All File Changes

v275_preview to v275_preview2 (2012-10-16 to 2012-10-23) v275

• src/hg/geneBounds/estLibStats/makefile
  • lines changed 1, context: html, text, full: html, text
    rearrange -lm to be after mysqllibs redmine 9101
• src/hg/hgCustom/hgCustom.c
  • lines changed 2, context: html, text, full: html, text
    Adding links to broadPeak and narrowPeak on hgCustom CGI since they are acceptable formats RM 9286, MLQ 9283
• src/hg/htdocs/ENCODE/analysisTools.html
  • lines changed 15, context: html, text, full: html, text
    Incorporated changes requested by Mike Pazin (redmine #9316)
• src/hg/htdocs/ENCODE/experiment_guidelines.html
  • lines changed 8, context: html, text, full: html, text
    Incorporated changes requested by Mike Pazin (redmine #9316)
• src/hg/htdocs/ENCODE/pubs.html
  • lines changed 3, context: html, text, full: html, text
    Incorporated changes requested by Mike Pazin (redmine #9316)
• src/hg/htdocs/ENCODE/pubsEncode.html
  • lines changed 3286, context: html, text, full: html, text
    Incorporated changes requested by Mike Pazin (redmine #9316)
• src/hg/htdocs/ENCODE/pubsOther.html
  • lines changed 1026, context: html, text, full: html, text
    Incorporated changes requested by Mike Pazin (redmine #9316)
• src/hg/htdocs/ENCODE/qualityMetrics.html
  • lines changed 44, context: html, text, full: html, text
    Incorporated changes requested by Mike Pazin (redmine #9316)
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 15, context: html, text, full: html, text
    Adding custom track and FAQformat information for broadPeak and narrowPeak which require track type= attribute to display RM# 9286
• src/hg/htdocs/goldenPath/help/customTrackLoad.html
  • lines changed 4, context: html, text, full: html, text
    Adding custom track and FAQformat information for broadPeak and narrowPeak which require track type= attribute to display RM# 9286
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 1, context: html, text, full: html, text
    Added an apostrophe.
  • lines changed 27, context: html, text, full: html, text
    Adding custom track and FAQformat information for broadPeak and narrowPeak which require track type= attribute to display RM# 9286
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 1, context: html, text, full: html, text
    fixed misspelling pointed out by a user
• src/hg/htdocs/indexNews.html
  • lines changed 1, context: html, text, full: html, text
    fixed misspelling pointed out by a user
• src/hg/lib/customTrack.c
  • lines changed 8, context: html, text, full: html, text
    fix for #9390 - tolerating url-encoded urls when detecting file compression type
• src/hg/lib/hubConnect.c
  • lines changed 6, context: html, text, full: html, text
    output error message ( and set them in hub status) when there are errors in hub.txt or genome.txt (#8848)
  • lines changed 3, context: html, text, full: html, text
    oops... a little error in my last commit to fix error messages on problems in genome.txt and hub.txt (#8848)
• src/hg/makeDb/doc/allMis1.txt
  • lines changed 367, context: html, text, full: html, text
    trying to get a unique RM library from Robert Hubley
• src/hg/makeDb/doc/blastTab.txt
  • lines changed 399, context: html, text, full: html, text
    drBlastTab reload for danRer7 Ensembl update
• src/hg/makeDb/doc/braFlo2.txt
  • lines changed 418, context: html, text, full: html, text
    starting new Lancelet assembly v2.0
  • lines changed 82, context: html, text, full: html, text
    running genbank
  • lines changed 46, context: html, text, full: html, text
    done with genbank alignments
  • lines changed 24, context: html, text, full: html, text
    lastz Lamprey <-> Lancelet
• src/hg/makeDb/doc/cerSim1.txt
  • lines changed 7, context: html, text, full: html, text
    ready for default position and pushQ entry
• src/hg/makeDb/doc/hg19.txt
  • lines changed 137, context: html, text, full: html, text
    running lastz for petMar2 and cerSim1
• src/hg/makeDb/doc/mm10.txt
  • lines changed 29, context: html, text, full: html, text
    adding cytoband tables for Chromosome Band track
  • lines changed 6, context: html, text, full: html, text
    better generic location for these ideogram files
• src/hg/makeDb/doc/petMar1.txt
  • lines changed 19, context: html, text, full: html, text
    petMar2 liftOver constructed and blanks at ends of lines removed
• src/hg/makeDb/doc/petMar2.txt
  • lines changed 194, context: html, text, full: html, text
    resolve GIT conflict
  • lines changed 46, context: html, text, full: html, text
    lastz Lamprey <-> Lancelet
• src/hg/makeDb/doc/rheMac3.txt
  • lines changed 188, context: html, text, full: html, text
    Finished genscan tracks and ctgPos2.html for rheMac3.
