All File Changes

v287_preview2 to v287_base (2013-07-23 to 2013-07-30) v287

• confs/genome-browser-mirror.hg.conf
  • lines changed 109, context: html, text, full: html, text
    check in hg.conf files for euronode, preview, and the RR refs #8383
  • lines changed 3, context: html, text, full: html, text
    note 46 of redmiine 8383.
  • lines changed 3, context: html, text, full: html, text
    Per redmine 8383 note 49.
• confs/hgwbeta-public.hg.conf
  • lines changed 1, context: html, text, full: html, text
    note 46 of redmiine 8383.
• confs/preview.hg.conf
  • lines changed 245, context: html, text, full: html, text
    check in hg.conf files for euronode, preview, and the RR refs #8383
• confs/rr.hg.conf
  • lines changed 112, context: html, text, full: html, text
    check in hg.conf files for euronode, preview, and the RR refs #8383
  • lines changed 3, context: html, text, full: html, text
    note 46 of redmiine 8383.
  • lines changed 3, context: html, text, full: html, text
    Per redmine 8383 note 49.
• src/hg/encode3/encodeDataWarehouse/edwAddQaContamTarget/edwAddQaContamTarget.c
  • lines changed 52, context: html, text, full: html, text
    Seems to work.
• src/hg/encode3/encodeDataWarehouse/edwAddQaContamTarget/makefile
  • lines changed 4, context: html, text, full: html, text
    Seems to work.
• src/hg/encode3/encodeDataWarehouse/edwAddQaContamTarget/makk
  • lines changed 3, context: html, text, full: html, text
    Seems to work.
• src/hg/encode3/encodeDataWarehouse/edwAddQaEnrichTarget/edwAddQaEnrichTarget.c
  • lines changed 1, context: html, text, full: html, text
    Changing connect to use librrary routine.
• src/hg/encode3/encodeDataWarehouse/edwChangeFormat/edwChangeFormat.c
  • lines changed 47, context: html, text, full: html, text
    Making new edwCorrectFileTags utility to correct file tags after upload. Moving stuff from edwChangeFormat to library to reuse in this context.
• src/hg/encode3/encodeDataWarehouse/edwCorrectFileTags/edwCorrectFileTags.c
  • lines changed 104, context: html, text, full: html, text
    Making new edwCorrectFileTags utility to correct file tags after upload. Moving stuff from edwChangeFormat to library to reuse in this context.
• src/hg/encode3/encodeDataWarehouse/edwCorrectFileTags/makefile
  • lines changed 4, context: html, text, full: html, text
    Making new edwCorrectFileTags utility to correct file tags after upload. Moving stuff from edwChangeFormat to library to reuse in this context.
• src/hg/encode3/encodeDataWarehouse/edwCorrectFileTags/makk
  • lines changed 3, context: html, text, full: html, text
    Making new edwCorrectFileTags utility to correct file tags after upload. Moving stuff from edwChangeFormat to library to reuse in this context.
• src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/edwMakeValidFile.c
  • lines changed 58, context: html, text, full: html, text
    refactored rcc and idat validationi code into encode3Valid.c; use it in edwMakeValidFile.c and validateFiles.c; call vf from vm for rcc, idat, and also added fasta type
  • lines changed 133, context: html, text, full: html, text
    Moving several routines to library. Supporting fasta files.
• src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c
  • lines changed 112, context: html, text, full: html, text
    Adding support for replacement operations.
  • lines changed 1, context: html, text, full: html, text
    Adding fasta files.
• src/hg/encode3/encodeDataWarehouse/edwWebDeprecate/edwWebDeprecate.c
  • lines changed 163, context: html, text, full: html, text
    First cut seems to work.
  • lines changed 3, context: html, text, full: html, text
    Improving memory management.
• src/hg/encode3/encodeDataWarehouse/edwWebDeprecate/makefile
  • lines changed 16, context: html, text, full: html, text
    First cut seems to work.
• src/hg/encode3/encodeDataWarehouse/edwWebDeprecate/makk
  • lines changed 3, context: html, text, full: html, text
    Adding little script to send it to San Diego.
• src/hg/encode3/encodeDataWarehouse/edwWebSubmit/edwWebSubmit.c
  • lines changed 1, context: html, text, full: html, text
    Improving comment.
• src/hg/encode3/encodeDataWarehouse/inc/edwLib.h
  • lines changed 4, context: html, text, full: html, text
    Making new edwCorrectFileTags utility to correct file tags after upload. Moving stuff from edwChangeFormat to library to reuse in this context.
  • lines changed 5, context: html, text, full: html, text
    Moving edwAlignFastqMakeBed from edwMakeValid file to library so it can be shared.
• src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h
  • lines changed 152, context: html, text, full: html, text
    Defining tables for contamination screening.
• src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
  • lines changed 31, context: html, text, full: html, text
    Making new edwCorrectFileTags utility to correct file tags after upload. Moving stuff from edwChangeFormat to library to reuse in this context.
  • lines changed 87, context: html, text, full: html, text
    Moving edwAlignFastqMakeBed from edwMakeValid file to library so it can be shared.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as
  • lines changed 17, context: html, text, full: html, text
    Defining tables for contamination screening.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c
  • lines changed 355, context: html, text, full: html, text
    Defining tables for contamination screening.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql
  • lines changed 21, context: html, text, full: html, text
    Defining tables for contamination screening.
• src/hg/encode3/encodeDataWarehouse/lib/resetEdw
  • lines changed 2, context: html, text, full: html, text
    Whitelisting Cricket under her Stanford email.
  • lines changed 12, context: html, text, full: html, text
    Adding a bunch of assemblies for use as contamination targets. Adding Katrina and Chin to white list.
• src/hg/encode3/encodeDataWarehouse/makefile
