All File Changes

v285_base to v286_preview (2013-06-18 to 2013-06-24) v286

• confs/hgwbeta-public.hg.conf
  • lines changed 16, context: html, text, full: html, text
    add the hg.conf for hgwbeta-public, update the hgwbeta and hgwdev versions to the currently in use versions
• confs/hgwbeta.hg.conf
  • lines changed 14, context: html, text, full: html, text
    add the hg.conf for hgwbeta-public, update the hgwbeta and hgwdev versions to the currently in use versions
  • lines changed 4, context: html, text, full: html, text
    take out the hgSuggest variables that we don't want people to know
• confs/hgwdev.hg.conf
  • lines changed 21, context: html, text, full: html, text
    add the hg.conf for hgwbeta-public, update the hgwbeta and hgwdev versions to the currently in use versions
  • lines changed 4, context: html, text, full: html, text
    take out the hgSuggest variables that we don't want people to know
• src/hg/hgGene/pathways.c
  • lines changed 3, context: html, text, full: html, text
    fix link-out to bioCyc
• src/hg/hgGene/synonym.c
  • lines changed 1, context: html, text, full: html, text
    add a missing slash that Fan failed to add in 2009. RIP. This fixes link-outs in "Other names" in the case of splice isoforms.
• src/hg/hgTables/bedList.c
  • lines changed 1, context: html, text, full: html, text
    Fixing problems with the way hgTables and hgVai handled failed position searches.fixes #10964, refs #6152
    
• src/hg/hgTables/compositeTrack.c
  • lines changed 2, context: html, text, full: html, text
    Fixing problems with the way hgTables and hgVai handled failed position searches.fixes #10964, refs #6152
    
• src/hg/hgTables/correlate.c
  • lines changed 1, context: html, text, full: html, text
    Fixing problems with the way hgTables and hgVai handled failed position searches.fixes #10964, refs #6152
    
• src/hg/hgTables/custom.c
  • lines changed 1, context: html, text, full: html, text
    Fixing problems with the way hgTables and hgVai handled failed position searches.fixes #10964, refs #6152
    
• src/hg/hgTables/filterFields.c
  • lines changed 2, context: html, text, full: html, text
    Fixing problems with the way hgTables and hgVai handled failed position searches.fixes #10964, refs #6152
    
• src/hg/hgTables/hgTables.c
  • lines changed 16, context: html, text, full: html, text
    Fixing problems with the way hgTables and hgVai handled failed position searches.fixes #10964, refs #6152
    
• src/hg/hgTables/hgTables.h
  • lines changed 1, context: html, text, full: html, text
    Fixing problems with the way hgTables and hgVai handled failed position searches.fixes #10964, refs #6152
    
• src/hg/hgTables/intersect.c
  • lines changed 2, context: html, text, full: html, text
    Fixing problems with the way hgTables and hgVai handled failed position searches.fixes #10964, refs #6152
    
• src/hg/hgTables/mainPage.c
  • lines changed 2, context: html, text, full: html, text
    Fixing problems with the way hgTables and hgVai handled failed position searches.fixes #10964, refs #6152
    
• src/hg/hgTracks/chainTrack.c
  • lines changed 1, context: html, text, full: html, text
    fixing "force index (bin)" with %-s
• src/hg/hgTracks/pubsTracks.c
  • lines changed 41, context: html, text, full: html, text
    fixed performance bug #6833, forgot to check for dense mode
• src/hg/hgTracks/simpleTracks.c
  • lines changed 2, context: html, text, full: html, text
    fixes errors about: multiple occurrences of NOSQLINJ; and buffer overflow, size 32; in hgTracks found with bac end pairs track
• src/hg/hgTracks/snakeTrack.c
  • lines changed 1, context: html, text, full: html, text
    fixing "force index (bin)" with %-s
• src/hg/hgVai/hgVai.c
  • lines changed 15, context: html, text, full: html, text
    Last-minute bugfixes and wording tweaks. refs #6152
  • lines changed 3, context: html, text, full: html, text
    Oops, .bed4 wasn't taking precedence as intended.
  • lines changed 12, context: html, text, full: html, text
    Fixing problems with the way hgTables and hgVai handled failed position searches.fixes #10964, refs #6152
    