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    adding petMar2
  • lines changed 1, context: html, text, full: html, text
    Added braFlo2.
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 17, context: html, text, full: html, text
    adding petMar2 Lamprey redmine 9153
  • lines changed 17, context: html, text, full: html, text
    adding braFlo2 - Lancelet - Branchiostoma floridae
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    adding petMar2
  • lines changed 1, context: html, text, full: html, text
    Added braFlo2.
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 1, context: html, text, full: html, text
    adding additional Lancelet names for Branchiostoma
• src/hg/makeDb/hgGcPercent/makefile
  • lines changed 8, context: html, text, full: html, text
    adding hgGcPercent to the userApps delivery
• src/hg/makeDb/schema/all.joiner
  • lines changed 31, context: html, text, full: html, text
    adding cerSim1 and petMar2 completely clean
  • lines changed 1, context: html, text, full: html, text
    do not need to check refLink with kgProtAlias on dm3
• src/hg/makeDb/trackDb/birds/melUnd1/trackDb.chainNet.ra
  • lines changed 1, context: html, text, full: html, text
    Added chainNet overrides to match getChainLines.csh and getMatrixLines.csh output.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 5, context: html, text, full: html, text
    Adding labels to some cell lines so the underscores that are space holders are not present
  • lines changed 13, context: html, text, full: html, text
    Adding the Human_-_ where missing and fixing the space in the Negative Control
  • lines changed 20, context: html, text, full: html, text
    Filling in missing validation lines. Removing the term that has no validation but is not used
  • lines changed 1, context: html, text, full: html, text
    Trying to indicate that a file is really for mouse
  • lines changed 3, context: html, text, full: html, text
    Correcting Typos for Antibody, moving antibody file for mouse BHLHE40 to correct BHLHE40 (NB100-1800)
  • lines changed 125, context: html, text, full: html, text
    More validation name standardizations
  • lines changed 1, context: html, text, full: html, text
    Adding a period at the end of targetDescription for KAP1
  • lines changed 3, context: html, text, full: html, text
    Adding a period at the end of targetDescription for three antibodies.
  • lines changed 4, context: html, text, full: html, text
    Fixing errors found in http://redmine.soe.ucsc.edu/issues/9305#note-10
  • lines changed 14, context: html, text, full: html, text
    Fixing merge conflict
  • lines changed 47, context: html, text, full: html, text
    Adding the validation methods for the missing one. Changed SC to sc
  • lines changed 1, context: html, text, full: html, text
    Adding parenthesis around SC-66884, and making it lowercase
  • lines changed 1, context: html, text, full: html, text
    Changing filename to mouse from human to match data, RM#9159, note#20
  • lines changed 8, context: html, text, full: html, text
    Changing file name to have correct lab, from Epstein to Bernstein
  • lines changed 3, context: html, text, full: html, text
    Adding lab Crawford missing from validation for c-Myc, direcing AP-2 gamma to correct validation, removing . from name for PU.1 to become PU1
  • lines changed 7, context: html, text, full: html, text
    Adding lot info from validation dock, adding affinity purified from val-doc, updating html link for sc-81188, updating file name too.
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 33, context: html, text, full: html, text
    Copying alpha/cv.ra to beta/cv.ra, changes to labels, unifying antibody targets and descriptions
  • lines changed 1, context: html, text, full: html, text
    Shortening URL length, Code Review 9369
  • lines changed 187, context: html, text, full: html, text
    copying alpha/cv.ra to beta/cv.ra, steps to unify validation line, lowercasing SC to sc-Antibody and ChIP to all ChIP-seq, ect.
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 287, context: html, text, full: html, text
    moving beta to public, the issues were small enough that they will be gotten next week
• src/hg/makeDb/trackDb/gadMor/trackDb.chainNet.ra
  • lines changed 4, context: html, text, full: html, text
    Added chainNet overrides to match getChainLines.csh and getMatrixLines.csh output.
