub pages per code review refs #13914
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 2, context: html, text, full: html, text
    Adding a note about not having periods in tags when using subGroups in composites refs #13923
  • lines changed 1, context: html, text, full: html, text
    Changing bars to bar per users input about graphTypeDefault documentation refs #13941
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 28, context: html, text, full: html, text
    Adding announcements for FaceBase hub and track, refs #12607
  • lines changed 18, context: html, text, full: html, text
    Adding news about ENCODE website change and lowering ENCODE/Neandertal per Jim note80 refs #13616
• src/hg/htdocs/images/phylo/dm6_27way.png
  • lines changed 0, context: html, text, full: html, text
    27-way phylo tree for dm6 refs #4049
• src/hg/htdocs/index.html
  • lines changed 8, context: html, text, full: html, text
    Adding news about ENCODE website change and lowering ENCODE/Neandertal per Jim note80 refs #13616
• src/hg/htdocs/indexNews.html
  • lines changed 74, context: html, text, full: html, text
    Adding announcements for FaceBase hub and track, refs #12607
  • lines changed 71, context: html, text, full: html, text
    Adding news about ENCODE website change and lowering ENCODE/Neandertal per Jim note80 refs #13616
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    up the size of a buffer
• src/hg/makeDb/doc/bosTau8.txt
  • lines changed 154, context: html, text, full: html, text
    Added initial bosTau8 make doc; refs #13852
• src/hg/makeDb/doc/dm6.txt
  • lines changed 160, context: html, text, full: html, text
    lastz runs completed refs #4049
• src/hg/makeDb/doc/encode3/hg38_encode2_dnase1.txt
  • lines changed 166, context: html, text, full: html, text
    Adding info on dnaseI build for hg38
• src/hg/makeDb/doc/encodeRegHg19.txt
  • lines changed 27, context: html, text, full: html, text
    Fix filtering step, problem caught by QA, tnx Jonathan. refs #13490
• src/hg/makeDb/doc/hg38.txt
  • lines changed 76, context: html, text, full: html, text
    running up ponAbe2 for snp141 build refs #13309
  • lines changed 6, context: html, text, full: html, text
    finished lastz ponAbe2 for snp141 build refs #13309
  • lines changed 4, context: html, text, full: html, text
    Adding build reference to DNAse build instructions to main hg38 doc.
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 1, context: html, text, full: html, text
    no per chrom tables on dm6
• src/hg/makeDb/outside/uwDnaseTrackHub/makefile
  • lines changed 3, context: html, text, full: html, text
    Program to make a track hub out of UW DNAse I data seems to work.
• src/hg/makeDb/outside/uwDnaseTrackHub/uwDnaseTrackHub.c
  • lines changed 378, context: html, text, full: html, text
    Program to make a track hub out of UW DNAse I data seems to work.
• src/hg/makeDb/schema/all.joiner
  • lines changed 17, context: html, text, full: html, text
    Add joiner info. refs #13230
  • lines changed 5, context: html, text, full: html, text
    More schema linking for DNase tracks. refs #13490
  • lines changed 1, context: html, text, full: html, text
    Fix comment
• src/hg/makeDb/trackDb/drosophila/dm6/trackDb.27way.ra
  • lines changed 106, context: html, text, full: html, text
    27-way phylo tree added refs #4096
• src/hg/makeDb/trackDb/drosophila/dm6/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    27-way phylo tree added refs #4096
• src/hg/makeDb/trackDb/drosophila/droSec1/description.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on droSec1, loxAfr3, calJac3, and macEug2 gateway description pages
• src/hg/makeDb/trackDb/elephant/loxAfr3/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on droSec1, loxAfr3, calJac3, and macEug2 gateway description pages
• src/hg/makeDb/trackDb/fishClones.html
  • lines changed 11, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/fosEndPairs.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/cytoBand.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/gnfAtlas2.html
  • lines changed 10, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/gwasCatalog.html
  • lines changed 10, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/hg19/acembly.html
  • lines changed 7, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/hg19/cosmic.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/hg19/exoniphy.html
  • lines changed 23, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/human/hg19/trackDb.cacTest100way.ra
  • lines changed 243, context: html, text, full: html, text
    now displaying cactus 100-way alignment refs #11636
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    now displaying cactus 100-way alignment refs #11636
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgDnaseMasterSites.html
  • lines changed 2, context: html, text, full: html, text
    Fix broken links. refs #13230
• src/hg/makeDb/trackDb/human/ntHumChimpCodingDiff.html
  • lines changed 11, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/marmoset/calJac3/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on droSec1, loxAfr3, calJac3, and macEug2 gateway description pages
• src/hg/makeDb/trackDb/rockHyrax/proCap1/description.html
  • lines changed 2, context: html, text, full: html, text
    Changing links on Rock Hyrax (proCap1) track description pages
• src/hg/makeDb/trackDb/rockHyrax/proCap1/gap.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on Rock Hyrax (proCap1) track description pages
• src/hg/makeDb/trackDb/rockHyrax/proCap1/gold.html
  • lines changed 3, context: html, text, full: html, text
    Changing links on Rock Hyrax (proCap1) track description pages
• src/hg/makeDb/trackDb/snp135.shared.html
  • lines changed 5, context: html, text, full: html, text
    Changing links on human (hg19) track description pages
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 2, context: html, text, full: html, text
    sGroups for dm6 27-way refs #4049
• src/hg/makeDb/trackDb/wallaby/macEug2/description.html
  • lines changed 1, context: html, text, full: html, text
    Changing links on droSec1, loxAfr3, calJac3, and macEug2 gateway description pages
• src/hg/utils/automation/doBlastzChainNet.pl
  • lines changed 1, context: html, text, full: html, text
    do not want to fail on remaking md5sum.txt if the query is the only entry in that file to begin with refs #13300
• src/hg/utils/phyloTrees/dm6.27way.nh
  • lines changed 27, context: html, text, full: html, text
    first pass at 27-way tree refs #4049
• src/hg/utils/phyloTrees/dm6.27way.scientificNames.nh
  • lines changed 27, context: html, text, full: html, text
    first pass at 27-way tree refs #4049
• src/lib/hacTree.c
  • lines changed 1, context: html, text, full: html, text
    Fixed typo in comment.
• src/oneShot/bigWigCluster/bigWigCluster.c
  • lines changed 399, context: html, text, full: html, text
    Removing code that has been moved out of one shot and into production
• src/oneShot/bigWigCluster/makefile
  • lines changed 3, context: html, text, full: html, text
    Removing code that has been moved out of one shot and into production
• src/oneShot/hacTreeTest/hacTreeTest.c
  • lines changed 5, context: html, text, full: html, text
    Updating tests
• src/oneShot/hacTreeTest/testIt
  • lines changed 2, context: html, text, full: html, text
    Updating tests
• src/utils/bedToBigBed/bedToBigBed.c
  • lines changed 1, context: html, text, full: html, text
    fix a crashing bug when the user requests an extraIndex on a field thatdoesn't exist #13928
    
• src/utils/bigWigCluster/bigWigCluster.c
  • lines changed 9, context: html, text, full: html, text
    Making tmp dir a command line option. Adding id to merged wigs, which will keep temp files from clashing better (oops).
• src/utils/qa/copyHgcentral
  • lines changed 18, context: html, text, full: html, text
    Changed the way the organism name is retrieved. Now obtained from dbDb.organism field instead of chopping number from assembly name and obtaining from defaultDb.genome. This addresses a rare issue where calMil0 and calMil1 have different values for the organism name; refs #13121
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v306 preview1 refs #13954

• lines changed: 2474
• files changed: 75