All File Changes

v288_preview2 to v288_base (2013-08-13 to 2013-08-19) v288

• confs/rr.hg.conf
  • lines changed 1, context: html, text, full: html, text
    fixing exception bottleneck ip to new hgwdev ip address
• src/hg/cartDump/cartDump.c
  • lines changed 1, context: html, text, full: html, text
    cartDump needs to call setUdcCacheDir() like the other CGIs; otherwise, when it opens the cart and fetches hubs, it uses the default /tmp/udcCache.
• src/hg/checkTableCoords/tests/input/fakeChromInfo.sql
  • lines changed 1, context: html, text, full: html, text
    MySQL 5.6 uses the ENGINE variable in place of TYPE refs #8875
• src/hg/hgGetAnn/tests/makefile
  • lines changed 6, context: html, text, full: html, text
    fixup sorting of outputs and expected to avoid MySQL sorting differences refs #9149
• src/hg/hgLogin/hgLogin.c
  • lines changed 2, context: html, text, full: html, text
    Bug 11547 When creating account realName (from good old wiki days) need to be set even it is not use anymore
• src/hg/hgTables/hal.c
  • lines changed 61, context: html, text, full: html, text
    make HAL linked in by default, fix the problem with mismatched bases nothaving the right chars in them, start adding HAL to the table browser.
    refs #10637
    
• src/hg/hgTables/hgTables.c
  • lines changed 4, context: html, text, full: html, text
    make HAL linked in by default, fix the problem with mismatched bases nothaving the right chars in them, start adding HAL to the table browser.
    refs #10637
    
• src/hg/hgTables/hgTables.h
  • lines changed 9, context: html, text, full: html, text
    make HAL linked in by default, fix the problem with mismatched bases nothaving the right chars in them, start adding HAL to the table browser.
    refs #10637
    
• src/hg/hgTables/joining.c
  • lines changed 12, context: html, text, full: html, text
    make HAL linked in by default, fix the problem with mismatched bases nothaving the right chars in them, start adding HAL to the table browser.
    refs #10637
    
• src/hg/hgTables/makefile
  • lines changed 1, context: html, text, full: html, text
    make HAL linked in by default, fix the problem with mismatched bases nothaving the right chars in them, start adding HAL to the table browser.
    refs #10637
    
• src/hg/hgTracks/bamTrack.c
  • lines changed 4, context: html, text, full: html, text
    Code review feedback from Kate. refs #11525
• src/hg/hgTracks/snakeTrack.c
  • lines changed 12, context: html, text, full: html, text
    make HAL linked in by default, fix the problem with mismatched bases nothaving the right chars in them, start adding HAL to the table browser.
    refs #10637
    