  • lines changed 1, context: html, text, full: html, text
    Fixing my harebrained JS that caused IE 9/10 to never successfully submit the form, as reported by Brooke in #6152 note 67.refs #6152
    
• src/hg/hgVai/libifyMe.c
  • lines changed 1, context: html, text, full: html, text
    Fixing problems with the way hgTables and hgVai handled failed position searches.fixes #10964, refs #6152
    
• src/hg/hgc/gencodeClick.c
  • lines changed 2, context: html, text, full: html, text
    gencode V17 import
• src/hg/hgc/pubs.c
  • lines changed 30, context: html, text, full: html, text
    working around a sqlinj messages
  • lines changed 1, context: html, text, full: html, text
    changing sqlinc printf to use %-s instead of append
  • lines changed 24, context: html, text, full: html, text
    going back to using %-s in sqlSafef rather than the sqlDyString functions
• src/hg/htdocs/contacts.html
  • lines changed 2, context: html, text, full: html, text
    Changed suggestion cgi link to be relative, refs #11002
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 13, context: html, text, full: html, text
    Cleaning up Table of Contents to correspond to actual section headings. refs #8072
• src/hg/htdocs/goldenPath/help/hgVaiHelpText.html
  • lines changed 9, context: html, text, full: html, text
    Added note saying that this is the initial release of hgVai and soliciting feedback and bug reports.
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 1, context: html, text, full: html, text
    Correcting link to downloads for #Ferret to #ferret, code review refs #11093
• src/hg/htdocs/indexNews.html
  • lines changed 1, context: html, text, full: html, text
    Correcting link to downloads for #Ferret to #ferret, code review refs #11093
• src/hg/lib/annoFormatVep.c
  • lines changed 46, context: html, text, full: html, text
    Last-minute bugfixes and wording tweaks. refs #6152
• src/hg/lib/annoStreamDb.c
  • lines changed 12, context: html, text, full: html, text
    found sql code that needed protection against sql injection
• src/hg/lib/hdb.c
  • lines changed 1, context: html, text, full: html, text
    unneeded %s for literal query
  • lines changed 1, context: html, text, full: html, text
    make a small buffer bigger
• src/hg/lib/hgFind.c
  • lines changed 1, context: html, text, full: html, text
    Fixing problems with the way hgTables and hgVai handled failed position searches.fixes #10964, refs #6152
    
