All File Changes

v289_preview to v289_preview2 (2013-08-26 to 2013-09-02) v289

• confs/genome-browser-mirror.hg.conf
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    do not want bottleneck references in hg.conf, should be in hg.conf.private both for security and consistency
• confs/preview.hg.conf
  • lines changed 4, context: html, text, full: html, text
    do not want bottleneck references in hg.conf, should be in hg.conf.private both for security and consistency
• confs/rr.hg.conf
  • lines changed 6, context: html, text, full: html, text
    do not want bottleneck references in hg.conf, should be in hg.conf.private both for security and consistency
• src/hg/checkTableCoords/tests/makefile
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    Don't hardcode the path of true as /bin/true; not the same on all systems.
• src/hg/encode3/encodeDataWarehouse/README
  • lines changed 40, context: html, text, full: html, text
    Add process description and trouble-shooting tips from JK emails
• src/hg/encode3/encodeDataWarehouse/edwWebDeprecate/edwWebDeprecate.c
  • lines changed 29, context: html, text, full: html, text
    Add 'Allow me to deprecate files not uploaded by me' check box function to edwWebDeprecate.c
  • lines changed 2, context: html, text, full: html, text
    Add comments to checkOwnership() and okToDeprecateThisFile().
  • lines changed 5, context: html, text, full: html, text
    Style change plus using fileList = cgiString("fileList")
  • lines changed 21, context: html, text, full: html, text
    Move okToDeprecateThisFile check inside the process licensePlate loop.
• src/hg/encode3/encodeDataWarehouse/inc/edwLib.h
  • lines changed 3, context: html, text, full: html, text
    Add edwUserNameFromFileId() -- given submitted file id, returns user's name (email address).
• src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
  • lines changed 10, context: html, text, full: html, text
    Add edwUserNameFromFileId() -- given submitted file id, returns user's name (email address).
• src/hg/hgLogin/hgLogin.c
  • lines changed 1, context: html, text, full: html, text
    redmine bug 11652 Expand userList[256] to 512, should be long enough for any user.
• src/hg/hgTracks/makefile
  • lines changed 1, context: html, text, full: html, text
    add snake configuration options, only link in HAL libraries in hgTracks,temporarily(?) remove support for snakes based on chains #10637
    
• src/hg/hgTracks/makefile.hgRenderTracks
  • lines changed 1, context: html, text, full: html, text
    add snake configuration options, only link in HAL libraries in hgTracks,temporarily(?) remove support for snakes based on chains #10637
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 2, context: html, text, full: html, text
    add snake configuration options, only link in HAL libraries in hgTracks,temporarily(?) remove support for snakes based on chains #10637
    
• src/hg/hgTracks/snakeTrack.c
  • lines changed 3, context: html, text, full: html, text
    for the moment, always color blocks blue (per David)
  • lines changed 37, context: html, text, full: html, text
    add snake configuration options, only link in HAL libraries in hgTracks,temporarily(?) remove support for snakes based on chains #10637
    
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 1, context: html, text, full: html, text
    Correcting typo, removing double quote to single quote Code Review RM# 11621
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 10, context: html, text, full: html, text
    Added Sanborn et al. pub per David request.
• src/hg/inc/snakeUi.h
  • lines changed 27, context: html, text, full: html, text
    oops... forgot to add snakeUi.h
• src/hg/inc/trackDb.h
  • lines changed 1, context: html, text, full: html, text
    add snake configuration options, only link in HAL libraries in hgTracks,temporarily(?) remove support for snakes based on chains #10637
    
• src/hg/lib/annoStreamDb.c
  • lines changed 7, context: html, text, full: html, text
    Oops, forgot to check self->notSorted in chunking queries. fixes #11625
• src/hg/lib/hgFind.c
  • lines changed 11, context: html, text, full: html, text
    Searches on excessively broad terms (like 'test') were leading to CGI 504 timeouts. This was tracked to almost 5000 queries to gbCdnaInfo, a 93 million row table. Since the page presented to the user only shows the first 500 results, this one mRNA search will now be curtailed after the first 500 results. Redmine #11626.
• src/hg/lib/hubStatus.as
  • lines changed 1, context: html, text, full: html, text
    change dbList in hubStatus to be a blob instead of a varchar(255)
• src/hg/lib/hubStatus.sql
  • lines changed 1, context: html, text, full: html, text
    change dbList in hubStatus to be a blob instead of a varchar(255)
• src/hg/lib/hui.c
  • lines changed 3, context: html, text, full: html, text
    add snake configuration options, only link in HAL libraries in hgTracks,temporarily(?) remove support for snakes based on chains #10637
    
