All File Changes

v298_preview2 to v298_base (2014-03-31 to 2014-04-07) v298

• src/hg/encode3/eap/eapAddStep/eapAddStep.c
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    Add SPP single-end peak-calling (first cut, prior to info from Anshul)
  • lines changed 2, context: html, text, full: html, text
    Adding initial cut of SPP ChIP-seq peak calling from bams (exploratory work ahead of spec from DAC)
  • lines changed 65, context: html, text, full: html, text
    Merge
• src/hg/encode3/eap/eapRunAddJson/eapRunAddJson.c
  • lines changed 366, context: html, text, full: html, text
    Move eapRunAddJson to oneShot dir
• src/hg/encode3/eap/eapRunAddJson/makefile
  • lines changed 4, context: html, text, full: html, text
    Move eapRunAddJson to oneShot dir
• src/hg/encode3/eap/eapSchedule/eapSchedule.c
  • lines changed 77, context: html, text, full: html, text
    Adding initial cut of SPP ChIP-seq peak calling from bams (exploratory work ahead of spec from DAC)
  • lines changed 4, context: html, text, full: html, text
    Merge
  • lines changed 4, context: html, text, full: html, text
    Tweaks for ChIP scheduling
• src/hg/encode3/eap/lib/resetDb
  • lines changed 2, context: html, text, full: html, text
    Adding initial cut of SPP ChIP-seq peak calling from bams (exploratory work ahead of spec from DAC)
  • lines changed 11, context: html, text, full: html, text
    Merge
  • lines changed 2, context: html, text, full: html, text
    Rscript is 3rdparty
• src/hg/encode3/eap/makefile
  • lines changed 1, context: html, text, full: html, text
    Remove obsolete tool
• src/hg/encode3/eap/oneShot/eapRunAddJson/eapRunAddJson.c
  • lines changed 366, context: html, text, full: html, text
    Move eapRunAddJson to oneShot dir
• src/hg/encode3/eap/oneShot/eapRunAddJson/makefile
  • lines changed 4, context: html, text, full: html, text
    Move eapRunAddJson to oneShot dir
• src/hg/encode3/encodeDataWarehouse/edwWebCreateUser/edwWebCreateUser.c
  • lines changed 1, context: html, text, full: html, text
    Only administrator can create new user in edwWebCreateUser.
• src/hg/encode3/encodeDataWarehouse/edwWebDeprecate/edwWebDeprecate.c
  • lines changed 9, context: html, text, full: html, text
    Make "Allow me to deprecate files not uploaded by me:" optionin edwWebDeprecate CGI available only for user who is an administrator.
    
• src/hg/encode3/encodeDataWarehouse/inc/edwLib.h
  • lines changed 3, context: html, text, full: html, text
    Make "Allow me to deprecate files not uploaded by me:" optionin edwWebDeprecate CGI available only for user who is an administrator.
    
• src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
  • lines changed 10, context: html, text, full: html, text
    Make "Allow me to deprecate files not uploaded by me:" optionin edwWebDeprecate CGI available only for user who is an administrator.
    
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 58, context: html, text, full: html, text
    Fixes #12602. Deal with long assembly lists by making a click-able expansion/contraction of long lists in the table. It tries to keep the assembly list to about 40 charachters.
• src/hg/hgLiftOver/hgLiftOver.c
  • lines changed 2, context: html, text, full: html, text
    changing hgLiftOver strategy in the browserbox: downloading liftoverfiles to local disk instead of streaming them through http, refs #11957
    and refs #12717
    
• src/hg/hgTables/hgTables.c
  • lines changed 12, context: html, text, full: html, text
    When we have multiple position matches, restore lastPosition(or defaultPosition).
    fixes #13009
    
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 4, context: html, text, full: html, text
    fixup ensGene name display from code review refs #12957
• src/hg/hgTracks/hgTracks.c
  • lines changed 6, context: html, text, full: html, text
    When we have multiple position matches, restore lastPosition(or defaultPosition).
    fixes #13009
    
• src/hg/hgTracks/menu.c
  • lines changed 3, context: html, text, full: html, text
    no mapviewer for hg18 and hg19 now uses build=previous and add hg38 link to NCBI refs #12871
• src/hg/hgTracks/simpleTracks.c
  • lines changed 4, context: html, text, full: html, text
    fixup ensGene name display from code review refs #12957
• src/hg/hgVai/hgVai.c
  • lines changed 3, context: html, text, full: html, text
    Fixing hgVai again for gbib, refs #11957 and refs #12717. One problemwas that show tables cannot fail over. Probably need to libify
    one day as a sqlShowTables() function. Another problem are the nib
    directories in hg18. Working towards replacing all nib directories with their
    twoBit versions via a hg.conf statement.
    
