All File Changes

v288_base to v289_preview (2013-08-19 to 2013-08-26) v289

• java/src/edu/ucsc/genome/util/LiftOverTest.props
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    Fix for mysql permissions issue with LiftOverTest - needs to use localhost instead of hgwdev by name
• src/hg/encode3/encodeDataWarehouse/inc/edwLib.h
  • lines changed 6, context: html, text, full: html, text
    Add new functions edwUserFromId and edwUserIdFromFileId to get user information from id of submitted file.
• src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
  • lines changed 19, context: html, text, full: html, text
    Add new functions edwUserFromId and edwUserIdFromFileId to get user information from id of submitted file.
• src/hg/hgTables/hgTables.c
  • lines changed 10, context: html, text, full: html, text
    fix bug in #11441 where switching to an assembly with a non-existantgroup would cause an internal error.
    
• src/hg/hgTracks/snakeTrack.c
  • lines changed 3, context: html, text, full: html, text
    use MAXLONG for maximum length of chrom
• src/hg/hgc/peakClusters.c
  • lines changed 17, context: html, text, full: html, text
    Special handling of antibody target ('factor') CV links. As a single factor may have multiple antibodies, show all for the factor. Response to QA question 6, note 52. refs #100097
• src/hg/hgc/pubs.c
  • lines changed 79, context: html, text, full: html, text
    fixing a layout bug, adding cgi param for ensembl to linkout to hgc
  • lines changed 162, context: html, text, full: html, text
    revamping the pubs marker page integrating all of Brookes comments that I can remember, adding javascript for "more" links, allowing additional filters for future ensembl incoming links, #6833
  • lines changed 15, context: html, text, full: html, text
    small changes to limit text
  • lines changed 17, context: html, text, full: html, text
    bugfix, forgot hits in supplements
• src/hg/htdocs/ENCODE/FAQ/index.html
  • lines changed 31, context: html, text, full: html, text
    Making changes to Hub FAQ in ENCODE per CR feedback refs# 11568
  • lines changed 3, context: html, text, full: html, text
    Adding Hiram's recommendation to use rsync for ENCODE data refs #11583
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 4, context: html, text, full: html, text
    Adding recommendation to use rysnc from Hiram MLQ refs #11579
• src/hg/htdocs/ENCODE/downloadsMouse.html
  • lines changed 4, context: html, text, full: html, text
    Adding Hiram's recommendation to use rsync for ENCODE data refs #11583
• src/hg/htdocs/ENCODE/search.html
  • lines changed 4, context: html, text, full: html, text
    Adding Hiram's recommendation to use rsync for ENCODE data refs #11583
• src/hg/htdocs/FAQ/FAQlicense.html
  • lines changed 2, context: html, text, full: html, text
    added links to google groups forum
• src/hg/htdocs/FAQ/FAQmaillist.html
  • lines changed 2, context: html, text, full: html, text
    added links to google groups forum, refs #11568
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 5, context: html, text, full: html, text
    added links to google groups forum
• src/hg/htdocs/admin/mirror.html
  • lines changed 2, context: html, text, full: html, text
    added links to google groups forum, refs #11568
• src/hg/htdocs/contacts.html
  • lines changed 3, context: html, text, full: html, text
    added links to google groups forum, refs #11568
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 2, context: html, text, full: html, text
    added links to google groups forum
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 2, context: html, text, full: html, text
    Adding recommendation to use HTTP versus FTP for hubs refs #11561
  • lines changed 3, context: html, text, full: html, text
    Adding link to Public Hub Guidelines Wiki on Hub User Guide page refs #11251
• src/hg/htdocs/goldenPath/help/mysql.html
  • lines changed 2, context: html, text, full: html, text
    added links to google groups forum
  • lines changed 20, context: html, text, full: html, text
    added encrypted email addresses
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 2, context: html, text, full: html, text