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    add snake configuration options, only link in HAL libraries in hgTracks,temporarily(?) remove support for snakes based on chains #10637
    
• src/hg/lib/snakeUi.c
  • lines changed 65, context: html, text, full: html, text
    double oops... need snakeUi.c too, obvs
• src/hg/lib/sqlProg.c
  • lines changed 63, context: html, text, full: html, text
    hgsql and friends utils: trying to make it so that the temp file and the child mysql process gets terminated when various signals such as Control-c, SIGINT, SIGABRT, SIGTERM etc are received
• src/hg/lib/trackDbCustom.c
  • lines changed 2, context: html, text, full: html, text
    add snake configuration options, only link in HAL libraries in hgTracks,temporarily(?) remove support for snakes based on chains #10637
    
• src/hg/makeDb/doc/encodeDccHg19/haibMethyl450.txt
  • lines changed 22, context: html, text, full: html, text
    Fix coords in bad Methyl450 table
• src/hg/makeDb/doc/hg19.txt
  • lines changed 206, context: html, text, full: html, text
    done with lastz runs on turTru2 orcOrc1 lipVex1 apaSpi1 cheMyd1 micOch1 refs #10272
  • lines changed 474, context: html, text, full: html, text
    Building snp138*. Initial config should not have ignoreDbSnpContigsWhatever. The first run will complain about not finding patch contigs. Use that run's suggestedLft as the list of contigs to ignore, after inspecting it first. It would be better to use a copy of it just in case somehow it gets overwritten with even more unfound contigs if we re-run or something... because the overwritten version would have only the newly unfound contigs.
  • lines changed 109, context: html, text, full: html, text
    wrapping up lastz runs for xipMac1 lipVex1 apaSpi1 cheMyd1 refs #10272
  • lines changed 193, context: html, text, full: html, text
    starting xenTro7 susScr3 speTri2 refs #10272
  • lines changed 85, context: html, text, full: html, text
    done with lastz for lipVex1 cheMyd1 xipMac1 and starting oreNil2 refs @10272
  • lines changed 34, context: html, text, full: html, text
    swapping lastz for xenTro7 susScr3 speTri2 oreNil2 refs #10272
  • lines changed 327, context: html, text, full: html, text
    finished lastz for xenTro7 and oreNil2 starting lastz for gadMor1 chrPic1 myoLuc2 chiLan1 pelSin1 refs #10272
  • lines changed 70, context: html, text, full: html, text
    catching up some older recipBest and synNet lastz runs and finishing off ponAbe2 gorGor3 cerSim1 orcOrc1 micOch1 susScr3 speTri2 chrPic1 myoLuc2 chiLan1 pelSin1 refs #10272
  • lines changed 372, context: html, text, full: html, text
    starting lastz runs for criGri1 mesAur1 pteAle1 myoDav1 eptFus1 takFla1 refs #10272
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 1, context: html, text, full: html, text
    Adding echTel2 to GenBank updates on beta (redmine #9693)
  • lines changed 1, context: html, text, full: html, text
    Adding oviAri3 to genbank update list on hgwbeta, refs #9409
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 1, context: html, text, full: html, text
    Added echTel2 (redmine #9693)
  • lines changed 1, context: html, text, full: html, text
    Adding oviAri3 to RR genbank update list, refs #9409
• src/hg/makeDb/schema/all.joiner
  • lines changed 12, context: html, text, full: html, text
    Adding snp138 to all.joiner. refs #11438
• src/hg/makeDb/trackDb/cpgIslandExt.html
  • lines changed 8, context: html, text, full: html, text
    Updated references
• src/hg/makeDb/trackDb/genscan.html
  • lines changed 1, context: html, text, full: html, text
    Edited Burge/Karlin reference
• src/hg/makeDb/trackDb/human/hg19/chainNetPlacental.ra
  • lines changed 2, context: html, text, full: html, text
    Edited .ra files for release of echTel2 (redmine #9693)
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 1, context: html, text, full: html, text
    Error notice for CSHL Long RNA-seq. refs #11005
  • lines changed 1, context: html, text, full: html, text
    Refresh magic number for metaDb
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeCshlLongRnaSeq.ra
  • lines changed 2, context: html, text, full: html, text
    Staging new metaData for errata of file refs #11005
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeCshlLongRnaSeq.ra
