All File Changes

v286_preview to v286_preview2 (2013-06-24 to 2013-07-02) v286

• python/lib/ucscGb/qa/tables/positionalQa.py
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    Added pgSnp track types to chromTypes list.
• src/fuzzyFind/ffapp.c
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    removing unneeded carefulCheckHeap calls since pushCarefulMemHandler was not being used and thus the check did absolutely nothing.
• src/hg/dnaGene/dnaGene.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/gsid/pbGsid/pbGsid.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/hgGateway/hgGateway.c
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    fixes #11192 -- handling https in redirects between ucsc and other official mirror sites like genome-euro
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    oops.
• src/hg/hgGene/ctd.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/hgGene/pathways.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/hgGene/pseudoGene.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/hgGene/synonym.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/hgTracks/pubsTracks.c
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    fixing comment CR #11140
• src/hg/hgTracks/retroGene.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/hgTracks/simpleTracks.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/hgUserSuggestion/hgUserSuggestion.c
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    To DO 11139 Upgrade to hgUserSuggestion spam blocking.
• src/hg/hgc/hgc.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/hgc/virusClick.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/htdocs/ENCODE/pubsEncode.html
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    Adding 2013 Year 5 update to ENCODE pubs html page
• src/hg/htdocs/FAQ/FAQdownloads.html
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    Changing track name in FAQ example, based on MLQ input refs #11154
• src/hg/htdocs/goldenPath/help/bigBed.html
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    some more changes to the doc for assembly hubs and track item search
• src/hg/htdocs/goldenPath/help/genomeEuro.html
  • lines changed 16, context: html, text, full: html, text
    Made changes suggested by b0b (redmine #3000,7481)
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    made the link to genome-euro bold
• src/hg/htdocs/goldenPath/help/haplotypes.html
  • lines changed 33, context: html, text, full: html, text
    Changed population and scoring sections to match style of other sections and fixed some typos and punctuation.
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
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    Uncommented line linking to genome-euro (redmine #9767)
• src/hg/htdocs/goldenPath/help/hgVaiHelpText.html
  • lines changed 322, context: html, text, full: html, text
    First draft of hgVai documentation. refs #6152
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    minor tweak: put tool's short/common name first, followed by long name.
• src/hg/htdocs/goldenPath/help/trix.html
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    some more changes to the doc for assembly hubs and track item search
• src/hg/htdocs/goldenPath/help/twoBit.html
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    some more changes to the doc for assembly hubs and track item search
• src/hg/htdocs/goldenPath/newsarch.html
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    Added news about suggestion box feature, refs #9142
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    Forgot to remove a comment from the html
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    removed some whitespace at the beginning of ~1000 lines at top of file
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    announcing euronode release
  • lines changed 37, context: html, text, full: html, text
    added news announcement for hg19 ucsc genes
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 21, context: html, text, full: html, text
    Added 3 new pubs.
• src/hg/htdocs/indexNews.html
  • lines changed 10, context: html, text, full: html, text
    added Ferret announcement to archive section, but commented out for now
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    Added news about suggestion box feature, refs #9142
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    fixed a missing tag opening
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    removed leading tabs and dropped 8 white spaces from each line
  • lines changed 111, context: html, text, full: html, text
    Resolved merge - edit conflicts between b0b and me
  • lines changed 18, context: html, text, full: html, text
    Added shortened suggestion announcement in a comment for archival use
  • lines changed 71, context: html, text, full: html, text
    announcing euronode release
  • lines changed 32, context: html, text, full: html, text
    added news announcement for hg19 ucsc genes
  • lines changed 1, context: html, text, full: html, text
    closed a broken tag that did not seem to break anything
• src/hg/htdocs/mirror.html
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    Added genome-euro to the list of mirrors (redmine #9769)
• src/hg/lib/hdb.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/lib/hgFind.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/lib/hubConnect.c
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    fix bug caused by my freeing memory that I was using as a cache. D'oh! refs #11165
• src/hg/lib/jksql.c
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    taking out unneeded debugging info in verbose=2 which was messing up genbank logging anyway
  • lines changed 12, context: html, text, full: html, text
    making the output a little safer for ignore situations so logs will not fill up with messages no one cares about
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    fixing dumpstack to use _exit instead of exit so that the child cleanup will not close the mysql connections that are shared with the parent process.