    Adding recommendation to use HTTP versus FTP for hubs refs #11561
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 36, context: html, text, full: html, text
    Added announcement for new LOVD, HGMD, and UniProt Variants tracks
• src/hg/htdocs/indexNews.html
  • lines changed 86, context: html, text, full: html, text
    Added announcement for new LOVD, HGMD, and UniProt Variants tracks
• src/hg/htdocs/mirror.html
  • lines changed 1, context: html, text, full: html, text
    added links to google groups forum, refs #11568
• src/hg/lib/sqlProg.c
  • lines changed 51, context: html, text, full: html, text
    Initial fix for hgsql warning message re command line password, refs #11516
  • lines changed 109, context: html, text, full: html, text
    Placed all config values in temp file instead of just password, propagated change to related functions
  • lines changed 84, context: html, text, full: html, text
    Removed redundancy from sqlExecProg* functions, added test and error message for crash of execvp()
  • lines changed 51, context: html, text, full: html, text
    fixing sqlProg (used by hgsql and friends) to use defaults file instead of the defaults-file-extra so that it can override the host/user/password in ~/my.cnf yet still it reads the known config files to capture mysql defaults
  • lines changed 4, context: html, text, full: html, text
    Fixed small memory leak
• src/hg/lib/trackHub.c
  • lines changed 10, context: html, text, full: html, text
    add vcfTabix support to hubCheck
• src/hg/lib/web.c
  • lines changed 13, context: html, text, full: html, text
    adding support for non-versioned links which work better for qaPushQ
• src/hg/makeDb/doc/ailMel1.txt
  • lines changed 15, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/anoCar2.txt
  • lines changed 13, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/bosTau7.txt
  • lines changed 13, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/calJac3.txt
  • lines changed 13, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/canFam3.txt
  • lines changed 13, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/cavPor3.txt
  • lines changed 13, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
  • lines changed 2, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/cerSim1.txt
  • lines changed 19, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/chrPic1.txt
  • lines changed 19, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/danRer7.txt
  • lines changed 22, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/dasNov3.txt
  • lines changed 19, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/encodeRegHg19.txt
  • lines changed 17, context: html, text, full: html, text
    Update downloads for reformatted V3 clusters file. refs #10097
• src/hg/makeDb/doc/felCat5.txt
  • lines changed 20, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/fr3.txt
  • lines changed 19, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/gadMor1.txt
  • lines changed 20, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/galGal4.txt
  • lines changed 27, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/geoFor1.txt
  • lines changed 19, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/hal.txt
  • lines changed 26, context: html, text, full: html, text
    instructions for building the HAL libraries.
• src/hg/makeDb/doc/hetGla2.txt
  • lines changed 19, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/hg19.txt
  • lines changed 67, context: html, text, full: html, text
    running lastz for fr3 refs #10272
  • lines changed 136, context: html, text, full: html, text
    baboon and dolphin for skunk project (marine mammal consortium)
  • lines changed 14, context: html, text, full: html, text
    done with fr3 lastz refs #10272
  • lines changed 96, context: html, text, full: html, text
    MLQs #11474 and #11504 alerted us to strand errors for some SNPs thatcaused incorrect allele frequencies, sometimes making a rare SNP seem
    common e.g. when the alleles are C/G and dbSNP's SNPAlleleFreq contains
    - strand data while dbSNP's SNPAlleleFreq_TGP (1000 Genomes) always has
    + strand data. I was using an insufficient kludge to detect strand-swapping.