• src/hg/lib/jksql.c
  • lines changed 11, context: html, text, full: html, text
    dealing with code looking for split tableNames which unfortunately use chrom names with dashes which mysql does not allow.
• src/hg/lib/liftOverChain.c
  • lines changed 1, context: html, text, full: html, text
    oops, I accidentally deleted the single quotes around the path field somehow, this puts them back the way it was.
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    add localEnvironment.mk include so local makes can work here for userApps refs #9149
• src/hg/makeDb/doc/ailMel1.txt
  • lines changed 21, context: html, text, full: html, text
    catching up windowMasker on all 100+ assemblies refs #10272
• src/hg/makeDb/doc/calJac3.txt
  • lines changed 21, context: html, text, full: html, text
    catching up windowMasker on all 100+ assemblies refs #10272
• src/hg/makeDb/doc/danRer7.txt
  • lines changed 28, context: html, text, full: html, text
    catching up windowMasker on all 100+ assemblies refs #10272
• src/hg/makeDb/doc/echTel2.txt
  • lines changed 82, context: html, text, full: html, text
    lastz to echTel2 and sorAra2 refs #9348 #9693
• src/hg/makeDb/doc/encodeRegHg19.txt
  • lines changed 31, context: html, text, full: html, text
    Drop display at >10Mbp window to prevent performance degradation. Not very interesting to view at this zoom level, so not much lost. Alternative would be to trim schema so sparse expScores are represented as a list of non-zero scores, and a list of eexpNums to identify (abandon microarray convention). refs #10097
• src/hg/makeDb/doc/equCab2.txt
  • lines changed 21, context: html, text, full: html, text
    catching up windowMasker on all 100+ assemblies refs #10272
• src/hg/makeDb/doc/gorGor3.txt
  • lines changed 19, context: html, text, full: html, text
    catching up windowMasker on all 100+ assemblies refs #10272
• src/hg/makeDb/doc/hg19.txt
  • lines changed 4, context: html, text, full: html, text
    updated GENCODE publications list
  • lines changed 3, context: html, text, full: html, text
    make current GENCODE public pack by default within supertrack
  • lines changed 342, context: html, text, full: html, text
    running lastz runs for ochPri3 oviAri3 sorAra2 taeGut2 vicPac2 refs #9347 #9409 #9348 #10190 #10833
  • lines changed 74, context: html, text, full: html, text
    gencode V17 import
  • lines changed 42, context: html, text, full: html, text
    running lastz runs for ochPri3 oviAri3 sorAra2 taeGut2 vicPac2 refs #9347 #9409 #9348 #10190 #10833
• src/hg/makeDb/doc/hgFixed.txt
  • lines changed 26, context: html, text, full: html, text
    load ctdSorted table
• src/hg/makeDb/doc/loxAfr1.txt
  • lines changed 21, context: html, text, full: html, text
    construct liftOvers to loxAfr3 refs #11064
• src/hg/makeDb/doc/loxAfr2.txt
  • lines changed 21, context: html, text, full: html, text
    construct liftOvers to loxAfr3 refs #11064
• src/hg/makeDb/doc/loxAfr3.txt
  • lines changed 21, context: html, text, full: html, text
    catching up windowMasker on all 100+ assemblies refs #10272
• src/hg/makeDb/doc/melGal1.txt
  • lines changed 21, context: html, text, full: html, text
    catching up windowMasker on all 100+ assemblies refs #10272
• src/hg/makeDb/doc/mm10.txt
  • lines changed 130, context: html, text, full: html, text
    lastz to echTel2 and sorAra2 refs #9348 #9693
• src/hg/makeDb/doc/myoLuc2.txt
  • lines changed 21, context: html, text, full: html, text
    catching up windowMasker on all 100+ assemblies refs #10272
• src/hg/makeDb/doc/ochPri3.txt
  • lines changed 2074, context: html, text, full: html, text
    running masking refs #9347
  • lines changed 48, context: html, text, full: html, text
    masking done starting genscan cpgIslands and ready for genbank refs #9347
• src/hg/makeDb/doc/ornAna1.txt
  • lines changed 20, context: html, text, full: html, text
    catching up windowMasker on all 100+ assemblies refs #10272
• src/hg/makeDb/doc/oryCun2.txt
  • lines changed 21, context: html, text, full: html, text
    catching up windowMasker on all 100+ assemblies refs #10272
• src/hg/makeDb/doc/ponAbe2.txt
  • lines changed 21, context: html, text, full: html, text
    catching up windowMasker on all 100+ assemblies refs #10272
• src/hg/makeDb/doc/rn5.txt
  • lines changed 43, context: html, text, full: html, text
    prompted NCBI to fix the rn5 cytoband file, load up cytoBand and Ideo refs #8529
• src/hg/makeDb/doc/sorAra2.txt
  • lines changed 73, context: html, text, full: html, text
    lastz to echTel2 and sorAra2 refs #9348 #9693
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added vicPac2 to daily hgwdev build refs #10833
  • lines changed 1, context: html, text, full: html, text
    Added oviAri3. refs #9409
  • lines changed 1, context: html, text, full: html, text
    Added allMis1 refs #8750
  • lines changed 1, context: html, text, full: html, text
    added CHM1 assembly to genbank
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 17, context: html, text, full: html, text
    adding eriEur2 hedgehog refs #9419
  • lines changed 1, context: html, text, full: html, text
    don't add xenoMrna to taeGut2
  • lines changed 19, context: html, text, full: html, text
    added CHM1 assembly to genbank