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    fixing typo
  • lines changed 1, context: html, text, full: html, text
    suppressing strand if strand field is empty in bed tracks, see #10935
  • lines changed 11, context: html, text, full: html, text
    changing the order of fields in bedDetail to match normal bed order, as requested by QA in #10687
  • lines changed 2, context: html, text, full: html, text
    removing one linebreak from bedDetails forms, #10687
  • lines changed 1, context: html, text, full: html, text
    correction to last commit, #10687
• src/hg/htdocs/ENCODE/FAQ/index.html
  • lines changed 9, context: html, text, full: html, text
    removed ML archives search box
  • lines changed 23, context: html, text, full: html, text
    Chaning ENCODE FAQ to test git commit and will add new entry
  • lines changed 28, context: html, text, full: html, text
    Adding a new FAQ to ENCODE FAQ refs #11546
• src/hg/htdocs/FAQ/FAQmaillist.html
  • lines changed 28, context: html, text, full: html, text
    changed some wording and updated with links to google groups, refs #11518
• src/hg/htdocs/FAQ/index.html
  • lines changed 8, context: html, text, full: html, text
    removed ML archives search box & changed wording
• src/hg/htdocs/admin/mirror.html
  • lines changed 12, context: html, text, full: html, text
    changed wording, removed ML archives search box
• src/hg/htdocs/contacts.html
  • lines changed 24, context: html, text, full: html, text
    removed ML archives search box & changed wording
  • lines changed 13, context: html, text, full: html, text
    made changes to mirror section, removed ML archives search box
• src/hg/htdocs/goldenPath/help/hgGenomeHelp.html
  • lines changed 13, context: html, text, full: html, text
    removed ML archives search box and updated link, refs #11518
• src/hg/htdocs/goldenPath/help/hgSessionHelp.html
  • lines changed 14, context: html, text, full: html, text
    removed ML archives search box & updated link, refs #11518
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 8, context: html, text, full: html, text
    removed ML archives search box & updated link, refs #11518
• src/hg/htdocs/mirror.html
  • lines changed 11, context: html, text, full: html, text
    changed wording and removed ML archives search box, refs #11518
  • lines changed 1, context: html, text, full: html, text
    added missing period
• src/hg/htdocs/training.html
  • lines changed 2, context: html, text, full: html, text
    updated mailing list link, refs #11518
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v288
• src/hg/lib/encode/unused/shortFrags.as
  • lines changed 31, context: html, text, full: html, text
    eliminate duplcated named file that has outlived usefulness refs #8875
• src/hg/lib/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    missing the build of the sqlCheck binary for the testing refs #8875
• src/hg/lib/ucscToINSDC.as
  • lines changed 8, context: html, text, full: html, text
    adding track INSDC name refs #11348
• src/hg/lib/ucscToINSDC.sql
  • lines changed 9, context: html, text, full: html, text
    adding track INSDC name refs #11348
• src/hg/lib/web.c
  • lines changed 1, context: html, text, full: html, text
    getting rid of a debugging line
  • lines changed 6, context: html, text, full: html, text
    adding support for null cart which is used in qaPushQ and maybe a few other places
• src/hg/makeDb/doc/gorGor3.txt
  • lines changed 81, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/hg19.txt
  • lines changed 28, context: html, text, full: html, text
    update cosmic to v66 refs #10158
  • lines changed 48, context: html, text, full: html, text
    adding track INSDC name refs #11348
  • lines changed 68, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/makeDb/doc/mm10.txt
  • lines changed 38, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/nomLeu3.txt
  • lines changed 88, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/oviAri3.txt
  • lines changed 1, context: html, text, full: html, text
    fixup comments about path name refs #9409
• src/hg/makeDb/doc/panPan1.txt
  • lines changed 57, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/panTro4.txt
  • lines changed 43, context: html, text, full: html, text
    adding ucscToINSDC track refs #11348
• src/hg/makeDb/doc/vicPac2.txt
  • lines changed 1, context: html, text, full: html, text
    fixup comments about path name refs #10833
• src/hg/makeDb/genbank/etc/euronode-copy
  • lines changed 1, context: html, text, full: html, text
    use hgwdev.sdsc.edu for euronode copy
• src/hg/makeDb/schema/all.joiner
  • lines changed 2, context: html, text, full: html, text
    Added hgmd and lovd to hg19 tablesIgnored (redmine #10687,10935)
  • lines changed 1, context: html, text, full: html, text
    Added spMut to the hg19 tablesIgnored list (redmine #9985)
• src/hg/makeDb/trackDb/cow/bosTau6/numtSeq2012.html
  • lines changed 16, context: html, text, full: html, text
    Updating references to include links to PMID/PMCID for cow numtS track, refs #8533
• src/hg/makeDb/trackDb/fishClones.html
  • lines changed 2, context: html, text, full: html, text
    Fixing broken links on track description pages
• src/hg/makeDb/trackDb/human/cytoBand.html
  • lines changed 2, context: html, text, full: html, text
    Fixing broken links on track description pages
• src/hg/makeDb/trackDb/human/evofold.html
  • lines changed 1, context: html, text, full: html, text
    Fixing broken links on track description pages
• src/hg/makeDb/trackDb/human/hg19/chainNetVertebrate.ra
  • lines changed 19, context: html, text, full: html, text
    Made chain/net changes; created new files for sarHar1 so appropriate values would appear in chain/net description page; edited hg19 files so tasmanian devil would appear properly (redmine #11552)
• src/hg/makeDb/trackDb/human/hg19/consIndelsHgMmCanFam.html
  • lines changed 1, context: html, text, full: html, text
    Fixing broken links on track description pages
• src/hg/makeDb/trackDb/human/hg19/hg19vertChainNet.html
  • lines changed 4, context: html, text, full: html, text
    Made chain/net changes; created new files for sarHar1 so appropriate values would appear in chain/net description page; edited hg19 files so tasmanian devil would appear properly (redmine #11552)
• src/hg/makeDb/trackDb/human/hg19/numtSeqHg19.html
  • lines changed 22, context: html, text, full: html, text
    Updating track referencesfor NumtS tracks, refs #11549
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 1, context: html, text, full: html, text
    Staging newer TFBS3 on beta refs #10097
• src/hg/makeDb/trackDb/human/hgIkmc.html
  • lines changed 1, context: html, text, full: html, text
    Fixing broken links on track description pages
• src/hg/makeDb/trackDb/human/hgmd.html
  • lines changed 52, context: html, text, full: html, text
    Made changes to the HGMD and LOVD description pages (redmine #10687,10935)
• src/hg/makeDb/trackDb/human/lovd.html
  • lines changed 45, context: html, text, full: html, text
    Made changes to the HGMD and LOVD description pages (redmine #10687,10935)
• src/hg/makeDb/trackDb/human/numtSeq.html
  • lines changed 20, context: html, text, full: html, text
    Updating track referencesfor NumtS tracks, refs #11549
• src/hg/makeDb/trackDb/human/spMut.html
  • lines changed 57, context: html, text, full: html, text
    Made various changes/corrections to the UniProt Variants description page (redmine #9985)
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Made slight changes to long labels of HGMD and LOVD (redmine #10935)
  • lines changed 3, context: html, text, full: html, text
    adding noScoreFilter to bigBed stanza (conflicts with docs), adding noScoreFilter to hgmd track as of #10935
  • lines changed 1, context: html, text, full: html, text
    removed login note, #10935
  • lines changed 1, context: html, text, full: html, text
    changed outlink label for lovd
  • lines changed 2, context: html, text, full: html, text
    Removed release tags from HGMD and LOVD (redmine #10687,10935)
  • lines changed 1, context: html, text, full: html, text
    Removed release tag for UniProt Variants track (redmine #9985)
• src/hg/makeDb/trackDb/makefile
  • lines changed 3, context: html, text, full: html, text
    reenable trix building in San Diego refs #8132
  • lines changed 1, context: html, text, full: html, text
    forget trix annulment clause, refs #8132
• src/hg/makeDb/trackDb/mouse/mm9/numtSeqMm9.html
  • lines changed 15, context: html, text, full: html, text
    Updating track referencesfor NumtS tracks, refs #11549
• src/hg/makeDb/trackDb/orfeomeMrna.html
  • lines changed 1, context: html, text, full: html, text