    Now strand is taken from bNNN_SNPContigLoc so we know exactly when to
    complement alleles before adding counts.
    fixes #11544
    
  • lines changed 63, context: html, text, full: html, text
    starting lipVex1 lastz refs #10272
  • lines changed 8, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/latCha1.txt
  • lines changed 19, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/loxAfr3.txt
  • lines changed 22, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/macEug2.txt
  • lines changed 19, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/melGal1.txt
  • lines changed 19, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/melUnd1.txt
  • lines changed 19, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/musFur1.txt
  • lines changed 13, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/myoLuc2.txt
  • lines changed 18, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/oreNil2.txt
  • lines changed 19, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/oryCun2.txt
  • lines changed 22, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/otoGar3.txt
  • lines changed 19, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/petMar2.txt
  • lines changed 18, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/rheMac3.txt
  • lines changed 19, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/rn5.txt
  • lines changed 19, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/saiBol1.txt
  • lines changed 19, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/sarHar1.txt
  • lines changed 17, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/speTri2.txt
  • lines changed 19, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/susScr3.txt
  • lines changed 19, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/triMan1.txt
  • lines changed 18, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/turTru2.txt
  • lines changed 19, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 1, context: html, text, full: html, text
    use new cluster in SD
• src/hg/makeDb/hgFindSpec/hgFindSpec.c
  • lines changed 8, context: html, text, full: html, text
    use sqlTablesExist instead of sqlTableExists which should only check for a single table.
• src/hg/makeDb/schema/all.joiner
  • lines changed 3, context: html, text, full: html, text
    Added Ortho and Expressed tables to ucscRetroInro rule.
  • lines changed 5, context: html, text, full: html, text
    adding ucscToINSDC checking refs #11348
  • lines changed 7, context: html, text, full: html, text
    Fixed alphabetic ordering of some of the groups
  • lines changed 1, context: html, text, full: html, text
    Added echTel2 to gbd group
  • lines changed 1, context: html, text, full: html, text
    Undid previous change - echTel2 was already part of gbd
• src/hg/makeDb/trackDb/cow/bosTau6/numtSeq2012.html
  • lines changed 20, context: html, text, full: html, text
    Fixing some reference links for numtS tracks, refs #11571
• src/hg/makeDb/trackDb/gator/trackDb.chainNet.ra
  • lines changed 6, context: html, text, full: html, text
    correct overrides for chain net settings on hg19 vs. allMis1 refs #8750
• src/hg/makeDb/trackDb/gator/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    correct overrides for chain net settings on hg19 vs. allMis1 refs #8750
• src/hg/makeDb/trackDb/human/hg19/consIndelsHgMmCanFam.html
  • lines changed 1, context: html, text, full: html, text
    Fixed html tag for opening link in new tab, refs #11571
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRegTfbsClustered.ra
  • lines changed 2, context: html, text, full: html, text
    Update md5sum for newly formatted V3 clusters file
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeRegTfbsClustered.ra
  • lines changed 2, context: html, text, full: html, text
    Staging new TFBS Clustered Metadata V3 on beta refs #10097
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeRegTfbsClustered.ra
  • lines changed 28, context: html, text, full: html, text
    Staging metaData to public for TFBS Clusters refs #10097
• src/hg/makeDb/trackDb/human/hg19/numtSeqHg19.html
  • lines changed 1, context: html, text, full: html, text
    Fixing some reference links for numtS tracks, refs #11571
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Changed Retroposed Genes short label to fit within 17-character limit (redmine #1513)
  • lines changed 6, context: html, text, full: html, text
    Removed date from long label for ucscRetroAli5, updated dataVersion and corrected search descriptions.