• src/hg/makeDb/trackDb/gadMor/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Added chainNet overrides to match getChainLines.csh and getMatrixLines.csh output.
• src/hg/makeDb/trackDb/gibbon/nomLeu1/description.html
  • lines changed 1, context: html, text, full: html, text
    Updated photo links
• src/hg/makeDb/trackDb/gibbon/nomLeu2/description.html
  • lines changed 1, context: html, text, full: html, text
    Updated photo links
• src/hg/makeDb/trackDb/guineaPig/cavPor3/description.html
  • lines changed 1, context: html, text, full: html, text
    Updated photo links
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeq.html
  • lines changed 5, context: html, text, full: html, text
    Changing Pol2(b) to be Pol2 as it is really POLR2A target
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeq.new.ra
  • lines changed 1405, context: html, text, full: html, text
    This file is not used anymore
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeq.ra
  • lines changed 19, context: html, text, full: html, text
    Changing Pol2(b) to be Pol2 as it is really POLR2A target
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeqRelease2.html
  • lines changed 142, context: html, text, full: html, text
    more files that are not being used
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeqRelease3original.html
  • lines changed 128, context: html, text, full: html, text
    more files that are not being used
• src/hg/makeDb/trackDb/human/hg19/trackDb.denisova.ra
  • lines changed 4, context: html, text, full: html, text
    Track #8886: shortening too-long longLabels for dhcHumDerDenAnc.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release3.html
  • lines changed 1, context: html, text, full: html, text
    Changing Pol2(b) to be Pol2 as it is really POLR2A target
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release3.ra
  • lines changed 24, context: html, text, full: html, text
    Changing Pol2(b) to be Pol2 as it is really POLR2A target
• src/hg/makeDb/trackDb/lancelet/braFlo2/description.html
  • lines changed 63, context: html, text, full: html, text
    adding Lancelet v2.0 braFlo2 to the build
• src/hg/makeDb/trackDb/lancelet/braFlo2/gap.html
  • lines changed 31, context: html, text, full: html, text
    adding Lancelet v2.0 braFlo2 to the build
• src/hg/makeDb/trackDb/lancelet/braFlo2/gold.html
  • lines changed 34, context: html, text, full: html, text
    adding Lancelet v2.0 braFlo2 to the build
• src/hg/makeDb/trackDb/lancelet/braFlo2/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    adding Lancelet v2.0 braFlo2 to the build
• src/hg/makeDb/trackDb/latCha/trackDb.chainNet.ra
  • lines changed 4, context: html, text, full: html, text
    Added chainNet overrides to match getChainLines.csh and getMatrixLines.csh output.
• src/hg/makeDb/trackDb/latCha/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Added chainNet overrides to match getChainLines.csh and getMatrixLines.csh output.
• src/hg/makeDb/trackDb/lizard/anoCar1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    override for quality table maximum limit
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding petMar2 to the build
  • lines changed 1, context: html, text, full: html, text
    adding Lancelet v2.0 braFlo2 to the build
• src/hg/makeDb/trackDb/mouse/mm10/cons60way.html
  • lines changed 3, context: html, text, full: html, text
    In table 2, moved mouse to UCSC Genes section, and changed Ensembl version to v68. Redmine #8876, note-18 and note-24/note-25.
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.euarchontoglireChainNet.ra
  • lines changed 242, context: html, text, full: html, text
    renaming primatesChainNet to euarchontoglireChainNet
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.gliresChainNet.ra
  • lines changed 17, context: html, text, full: html, text
    renaming primatesChainNet to euarchontoglireChainNet
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.primatesChainNet.ra
  • lines changed 226, context: html, text, full: html, text
    renaming primatesChainNet to euarchontoglireChainNet
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    renaming primatesChainNet to euarchontoglireChainNet
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeLicrTfbs.ra
  • lines changed 154, context: html, text, full: html, text
    Dropping metaData for Cricket for files Brooke discovered out-of-sync with RR and beta
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeLicrTfbs.ra
  • lines changed 154, context: html, text, full: html, text
    Dropping metaData for Cricket for files Brooke discovered out-of-sync with RR and beta
• src/hg/makeDb/trackDb/rhesus/rheMac3/ctgPos2.html
  • lines changed 3, context: html, text, full: html, text
    Finished genscan tracks and ctgPos2.html for rheMac3.