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    increasing the size of a couple of query arrays
• src/hg/lib/spDb.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/lib/web.c
  • lines changed 14, context: html, text, full: html, text
    fixes #11192 -- handling https in redirects between ucsc and other official mirror sites like genome-euro
• src/hg/makeDb/doc/allMis1.txt
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    done with genbank and blatServers entries refs #8750
• src/hg/makeDb/doc/echTel2.txt
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    done with genscan and lastz to mouse mm10 refs #9693
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    in the pushQ 007047 refs #9693
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    in the pushQ 007047 refs #9693
• src/hg/makeDb/doc/encodeRegHg19.txt
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    Performance work. refs #10097
• src/hg/makeDb/doc/eriEur1.txt
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    liftOver eriEur1 to eriEur2 refs #9419
• src/hg/makeDb/doc/hg19.txt
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    Added a cautionary note for the next dbSNP build, to look for rs IDs that havebeen mapped to assembly patch contigs but not the primary reference, because
    in at least some of those cases, mappings to the primary assembly show up on
    dbSNP's website but not in the download files. refs #8360
    
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    wrapping up lastz for echTel2 oviAri3 sorAra2 and starting lastz zonAlb2 refs #10272
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    done with lastz for zonAlb1 refs #10272
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    done with zonAlb1 lastz starting falChe1 falPer1 anaPla1 amaVit1 melUnd1 refs #10272
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    finishing up lastz for echTel2 oviAri3 falChe1 falPer1 anaPla1 amaVit1 allMis1 refs #10272
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    done with melUnd1 lastz refs #10272
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    done with falChe1 lastz refs #10272
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    starting lastz for colLiv1 ficAlb2 araMac1 galGal4 pseHum1 refs #10272
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    done with lastz for pseHum1 ficAlb2 colLiv1 refs #10272
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    done with lastz for araMac1 and galGal4 refs #10272
  • lines changed 59, context: html, text, full: html, text
    starting lastz on chlSab1 refs #10272
  • lines changed 72, context: html, text, full: html, text
    starting lastz on macFas3 refs #10272
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    starting lastz on saiBol1 and otoGar3 refs #10272
  • lines changed 87, context: html, text, full: html, text
    finishing off lastz for ochPri3 oviAri3 macFas5 saiBol1 otoGar3 refs #10272
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    done with lastz for allMis1 macFas5 ochPri3 refs #10272
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    running up swap lastz for tarSyr1 papHam1 tupBel1 pteVam1 refs #10272
• src/hg/makeDb/doc/mm10.txt
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    running lastz to vicPac2 refs #10833
• src/hg/makeDb/doc/oviAri1.txt
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    liftOver to oviAri3 refs #9409
• src/hg/makeDb/doc/oviAri3.txt
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    ready for all.joiner downloads and pushQ refs #9409
• src/hg/makeDb/doc/proteins/121210.txt
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    build a couple more tables in the proteins database
• src/hg/makeDb/doc/taeGut1.txt
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    liftOver taeGut1 to taeGut2 refs #10190
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes14.csh
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    rebuild after realizing I used rn4 instead of rheMac2 for zdb. D'oh!
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    generate new ucscGenePfam table
• src/hg/makeDb/doc/vicPac2.txt
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    in the pushQ 007048 refs #10833
• src/hg/makeDb/doc/xenTro7.txt
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    starting genbank refs #9868
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 2, context: html, text, full: html, text
    Added xenTro7. refs #9868
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    Added taeGut2. refs #10190
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    Added eriEur2 to daily hgwdev build refs #9419
• src/hg/makeDb/genbank/etc/genbank.conf
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    use less strengent filtering on CHM1
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    added native mRNAs and ESTs to CHM1
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    adding xenTro7 Xenopus (Silurana) tropicalis refs #9868
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    fix eriEur2 hedgehog entry for ooc file refs #9419
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added xenTro7. refs #9868
  • lines changed 1, context: html, text, full: html, text
    Added taeGut2. refs #10190
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    Added eriEur2 to daily hgwdev build refs #9419
• src/hg/makeDb/genbank/src/dbload/gbLoadRna.c
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    take out superflous printf on Hiram's request
• src/hg/makeDb/genbank/src/lib/sqlUpdater.c
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    make sqli play nice
• src/hg/makeDb/hgCalStat/hgCalStat.c
  • lines changed 9, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/makeDb/hgKgMrna/hgKgMrna.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/makeDb/outside/hgBioCyc/hgBioCyc.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/makeDb/outside/hgJaxQtl/hgJaxQtl.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/makeDb/outside/hgKegg/hgKegg.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/makeDb/outside/hgKegg2/hgKegg2.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/makeDb/outside/hgKegg3/hgKegg3.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/makeDb/outside/hgSuperfam/hgSuperfam.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/makeDb/schema/all.joiner
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    Replaced several personal genomes table names in the human tablesIgnored list with pg%. Angie approves. refs #683
• src/hg/makeDb/trackDb/cow/bosTau6/numtSeq2012.html
  • lines changed 110, context: html, text, full: html, text
    Finalized numtSeq2012.html for susScr2 and bosTau6
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    Make NumtS table searchable for susScr2 and bosTau6 redmine 8533.