  • lines changed 7, context: html, text, full: html, text
    Libifying yesterday's commit and applying another patch to hgVai to makeit work in the browserbox, refs #11957 and #12717
    
  • lines changed 9, context: html, text, full: html, text
    When we have multiple position matches, restore lastPosition(or defaultPosition).
    fixes #13009
    
• src/hg/hgc/bamClick.c
  • lines changed 2, context: html, text, full: html, text
    making hgc bam clicks gbib-ready, refs #11957 and refs #12717
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 3, context: html, text, full: html, text
    changes after code review, refs #12998
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 16, context: html, text, full: html, text
    Added 2 new entries by Karen Miga. I think this is our first citation of a blog post, so I made up a format :-). Linking to abstract of Genome Res. article until full-text article is officially in print.
• src/hg/htdocs/images/Callorhinchus_milii.jpg
  • lines changed 0, context: html, text, full: html, text
    Elephant shark photo from http://www.flagstaffotos.com.au/ Wikipedia refs #12976
• src/hg/htdocs/images/Cricetulus_griseus.jpg
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    Chinese hamster photo from WikiMedia commons refs #6506
• src/hg/htdocs/images/phylo/rn5_14way.png
  • lines changed 0, context: html, text, full: html, text
    Adding phylo for rn5 multiz track. refs #8212
• src/hg/htdocs/license/gblicense.pdf
  • lines changed 0, context: html, text, full: html, text
    Updated GB licensing agreement from Wil Hale.
• src/hg/inc/hdb.h
  • lines changed 9, context: html, text, full: html, text
    changing hgLiftOver strategy in the browserbox: downloading liftoverfiles to local disk instead of streaming them through http, refs #11957
    and refs #12717
    
• src/hg/inc/jksql.h
  • lines changed 3, context: html, text, full: html, text
    Fixing hgVai again for gbib, refs #11957 and refs #12717. One problemwas that show tables cannot fail over. Probably need to libify
    one day as a sqlShowTables() function. Another problem are the nib
    directories in hg18. Working towards replacing all nib directories with their
    twoBit versions via a hg.conf statement.
    
  • lines changed 3, context: html, text, full: html, text
    Fixing what I believe was a misspelled function header in ed552b421.
  • lines changed 4, context: html, text, full: html, text
    Libifying yesterday's commit and applying another patch to hgVai to makeit work in the browserbox, refs #11957 and #12717
    
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v298
• src/hg/lib/geneReviewsGeneGRshortNBKidGRtitle.sql
  • lines changed 7, context: html, text, full: html, text
    Add 3 sql file to create the 3 new tables used byTrack #11226 Change the geneReviews tables of hg19 and hg18 to match NCBI.
    geneReviewsGrshortNBKid.sql
    geneReviewsGrshortTitleNBKid.sql
    geneReviewsGeneGRshortNBKidGRtitle.sql
    
    lease enter the commit message for your changes. Lines starting
    
• src/hg/lib/geneReviewsGrshortNBKid.sql
  • lines changed 6, context: html, text, full: html, text
    Add 3 sql file to create the 3 new tables used byTrack #11226 Change the geneReviews tables of hg19 and hg18 to match NCBI.
    geneReviewsGrshortNBKid.sql
    geneReviewsGrshortTitleNBKid.sql
    geneReviewsGeneGRshortNBKidGRtitle.sql
    
    lease enter the commit message for your changes. Lines starting
    
• src/hg/lib/geneReviewsGrshortTitleNBKid.sql
  • lines changed 6, context: html, text, full: html, text
    Add 3 sql file to create the 3 new tables used byTrack #11226 Change the geneReviews tables of hg19 and hg18 to match NCBI.
    geneReviewsGrshortNBKid.sql
    geneReviewsGrshortTitleNBKid.sql
    geneReviewsGeneGRshortNBKidGRtitle.sql
    
    lease enter the commit message for your changes. Lines starting
    
• src/hg/lib/hdb.c
  • lines changed 61, context: html, text, full: html, text
    changing hgLiftOver strategy in the browserbox: downloading liftoverfiles to local disk instead of streaming them through http, refs #11957
    and refs #12717
    
  • lines changed 13, context: html, text, full: html, text
    Fixing hgVai again for gbib, refs #11957 and refs #12717. One problemwas that show tables cannot fail over. Probably need to libify
    one day as a sqlShowTables() function. Another problem are the nib
    directories in hg18. Working towards replacing all nib directories with their
    twoBit versions via a hg.conf statement.
    