• src/hg/makeDb/trackDb/turkey/melGal1/description.html
  • lines changed 2, context: html, text, full: html, text
    Updated photo links
• src/hg/makeDb/trackDb/worm/cb1/description.html
  • lines changed 1, context: html, text, full: html, text
    Updated photo link
• src/hg/makefile
  • lines changed 3, context: html, text, full: html, text
    Arrange hgLogin according to alphabetical order in BROWSER_BINS= list.
• src/hg/pslToBed/tests/expected/doTest2.bed
  • lines changed 11713, context: html, text, full: html, text
    fix expected test output of pslToBed to expect cdsStart to be txStart if cdsEnd = cdsStart. This is what the browser wants. It ignores values of cdsStart outside of the range txStart..txEnd. (#7045)
• src/hg/utils/automation/configFiles/cerSim1.config.ra
  • lines changed 23, context: html, text, full: html, text
    adding recent new assemblies, rhino, chinchilla, lamprey
• src/hg/utils/automation/configFiles/chiLan1.config.ra
  • lines changed 23, context: html, text, full: html, text
    adding recent new assemblies, rhino, chinchilla, lamprey
• src/hg/utils/automation/configFiles/petMar2.config.ra
  • lines changed 23, context: html, text, full: html, text
    adding recent new assemblies, rhino, chinchilla, lamprey
• src/hg/utils/automation/configFiles/rn5.config.ra
  • lines changed 1, context: html, text, full: html, text
    corrected ncbiAssemblyId
• src/hg/utils/bedExtendRanges/makefile
  • lines changed 6, context: html, text, full: html, text
    adding bedExtendRanges and makeTableList to the build
• src/hg/utils/gff3ToGenePred/gff3ToGenePred.c
  • lines changed 1, context: html, text, full: html, text
    Corrected typo in usage statement.
• src/hg/utils/makefile
  • lines changed 2, context: html, text, full: html, text
    adding bedExtendRanges and makeTableList to the build
• src/inc/common.mk
  • lines changed 35, context: html, text, full: html, text
    Feature #6336 (redistribution of samtools + tabix + KNETFILE_HOOKS patches):I made a combined, pre-patched package on github:
    https://github.com/AngieHinrichs/samtabix
    and modified common.mk to autodetect the /hive installation and use samtabix
    preferentially to separate installations of samtools and tabix.
    linefile.c is keeping some patch-specific function aliases for backwards
    compatibility with tabix.
    
• src/lib/linefile.c
  • lines changed 6, context: html, text, full: html, text
    Feature #6336 (redistribution of samtools + tabix + KNETFILE_HOOKS patches):I made a combined, pre-patched package on github:
    https://github.com/AngieHinrichs/samtabix
    and modified common.mk to autodetect the /hive installation and use samtabix
    preferentially to separate installations of samtools and tabix.
    linefile.c is keeping some patch-specific function aliases for backwards
    compatibility with tabix.
    
  • lines changed 20, context: html, text, full: html, text
    fix for #9390 - tolerating url-encoded urls when detecting file compression type
• src/lib/net.c
  • lines changed 8, context: html, text, full: html, text
    fix for #9390 - tolerating url-encoded urls when detecting file compression type
• src/makefile
  • lines changed 3, context: html, text, full: html, text
    adding hgGcPercent to the userApps delivery
• src/product/README.building.source
  • lines changed 12, context: html, text, full: html, text
    add note about dlopen routines in library -ldl
  • lines changed 13, context: html, text, full: html, text
    Added new environment variables USE_SAMTABIX and SAMTABIXDIR.
• src/utils/bedGraphToBigWig/bedGraphToBigWig.c
  • lines changed 1, context: html, text, full: html, text
    adding hgGcPercent to the userApps delivery
• src/utils/faRandomize/faRandomize.c
  • lines changed 8, context: html, text, full: html, text
    standardize usage message to place into the build
• src/utils/faRandomize/makefile
  • lines changed 3, context: html, text, full: html, text
    standardize usage message to place into the build
• src/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    adding faRandomize to the build
  • lines changed 1, context: html, text, full: html, text
    adding paraSync to the build
• src/utils/ncbi/createNcbiCytoBand.pl
  • lines changed 3, context: html, text, full: html, text
    update to handle mm10 correctly
• src/utils/ncbi/cytoBandVerify.pl
  • lines changed 1, context: html, text, full: html, text
    update to handle mm10 correctly
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v275 preview2

• lines changed: 21853
• files changed: 118