• src/hg/makeDb/trackDb/cow/bosTau6/trackDb.ra
  • lines changed 18, context: html, text, full: html, text
    Make NumtS table searchable for susScr2 and bosTau6 redmine 8533.
• src/hg/makeDb/trackDb/gator/allMis1/trackDb.ra
  • lines changed 27, context: html, text, full: html, text
    adjusting default visibilities refs #8750
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeHaibMethyl450.ra
  • lines changed 127, context: html, text, full: html, text
    Staging metaData correction for wgEncodeHaibMethyl450wgEncodeHaibMethyl450 track, removing file references, files have probe mappings, we display single base in table, refs #10447
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeHaibMethyl450.ra
  • lines changed 127, context: html, text, full: html, text
    Staging metaData correction for wgEncodeHaibMethyl450wgEncodeHaibMethyl450 track, removing file references, files have probe mappings, we display single base in table, refs #10447
• src/hg/makeDb/trackDb/human/hg19/pgSnp.html
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    Updating Complete Genomics samples and references. refs #683
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    Clarifying which Genome Variants subtracks are native to hg19 and whichwere lifted. Unfortunately the per-subtrack origAssembly/pennantIcon
    settings aren't reflected in the hgTrackUi table of subtracks; that
    would be a nice feature.
    
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    Standardized punctuation on lists, put publications in CBSE citation format, fixed a link that was getting redirected, made several small grammar/punctuation tweaks. refs 683
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    Updating links & small fixes - thanks Brooke! refs #683
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    Changed 1000 Genomes Pilot labels to 1000 Genomes March 2010, per note-42 from Angie. refs #683
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 28, context: html, text, full: html, text
    Clarifying which Genome Variants subtracks are native to hg19 and whichwere lifted. Unfortunately the per-subtrack origAssembly/pennantIcon
    settings aren't reflected in the hgTrackUi table of subtracks; that
    would be a nice feature.
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.html
  • lines changed 2, context: html, text, full: html, text
    Updating links in HAIB Methy wgEncodeHaibMethyl450 track to point from hgdownload-test to hgdownload refs #10447
• src/hg/makeDb/trackDb/human/trackDb.pgSnp.ra
  • lines changed 1, context: html, text, full: html, text
    Shortening too-longLabel per Brooke's suggestion. refs #683
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    Changed 1000 Genomes Pilot labels to 1000 Genomes March 2010, per note-42 from Angie. refs #683
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    Made only the PSU, Saqqaq and AK1 visible by default per note-40. refs 683
• src/hg/makeDb/trackDb/pig/susScr2/numtSeq2012.html
  • lines changed 2, context: html, text, full: html, text
    Per 8533 note 39, the stement about 'a link pointing to ...' is removed.
  • lines changed 3, context: html, text, full: html, text
    Finalized numtSeq2012.html for susScr2 and bosTau6
• src/hg/makeDb/trackDb/pig/susScr2/trackDb.ra
  • lines changed 23, context: html, text, full: html, text
    Make NumtS table searchable for susScr2 and bosTau6 redmine 8533.
• src/hg/makeDb/trackDb/tenrec/echTel2/trackDb.ra
  • lines changed 18, context: html, text, full: html, text
    setting default track visibilities refs #9693
• src/hg/makefile
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    redmine 10685 Do not make mkEncodeFrameset anymore.