  • lines changed 2, context: html, text, full: html, text
    oops forgot to check for null pointer in last commit.
  • lines changed 1, context: html, text, full: html, text
    further support to remove .nib access via an hg.conf option. refs #11957
• src/hg/lib/jksql.c
  • lines changed 7, context: html, text, full: html, text
    Fixing hgVai again for gbib, refs #11957 and refs #12717. One problemwas that show tables cannot fail over. Probably need to libify
    one day as a sqlShowTables() function. Another problem are the nib
    directories in hg18. Working towards replacing all nib directories with their
    twoBit versions via a hg.conf statement.
    
  • lines changed 24, context: html, text, full: html, text
    Libifying yesterday's commit and applying another patch to hgVai to makeit work in the browserbox, refs #11957 and #12717
    
  • lines changed 2, context: html, text, full: html, text
    fixing a mysqlinj bug in last commit
  • lines changed 37, context: html, text, full: html, text
    when using a failover connection but no table cache, merge the tablelists from both the failover connection and the main connection.
    Otherwise only local tracks show up. for this, extracting
    old code into a new function and calling it twice. (NB: This code change
    is very hard to see in the diff algorithm we use in the git reports.
    The "patience" algorithm is a lot better: git diff --patience jksql.c)
    
• src/hg/lib/liftOver.c
  • lines changed 1, context: html, text, full: html, text
    changing hgLiftOver strategy in the browserbox: downloading liftoverfiles to local disk instead of streaming them through http, refs #11957
    and refs #12717
    
• src/hg/makeDb/doc/balAcu1.txt
  • lines changed 68, context: html, text, full: html, text
    done with masking refs #12977
  • lines changed 210, context: html, text, full: html, text
    in the pushQ refs #12977
• src/hg/makeDb/doc/calMil1.txt
  • lines changed 347, context: html, text, full: html, text
    initial sequence and running masking refs #12976
  • lines changed 147, context: html, text, full: html, text
    genbank done constructing download files refs #12976
  • lines changed 8, context: html, text, full: html, text
    in the pushQ refs #12976
  • lines changed 4, context: html, text, full: html, text
    fix gap procedure steps refs #12976
• src/hg/makeDb/doc/hg19.txt
  • lines changed 130, context: html, text, full: html, text
    Rebuilt snp138* tables and files from scratch 3/28/14 - 3/31/14 afterfinding that the FTP files available when b138 was announced were
    outdated and were replaced a few weeks after the announcement.
    1.2M SNPs had been dropped because they were not in the fasta files.
    refs #12975 #11438
    
• src/hg/makeDb/doc/hg38.txt
  • lines changed 8, context: html, text, full: html, text
    Completed last swap steps to generate chain/net for rn5<->hg38. refs #8212
• src/hg/makeDb/doc/rn5.txt
  • lines changed 14, context: html, text, full: html, text
    Adding hg38 swap details to rn5 makedoc. refs #8212
  • lines changed 6, context: html, text, full: html, text
    start monDom5 swap refs #8212
  • lines changed 4, context: html, text, full: html, text
    syntenic net for hg38 for 14-way refs #8212
  • lines changed 1, context: html, text, full: html, text
    recip best for Panda for 13-way alignment refs #8212
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added balAcu1 to daily hgwdev build refs #12977
  • lines changed 1, context: html, text, full: html, text
    Added calMil1 to daily hgwdev build refs #12976
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 19, context: html, text, full: html, text
    adding balAcu1 Minke whale refs #12977
  • lines changed 19, context: html, text, full: html, text
    adding calMil1 Elephant shark refs #12976
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added balAcu1 to daily hgwdev build refs #12977
  • lines changed 1, context: html, text, full: html, text
    Added calMil1 to daily hgwdev build refs #12976
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 2, context: html, text, full: html, text
    adding definition for balAcuNames refs 12977
  • lines changed 1, context: html, text, full: html, text
    adding definition for balAcuNames refs 12977
  • lines changed 2, context: html, text, full: html, text
    adding calMil1 Elephant shark refs #12976
• src/hg/makeDb/schema/all.joiner
  • lines changed 12, context: html, text, full: html, text
    adding balAcu1 and calMil1 Minke whale and Elephant shark refs #12976 #12977
• src/hg/makeDb/trackDb/balAcu/balAcu1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    moving cpgIslandSuper composite track to the top for balAcu1 and calMil1 refs #12977 #12976
  • lines changed 7, context: html, text, full: html, text
    setting default track visibilities refs #12977
• src/hg/makeDb/trackDb/calMil/calMil1/description.html
  • lines changed 63, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #12976
• src/hg/makeDb/trackDb/calMil/calMil1/gap.html
  • lines changed 30, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #12976
• src/hg/makeDb/trackDb/calMil/calMil1/gold.html
  • lines changed 34, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #12976
• src/hg/makeDb/trackDb/calMil/calMil1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #12976
  • lines changed 2, context: html, text, full: html, text
    moving cpgIslandSuper composite track to the top for balAcu1 and calMil1 refs #12977 #12976
  • lines changed 8, context: html, text, full: html, text
    set default track visibilities refs #12976
• src/hg/makeDb/trackDb/cpgIslandSuper.html
  • lines changed 79, context: html, text, full: html, text
    moving cpgIslandSuper composite track to the top for balAcu1 and calMil1 refs #12977 #12976
  • lines changed 7, context: html, text, full: html, text
    change the discussion of masked and unmasked versions to eliminate the hg38 specific language refs #12976 #12977
• src/hg/makeDb/trackDb/criGri/criGri1/description.html
  • lines changed 63, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #6506
• src/hg/makeDb/trackDb/criGri/criGri1/gap.html
  • lines changed 30, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #6506
• src/hg/makeDb/trackDb/criGri/criGri1/gold.html
  • lines changed 34, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #6506
• src/hg/makeDb/trackDb/criGri/criGri1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #6506
• src/hg/makeDb/trackDb/human/chainNetPlacental.ra
  • lines changed 2, context: html, text, full: html, text
    chainNetPlacental.ra change to release felCat5/hg19 refs# 12744
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    removed hg18 pool ball icon
  • lines changed 1, context: html, text, full: html, text
    removing liftOver note
• src/hg/makeDb/trackDb/human/hg38/cpgIslandSuper.html
  • lines changed 79, context: html, text, full: html, text
    moving cpgIslandSuper composite track to the top for balAcu1 and calMil1 refs #12977 #12976
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    Fixing checkHgFindSpec -checkTermRegex warning that Jonathan found -when the termRegex doesn't match (all of) the terms in the table,
    we need to add a dontCheck regex to cover all of the non-matching terms.
    