  • lines changed 0, context: html, text, full: html, text
    Edited search labels (redmine #1513)
  • lines changed 24, context: html, text, full: html, text
    add multizMarine for skunk project (marine mamal consortia)
• src/hg/makeDb/trackDb/human/hg19/ucscRetroAli5.html
  • lines changed 91, context: html, text, full: html, text
    Made whitespace and html formatting changes only - no content changes (redmine #1513)
  • lines changed 75, context: html, text, full: html, text
    Made minor content corrections; fixed References section (redmine #1513)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 2, context: html, text, full: html, text
    Add description of new file format for clusters. refs #10097
  • lines changed 3, context: html, text, full: html, text
    Changing visibility of track from default dense to hide and short label to V3 per conversation with Kate for first release refs #10097
  • lines changed 1, context: html, text, full: html, text
    Chaning release tag to public for TFBS Clusters refs #10097
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTfbsClusteredV3.html
  • lines changed 6, context: html, text, full: html, text
    Add description of new file format for clusters. refs #10097
  • lines changed 23, context: html, text, full: html, text
    Adding details about score and related tables for TFBS Clusters V3 html page refs #10097
  • lines changed 13, context: html, text, full: html, text
    Attempts to simplify & clarify the Methods and Release Notes sections. refs #10097
  • lines changed 2, context: html, text, full: html, text
    Removing an underlying typo for release V3 TFBS Clusters refs# 10097
• src/hg/makeDb/trackDb/human/lovd.html
  • lines changed 3, context: html, text, full: html, text
    tiny lovd html change
• src/hg/makeDb/trackDb/human/numtSeq.html
  • lines changed 1, context: html, text, full: html, text
    Fixed a reference link, refs #11571
• src/hg/makeDb/trackDb/human/spMut.html
  • lines changed 4, context: html, text, full: html, text
    Made correction suggested in code review (redmine #11570)
• src/hg/makeDb/trackDb/human/trackDb.chainNet.ra
  • lines changed 7, context: html, text, full: html, text
    correct overrides for chain net settings on hg19 vs. allMis1 refs #8750
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    Removing rsync of cv.ra to beta-public; this will be done manually now refs #11601
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Changed Retroposed Genes short label to fit within 17-character limit (redmine #1513)
  • lines changed 6, context: html, text, full: html, text
    Removed date from long label for ucscRetroAli5, added dataVersion and removed date from search descriptions.
  • lines changed 1, context: html, text, full: html, text
    Added 'V2' to the Retroposed Genes long label (redmine #1513)
  • lines changed 1, context: html, text, full: html, text
    Edited search labels (redmine #1513)
• src/hg/makeDb/trackDb/mouse/mm10/ucscRetroAli2.html
  • lines changed 95, context: html, text, full: html, text
    Made whitespace and html formatting changes only - no content changes (redmine #1513)
  • lines changed 74, context: html, text, full: html, text
    Made minor content corrections; fixed References section (redmine #1513)
• src/hg/makeDb/trackDb/pig/susScr2/numtSeq2012.html
  • lines changed 1, context: html, text, full: html, text
    Fixing some reference links for numtS tracks, refs #11571
• src/hg/makeDb/trackDb/snail/bioGla0/trackDb.ra
  • lines changed 41, context: html, text, full: html, text
    a bioGla0 trackDb. Part of a skunk project for the snail consortium.
• src/hg/phyloGif/makefile
  • lines changed 1, context: html, text, full: html, text
    Tweaked phyloGif/makefile's installation to tolerate the use of the samedirectory for CGI binaries and utils.
    
• src/hg/utils/automation/HgAutomate.pm
  • lines changed 18, context: html, text, full: html, text
    moving to San Diego compute environment, adding the ku kluster to the mix refs #8875
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    Added a function to get the species name from dbDb.
  • lines changed 1, context: html, text, full: html, text
    fixup reference to hgcentraltest as localhost instead of genome-testdb refs #8875
• src/hg/utils/automation/doBlastzChainNet.pl
  • lines changed 4, context: html, text, full: html, text
    moving to San Diego compute environment, adding the ku kluster to the mix refs #8875
• src/hg/utils/automation/doCpgIslands.pl
  • lines changed 4, context: html, text, full: html, text
    moving to San Diego compute environment, adding the ku kluster to the mix refs #8875
• src/hg/utils/automation/doDbSnp.pl
  • lines changed 1, context: html, text, full: html, text
    MLQs #11474 and #11504 alerted us to strand errors for some SNPs thatcaused incorrect allele frequencies, sometimes making a rare SNP seem
    common e.g. when the alleles are C/G and dbSNP's SNPAlleleFreq contains
    - strand data while dbSNP's SNPAlleleFreq_TGP (1000 Genomes) always has
    + strand data. I was using an insufficient kludge to detect strand-swapping.