• src/hg/near/hgNear/hgNearData/Rat/rn4/orderDb.ra
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    fix the name similarity sort for rn4. refs #7129
• src/hg/oneShot/kgName/fbName.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/oneShot/kgName/kgName.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/pdbSP/pdbSP.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/fixAgp/fixAgp.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgAliasM/kgAliasM.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgAliasP/kgAliasP.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgBestMrna/kgPrepBestMrna.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgBestMrna/kgPrepBestMrna2.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgBestMrna/kgResultBestMrna.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgBestMrna2/kgPrepBestMrna2.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgBestMrna2/kgResultBestMrna2.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgBestRef2/kgPrepBestRef2.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgBestRef2/kgResultBestRef2.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgCheck/kgCheck.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgCheck2/kgCheck2.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgGetCds/kgGetCds.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgPepMrna/kgPepMrna.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgPick/kgPick.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgProtAlias/kgProtAlias.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgProtAliasNCBI/kgProtAliasNCBI.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgUniq/kgUniq.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgXref/kgXref.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/kgXref2/kgXref2.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/lib/doSam.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/lib/doStamps.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/lib/doTracks.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/lib/domains.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/lib/pbUtil.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/omimCheckAv/omimCheckAv.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/pbCalDist/pbCalDist.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/pbCalResStd/pbCalResStd.c
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    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/pbGlobal/pbGlobal.c
  • lines changed 12, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/pbTracks/pbTracks.c
  • lines changed 7, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/pfamXref/pfamXref.c
  • lines changed 1, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/rmKGPepMrna/rmKGPepMrna.c
  • lines changed 5, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/spToProteins/spToProteins.c
  • lines changed 3, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/spToProteinsVar/spToProteinsVar.c
  • lines changed 1, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/spXref3/spXref3.c
  • lines changed 2, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/spm6/spm6.c
  • lines changed 2, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/protein/spm7/spm7.c
  • lines changed 2, context: html, text, full: html, text
    fixing callers of sqlGetField to use sqlSafeFrag
• src/hg/pslReps/pslReps.c
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    removing unneeded carefulCheckHeap calls since pushCarefulMemHandler was not being used and thus the check did absolutely nothing.
• src/hg/utils/automation/doSimpleRepeat.pl
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    better cleaning of the TrfPart directory refs #10998
• src/hg/utils/automation/ensGeneScaffolds.pl
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    allow contig names to translate also refs #11114
• src/hg/utils/phyloTrees/108way.commonNames.nh
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    adding macFas5 chlSab1 araMac1 refs #10272
• src/hg/utils/phyloTrees/108way.nh
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    adding macFas5 chlSab1 araMac1 refs #10272
• src/hg/utils/phyloTrees/108way.scientificNames.nh
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    adding macFas5 chlSab1 araMac1 refs #10272
• src/hg/utils/phyloTrees/commonNames.sh
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    adding macFas5 chlSab1 araMac1 refs #10272
• src/hg/utils/phyloTrees/makefile
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    adding macFas5 chlSab1 araMac1 refs #10272
• src/hg/utils/phyloTrees/scientificNames.sh
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    adding macFas5 chlSab1 araMac1 refs #10272
• src/inc/common.h
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    fixing dumpstack to use _exit instead of exit so that the child cleanup will not close the mysql connections that are shared with the parent process.
• src/lib/errabort.c
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    fixing dumpstack to use _exit instead of exit so that the child cleanup will not close the mysql connections that are shared with the parent process.
• src/lib/memalloc.c
  • lines changed 21, context: html, text, full: html, text
    fixing bug in unlocking. There were too many places where returns and errAbort were leaving the routine without unlocking. It was easy to fix. Now I understand that if the user does not call pushCarefulMemHandler, then carefulParent is NULL and carefulCheckHeap exits early without doing anything. So only for routines that did NOT call pushCarefulMemHandler, but did call carefulCheckHeap multiple times was there a problem, and only pslReps util met those criteria
• src/lib/osunix.c
  • lines changed 22, context: html, text, full: html, text
    fixing dumpstack to use _exit instead of exit so that the child cleanup will not close the mysql connections that are shared with the parent process.
• src/lib/pipeline.c
  • lines changed 1, context: html, text, full: html, text
    fixing dumpstack to use _exit instead of exit so that the child cleanup will not close the mysql connections that are shared with the parent process.
• src/userApps/fetchKentSource.sh
  • lines changed 10, context: html, text, full: html, text
    ready for v286 with the beta branch fetch instead of HEAD refs #9149

• lines changed: 7770
• files changed: 181