    Fixing broken links on track description pages
• src/hg/makeDb/trackDb/pig/susScr2/numtSeq2012.html
  • lines changed 19, context: html, text, full: html, text
    Updating track referencesfor NumtS tracks, refs #11549
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    adding noScoreFilter to bigBed stanza (conflicts with docs), adding noScoreFilter to hgmd track as of #10935
• src/hg/makeDb/trackDb/tasmanianDevil/trackDb.chainNet.ra
  • lines changed 4, context: html, text, full: html, text
    Made chain/net changes; created new files for sarHar1 so appropriate values would appear in chain/net description page; edited hg19 files so tasmanian devil would appear properly (redmine #11552)
• src/hg/makeDb/trackDb/tasmanianDevil/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Made chain/net changes; created new files for sarHar1 so appropriate values would appear in chain/net description page; edited hg19 files so tasmanian devil would appear properly (redmine #11552)
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    adding track INSDC name refs #11348
  • lines changed 8, context: html, text, full: html, text
    adding search rule and html doc for ucscToINSDC track refs #11348
• src/hg/makeDb/trackDb/ucscToINSDC.html
  • lines changed 16, context: html, text, full: html, text
    adding search rule and html doc for ucscToINSDC track refs #11348
• src/hg/makefile
  • lines changed 5, context: html, text, full: html, text
    proper clean target for TEST_DIRS refs #9149
• src/hg/qaPushQ/makefile
  • lines changed 1, context: html, text, full: html, text
    fixing hgwbeta login after hardware move to san diego
• src/hg/qaPushQ/qaPushQ.c
  • lines changed 4, context: html, text, full: html, text
    fixing minor anti-sqli problems
• src/hg/utils/cpAndLinkToResourceFiles.pl
  • lines changed 1, context: html, text, full: html, text
    do not need the host hgwdevSD refs #8875
• src/hg/utils/decipher/buildDecipher
  • lines changed 42, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/decipher/checkDecipher.sh
  • lines changed 104, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/decipher/decipher.tables
  • lines changed 4, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/decipher/decipherWrapper.sh
  • lines changed 8, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/decipher/validateDecipher.sh
  • lines changed 30, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/gwas/checkGwas.sh
  • lines changed 76, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/gwas/expectedColumns.txt
  • lines changed 34, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/gwas/gwasWrapper.sh
  • lines changed 8, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/gwas/makefile
  • lines changed 23, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/gwas/perlParser.pl
  • lines changed 38, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/gwas/validateGwas.sh
  • lines changed 30, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/isca/buildISCA.csh
  • lines changed 55, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/isca/checkISCA.sh
  • lines changed 72, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/isca/isca.tables
  • lines changed 9, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/isca/iscaWrapper.sh
  • lines changed 8, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/isca/makefile
  • lines changed 20, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/isca/validateISCA.sh
  • lines changed 35, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/omim/buildOmimTracks.csh
  • lines changed 175, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/omim/checkOmim.sh
  • lines changed 148, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/omim/checkOmimUpload.sh
  • lines changed 80, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/omim/doOmimAv/doOmimAv.c
  • lines changed 219, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/omim/doOmimAv/makefile
  • lines changed 21, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/omim/doOmimGene2/doOmimGene2.c
  • lines changed 98, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/omim/doOmimGene2/makefile
  • lines changed 21, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/omim/doOmimGeneSymbols/doOmimGeneSymbols.c
  • lines changed 81, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/omim/doOmimGeneSymbols/makefile
  • lines changed 21, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/omim/doOmimLocation/doOmimLocation.c
  • lines changed 311, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/omim/doOmimLocation/makefile
  • lines changed 21, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/omim/makefile
  • lines changed 21, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/omim/omim.tables
  • lines changed 9, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/omim/omimUploadWrapper.sh
  • lines changed 9, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/omim/omimWrapper.sh
  • lines changed 8, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/omim/parseGeneMap.pl
  • lines changed 221, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/omim/validateOmim.sh
  • lines changed 35, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/decipher/buildDecipher
  • lines changed 42, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/decipher/checkDecipher.sh
  • lines changed 104, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/decipher/decipher.tables
  • lines changed 4, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/decipher/decipherWrapper.sh
  • lines changed 8, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/decipher/validateDecipher.sh
  • lines changed 30, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/gwas/checkGwas.sh
  • lines changed 76, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/gwas/expectedColumns.txt
  • lines changed 34, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/gwas/gwasWrapper.sh
  • lines changed 8, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/gwas/makefile
  • lines changed 23, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/gwas/perlParser.pl
  • lines changed 38, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/gwas/validateGwas.sh
  • lines changed 30, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/isca/buildISCA.csh
  • lines changed 55, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/isca/checkISCA.sh
  • lines changed 72, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/isca/isca.tables
  • lines changed 9, context: html, text, full: html, text
    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/isca/iscaWrapper.sh
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• src/hg/utils/otto/isca/makefile
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• src/hg/utils/otto/isca/validateISCA.sh
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    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/omim/buildOmimTracks.csh
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    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/omim/checkOmim.sh
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    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/omim/checkOmimUpload.sh
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• src/hg/utils/otto/omim/doOmimAv/doOmimAv.c
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• src/hg/utils/otto/omim/doOmimAv/makefile
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• src/hg/utils/otto/omim/doOmimGene2/doOmimGene2.c
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    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/omim/doOmimGene2/makefile
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• src/hg/utils/otto/omim/doOmimGeneSymbols/doOmimGeneSymbols.c
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• src/hg/utils/otto/omim/doOmimGeneSymbols/makefile
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• src/hg/utils/otto/omim/doOmimLocation/doOmimLocation.c
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• src/hg/utils/otto/omim/doOmimLocation/makefile
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• src/hg/utils/otto/omim/makefile
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• src/hg/utils/otto/omim/omim.tables
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• src/hg/utils/otto/omim/omimUploadWrapper.sh
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• src/hg/utils/otto/omim/omimWrapper.sh
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    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/omim/parseGeneMap.pl
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    redid the refGene.exonAA file for the 46-way on hg19, also somealignments of killer whale for skunk project
    