  • lines changed 1, context: html, text, full: html, text
    fix a regex for the OMIM SNP track
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding calMil1 to the build refs #12976
  • lines changed 1, context: html, text, full: html, text
    adding criGri1 to the build refs #6506
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.60way.ra
  • lines changed 1, context: html, text, full: html, text
    temporarily set cons60way to hide while maf table is reloaded refs #12260
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 28, context: html, text, full: html, text
    moving cpgIslandSuper composite track to the top for balAcu1 and calMil1 refs #12977 #12976
• src/hg/utils/automation/collectNcbiFuncAnnotations.pl
  • lines changed 3, context: html, text, full: html, text
    Prevent warning about uninitialized variables triggered by $refRow-only items.
• src/hg/utils/automation/makePushQSql.pl
  • lines changed 2, context: html, text, full: html, text
    connection to hgwbeta for commands requires extra business now refs #12977
  • lines changed 1, context: html, text, full: html, text
    mysql create table now requires ENGINE and not TYPE refs #12976
• src/hg/utils/makeTableList/makeTableList.c
  • lines changed 1, context: html, text, full: html, text
    making makeTableList work for Jorge who has no hg.conf and his hgcentralhave no user or sessionDb tables. refs #11957
    
• src/hg/utils/phyloTrees/commonNames.sh
  • lines changed 1, context: html, text, full: html, text
    Adding missing entry for hg38. refs #8212
• src/lib/paraFetch.c
  • lines changed 1, context: html, text, full: html, text
    fixing an error message
• src/makefile
  • lines changed 18, context: html, text, full: html, text
    adding a top level target for htdocs+js+css, refs #12717 note 27
• src/product/README.mysql.setup
  • lines changed 1, context: html, text, full: html, text
    added a little clarification to one line
• src/product/ex.hg.conf
  • lines changed 4, context: html, text, full: html, text
    hg.conf doc change after code review, refs #12998
  • lines changed 4, context: html, text, full: html, text
    Fixing hgVai again for gbib, refs #11957 and refs #12717. One problemwas that show tables cannot fail over. Probably need to libify
    one day as a sqlShowTables() function. Another problem are the nib
    directories in hg18. Working towards replacing all nib directories with their
    twoBit versions via a hg.conf statement.
    
• src/utils/qa/sessionStats.csh
  • lines changed 6, context: html, text, full: html, text
    Replaced MyQQL 'like' comparison of dates with an alternative that doesn't cause warnings
• src/utils/qa/updateTimes.csh
  • lines changed 8, context: html, text, full: html, text
    added a noEuro option for quick resulets. working with BrianLee
  • lines changed 4, context: html, text, full: html, text
    fixed bug reported by steve and another found while fixing. sorry. shoulda been tested more thoroughly
  • lines changed 11, context: html, text, full: html, text
    made it possible to run in verbose and noEuro modes together
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v298 final build refs #12803

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• files changed: 113