  • lines changed 7, context: html, text, full: html, text
    fixed problem with CHM1 genbank conf
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added vicPac2 to daily hgwdev build refs #10833
  • lines changed 1, context: html, text, full: html, text
    Added oviAri3. refs #9409
  • lines changed 1, context: html, text, full: html, text
    Added allMis1 refs #8750
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 1, context: html, text, full: html, text
    added CHM1 assembly to genbank
• src/hg/makeDb/schema/all.joiner
  • lines changed 17, context: html, text, full: html, text
    adding vicPac2 rules refs #10833
  • lines changed 11, context: html, text, full: html, text
    adding allMis1 rules refs #8750
  • lines changed 80, context: html, text, full: html, text
    gencode V17 import
  • lines changed 6, context: html, text, full: html, text
    added knownGeneOld6Id for old known gene check
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    Made changes necessary to add hg19 <-> panTro4 chain/net track (redmine #10795)
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    gencode V17 import
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV16.html
  • lines changed 10, context: html, text, full: html, text
    updated GENCODE publications list
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV16.ra
  • lines changed 1, context: html, text, full: html, text
    make current GENCODE public pack by default within supertrack
  • lines changed 1, context: html, text, full: html, text
    gencode V17 import
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV17.html
  • lines changed 347, context: html, text, full: html, text
    gencode V17 import
  • lines changed 1, context: html, text, full: html, text
    fixed typo in GENCODE V17 track description
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV17.ra
  • lines changed 263, context: html, text, full: html, text
    gencode V17 import
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 1, context: html, text, full: html, text
    Drop display at >10Mbp window to prevent performance degradation. Not very interesting to view at this zoom level, so not much lost. Alternative would be to trim schema so sparse expScores are represented as a list of non-zero scores, and a list of eexpNums to identify (abandon microarray convention). refs #10097
• src/hg/makeDb/trackDb/human/hgmd.html
  • lines changed 16, context: html, text, full: html, text
    changes to HGMD text after feedback from frank schacherer
  • lines changed 9, context: html, text, full: html, text
    table browser off for hgmd, some changes to the text
• src/hg/makeDb/trackDb/human/trackDb.chainNet.ra
  • lines changed 6, context: html, text, full: html, text
    Made changes necessary to add hg19 <-> panTro4 chain/net track (redmine #10795)
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    table browser off for hgmd, some changes to the text
• src/hg/makeDb/trackDb/makefile
  • lines changed 2, context: html, text, full: html, text
    adding pika/ochPri3 to the build refs #9347
• src/hg/makeDb/trackDb/pika/ochPri3/description.html
  • lines changed 63, context: html, text, full: html, text
    initial pika files ochPri3 from makeGenomeDb.pl refs #9347
• src/hg/makeDb/trackDb/pika/ochPri3/gap.html
  • lines changed 30, context: html, text, full: html, text
    initial pika files ochPri3 from makeGenomeDb.pl refs #9347
• src/hg/makeDb/trackDb/pika/ochPri3/gold.html
  • lines changed 34, context: html, text, full: html, text
    initial pika files ochPri3 from makeGenomeDb.pl refs #9347
• src/hg/makeDb/trackDb/pika/ochPri3/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial pika files ochPri3 from makeGenomeDb.pl refs #9347
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    Drop display at >10Mbp window to prevent performance degradation. Not very interesting to view at this zoom level, so not much lost. Alternative would be to trim schema so sparse expScores are represented as a list of non-zero scores, and a list of eexpNums to identify (abandon microarray convention). refs #10097
• src/hg/near/hgNear/go.c
  • lines changed 8, context: html, text, full: html, text
    fixes error in hgNear (found in rn4 partial fix for #7129) " %s value is NULL which is incorrect."
• src/hg/near/hgNear/hgNearData/Rat/rn4/columnDb.ra
  • lines changed 1, context: html, text, full: html, text
    fix sqli problem in gene sorter on RGD genes in rn4.
• src/hg/near/hgNear/knownGene.c
  • lines changed 12, context: html, text, full: html, text
    fix bug related to multiple NOSQLINJ prefixes found
• src/hg/utils/automation/EnsGeneAutomate.pm
  • lines changed 197, context: html, text, full: html, text
    adding ensGene v72 definitions, suspiciously identical to v71, refs #11114
• src/inc/common.mk
  • lines changed 15, context: html, text, full: html, text
    add new rules for finding mysql as found by compiling on beer30 refs #9149
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    add localEnvironment.mk include so local makes can work here for userApps refs #9149
• src/product/ex.hg.conf
  • lines changed 1, context: html, text, full: html, text
    Minor grammar edit, refs #11092
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v286 preview1

• lines changed: 4779
• files changed: 111