• src/hg/utils/otto/omim/validateOmim.sh
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• src/hg/utils/phyloTrees/vertebrates.txt
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    adding Ostrich - Struthio camelus refs #10272
• src/inc/cgi_build_rules.mk
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    install move should remove target first refs #9149
• src/inc/common.mk
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    make HAL linked in by default, fix the problem with mismatched bases nothaving the right chars in them, start adding HAL to the table browser.
    refs #10637
    
• src/lib/annoStreamVcf.c
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    Fix for #11519: annoStreamVcf wasn't chr-ifying VCF seq names (whichcan be 1, 2, 3 instead of chr1, chr2, chr3) before comparing with the
    current region chrom (or minChrom).
    
• src/lib/twoBit.c
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    Speedup for twoBitIsSequence: look up name in tbf->hash instead of scanning indexList.
• src/product/scripts/fetchMinimalGbdb.sh
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    inform messages about where log file exists for script results and echo messages to stederr refs #9104
• src/product/scripts/kentSrcUpdate.sh
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    inform messages about where log file exists for script results and echo messages to stederr refs #9104
• src/product/scripts/minimal.db.list.txt
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    inform messages about where log file exists for script results and echo messages to stederr refs #9104
• src/product/scripts/updateHtml.sh
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    inform messages about where log file exists for script results and echo messages to stederr refs #9104
• src/utils/qa/weeklybld/buildEnv.csh
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    v288 final build

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• files changed: 164