  • lines changed 2, context: html, text, full: html, text
    Staging new metaData for errata of file refs #11005
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release3.html
  • lines changed 5, context: html, text, full: html, text
    Error notice for CSHL Long RNA-seq. refs #11005
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.placentalsChainNet.ra
  • lines changed 6, context: html, text, full: html, text
    Edited .ra files for release of echTel2 (redmine #9693)
• src/hg/makeDb/trackDb/nestedRepeats.html
  • lines changed 3, context: html, text, full: html, text
    Updated references
• src/hg/makeDb/trackDb/rmsk.html
  • lines changed 3, context: html, text, full: html, text
    Updated references
• src/hg/makeDb/trackDb/simpleRepeat.html
  • lines changed 8, context: html, text, full: html, text
    Updated references
• src/hg/makeDb/trackDb/tenrec/echTel2/gap.html
  • lines changed 2, context: html, text, full: html, text
    Made minor formatting changes (redmine #9693)
• src/hg/makeDb/trackDb/tenrec/echTel2/gold.html
  • lines changed 3, context: html, text, full: html, text
    Made minor formatting changes (redmine #9693)
• src/hg/makeDb/trackDb/windowmaskerSdust.html
  • lines changed 1, context: html, text, full: html, text
    Updated references
• src/hg/makeDb/trackDb/xenoMrna.html
  • lines changed 1, context: html, text, full: html, text
    Adding a period at end of third paragraph of Display section
• src/hg/makeDb/trackDb/xenoRefGene.html
  • lines changed 9, context: html, text, full: html, text
    Updated references
• src/hg/snp/snpLoad/snpNcbiToUcsc.c
  • lines changed 8, context: html, text, full: html, text
    Building snp138*. Initial config should not have ignoreDbSnpContigsWhatever. The first run will complain about not finding patch contigs. Use that run's suggestedLft as the list of contigs to ignore, after inspecting it first. It would be better to use a copy of it just in case somehow it gets overwritten with even more unfound contigs if we re-run or something... because the overwritten version would have only the newly unfound contigs.
• src/hg/utils/automation/doDbSnp.pl
  • lines changed 1, context: html, text, full: html, text
    Building snp138*. Initial config should not have ignoreDbSnpContigsWhatever. The first run will complain about not finding patch contigs. Use that run's suggestedLft as the list of contigs to ignore, after inspecting it first. It would be better to use a copy of it just in case somehow it gets overwritten with even more unfound contigs if we re-run or something... because the overwritten version would have only the newly unfound contigs.
• src/hg/utils/automation/snpAddTGPAlleleFreq.pl
  • lines changed 84, context: html, text, full: html, text
    dbSNP has made yet another change to allele frequency info in snp138:now if there are no non-1000Genomes allele freq/counts, but there are
    1000Genomes freq/counts, the 1000Genomes freq/counts are copied into
    the otherwise non-1000Genomes table (SNPAlleleFreq_TGP data are copied
    into SNPAlleleFreq). Detect those cases of copying and don't add the
    duplicated freq/counts. refs #11438
    
• src/inc/common.mk
  • lines changed 6, context: html, text, full: html, text
    no librt on Mac OSX compile refs #11616
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    add snake configuration options, only link in HAL libraries in hgTracks,temporarily(?) remove support for snakes based on chains #10637
    
• src/utils/git-reports/git-reports.c
  • lines changed 11, context: html, text, full: html, text
    avoid problem of white space only diffs and missing zero length files refs #11571
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v289 preview2
• src/utils/qa/weeklybld/buildHgCentralSql.csh
  • lines changed 3, context: html, text, full: html, text
    fixup for SDSC MySQL 5.6 differences in the mysql dump command refs #11576
• src/utils/qa/weeklybld/doNewReview.csh
  • lines changed 1, context: html, text, full: html, text
    adding steve to the mail list refs #11576
• src/utils/qa/weeklybld/downloadBuildSettings.mk
  • lines changed 1, context: html, text, full: html, text
    need to build download files with SSL on since the new MySQL requires that, sorry, refs #11576

• lines changed: 2447
• files changed: 72