    Now strand is taken from bNNN_SNPContigLoc so we know exactly when to
    complement alleles before adding counts.
    fixes #11544
    
• src/hg/utils/automation/doGenscan.pl
  • lines changed 2, context: html, text, full: html, text
    moving to San Diego compute environment, adding the ku kluster to the mix refs #8875
• src/hg/utils/automation/doHgNearBlastp.pl
  • lines changed 4, context: html, text, full: html, text
    moving to San Diego compute environment, adding the ku kluster to the mix refs #8875
• src/hg/utils/automation/doRepeatMasker.pl
  • lines changed 5, context: html, text, full: html, text
    fixup use of ku kluster for options to engines for RM refs #8875
• src/hg/utils/automation/snpAddTGPAlleleFreq.pl
  • lines changed 95, context: html, text, full: html, text
    MLQs #11474 and #11504 alerted us to strand errors for some SNPs thatcaused incorrect allele frequencies, sometimes making a rare SNP seem
    common e.g. when the alleles are C/G and dbSNP's SNPAlleleFreq contains
    - strand data while dbSNP's SNPAlleleFreq_TGP (1000 Genomes) always has
    + strand data. I was using an insufficient kludge to detect strand-swapping.
    Now strand is taken from bNNN_SNPContigLoc so we know exactly when to
    complement alleles before adding counts.
    fixes #11544
    
• src/hg/utils/lovd/bedDetail4.sql
  • lines changed 16, context: html, text, full: html, text
    moving lovd otto scripts into otto dir
• src/hg/utils/lovd/checkAndLoad.sh
  • lines changed 54, context: html, text, full: html, text
    moving lovd otto scripts into otto dir
• src/hg/utils/lovd/doUpdate.sh
  • lines changed 2, context: html, text, full: html, text
    moving lovd otto scripts into otto dir
• src/hg/utils/lovd/download.sh
  • lines changed 24, context: html, text, full: html, text
    moving lovd otto scripts into otto dir
• src/hg/utils/otto/lovd/bedDetail4.sql
  • lines changed 16, context: html, text, full: html, text
    moving lovd otto scripts into otto dir
• src/hg/utils/otto/lovd/checkAndLoad.sh
  • lines changed 54, context: html, text, full: html, text
    moving lovd otto scripts into otto dir
• src/hg/utils/otto/lovd/doUpdate.sh
  • lines changed 2, context: html, text, full: html, text
    moving lovd otto scripts into otto dir
• src/hg/utils/otto/lovd/download.sh
  • lines changed 24, context: html, text, full: html, text
    moving lovd otto scripts into otto dir
• src/hg/utils/phyloTrees/placentals.txt
  • lines changed 7, context: html, text, full: html, text
    adding lipVex and myoBri Brandt's Myotis (bat) - Myotis brandtii and Yangtze River Dolphin Lipotes vexillifer refs @10272
• src/inc/common.mk
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    adding -lstdc++ and -lrt to all MYSQLLIBS in case of MySQL v5.6 refs #9149
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    If a non-standard $SSL_DIR has been specified, add the necessary lib and inc settings.
• src/utils/qa/weeklybld/buildEnv.csh
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    v289 preview1
• src/utils/qa/weeklybld/doHgTablesTestRobot.csh
  • lines changed 2, context: html, text, full: html, text
    adding steve to the notification email refs #8875
• src/utils/qa/weeklybld/doNewBranch.csh
  • lines changed 8, context: html, text, full: html, text
    using sendmail instead of mail because this mail is different than before refs #8875

• lines changed: 2870
• files changed: 146