  • lines changed 4, context: html, text, full: html, text
    Added several new edw programs to higher level make.
• src/hg/encode3/validateFiles/validateFiles.c
  • lines changed 20, context: html, text, full: html, text
    refactored rcc and idat validationi code into encode3Valid.c; use it in edwMakeValidFile.c and validateFiles.c; call vf from vm for rcc, idat, and also added fasta type
• src/hg/encode3/validateManifest/validateManifest.c
  • lines changed 19, context: html, text, full: html, text
    refactored rcc and idat validationi code into encode3Valid.c; use it in edwMakeValidFile.c and validateFiles.c; call vf from vm for rcc, idat, and also added fasta type
• src/hg/hgTracks/simpleTracks.c
  • lines changed 4, context: html, text, full: html, text
    Registering track handlers for snp138 tables.
• src/hg/hgc/gencodeClick.c
  • lines changed 1, context: html, text, full: html, text
    added target = _blank to a link per Jonathan
  • lines changed 23, context: html, text, full: html, text
    updated links to APPRIS, which now requires a species name
• src/hg/htdocs/ENCODE/index.html
  • lines changed 51, context: html, text, full: html, text
    Adding a news entry about addition of BLUEPRINT Hub and ENCODE PDF, per Kate note-36 refs #11050
• src/hg/htdocs/ENCODE/newsarch.html
  • lines changed 96, context: html, text, full: html, text
    Adding a news entry about addition of BLUEPRINT Hub and ENCODE PDF, per Kate note-36 refs #11050
• src/hg/htdocs/FAQ/FAQblat.html
  • lines changed 18, context: html, text, full: html, text
    Added paragraph to try to discourage users from trying to exactly replicate web-based blat on command-line blat, refs #11295
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 2, context: html, text, full: html, text
    Added line to assembly hubs section to point users to wiki page for more info
• src/hg/htdocs/goldenPath/help/hgVaiHelpText.html
  • lines changed 4, context: html, text, full: html, text
    Changed wording in acknowledgements as suggested by b0b in note-146. refs #6152
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 40, context: html, text, full: html, text
    Added announcement for hgVai to indexNews and newsarch, and changed announcements for Gene Alleles and UCSC Genes to their condensed versions on indexNews.
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 303, context: html, text, full: html, text
    Updating publications entries with new getTrackReferences, refs #11400
• src/hg/htdocs/indexNews.html
  • lines changed 134, context: html, text, full: html, text
    Added announcement for hgVai to indexNews and newsarch, and changed announcements for Gene Alleles and UCSC Genes to their condensed versions on indexNews.
• src/hg/htdocs/makefile
  • lines changed 1, context: html, text, full: html, text
    change make beta to update both hgwbeta and hgwdev-beta
• src/hg/htdocs/staff.html
  • lines changed 1, context: html, text, full: html, text
    Fixing colon position in my name refs #11373
• src/hg/htdocs/style/makefile
  • lines changed 2, context: html, text, full: html, text
    changes to facilitate beta builds on dev. Appropriating beta target, and assuming that USER=beta exists on dev.
• src/hg/inc/encode3/encode3Valid.h
  • lines changed 6, context: html, text, full: html, text
    refactored rcc and idat validationi code into encode3Valid.c; use it in edwMakeValidFile.c and validateFiles.c; call vf from vm for rcc, idat, and also added fasta type
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v287
• src/hg/js/makefile
  • lines changed 2, context: html, text, full: html, text
    changes to facilitate beta builds on dev. Appropriating beta target, and assuming that USER=beta exists on dev.
• src/hg/lib/annoStreamDb.c
  • lines changed 16, context: html, text, full: html, text
    Fixing bug reported by user in MLQ #11401. I missed a corner case:it's getFinestBin's job to set self->gotFinestBin, *but* nextRowFiltered
    calls nextRowRaw in a loop to skip past rows that precede minChrom,minEnd.
    nextRowRaw (nextRowFromBuffer) calls asdDoQueryChunking when it hits the
    end of the buffer, which it does when the entire buffer's contents precede
    the new minChrom,minEnd. In that case, getFinestBin is still waiting for
    a row so it has not yet set self->gotFinestBin. So before calling
    asdDoQueryChunking, nextRowFromBuffer needs to update self->gotFinestBin.
    While fixing that, I noticed that nextRowFromBuffer wasn't considering
    that rowBuf->size might be 0 if the query returns no rows.
    refs #11401
    
• src/hg/lib/encode3/encode3Valid.c
  • lines changed 80, context: html, text, full: html, text
    refactored rcc and idat validationi code into encode3Valid.c; use it in edwMakeValidFile.c and validateFiles.c; call vf from vm for rcc, idat, and also added fasta type
• src/hg/lib/web.c
  • lines changed 1, context: html, text, full: html, text
    changes to facilitate beta builds on dev. Appropriating beta target, and assuming that USER=beta exists on dev.
• src/hg/makeDb/schema/all.joiner
  • lines changed 2, context: html, text, full: html, text
    Added gadMor1 to ensGeneDb and ensGeneScaffold groups for Ensembl Genes v72 release (redmine #11114)
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
  • lines changed 6, context: html, text, full: html, text
    Added Vega version equivalence for gencode V17, added V17 to supertracks description
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV17.html
  • lines changed 13, context: html, text, full: html, text
    Fixed references, made a link open in a new window, added a filter description
  • lines changed 1, context: html, text, full: html, text
    Added Vega version equivalence for gencode V17, added V17 to supertracks description
• src/hg/makeDb/trackDb/makefile
  • lines changed 5, context: html, text, full: html, text
    build trix and cv.ra files for hgwdev-beta when there is a make beta.
• src/hg/makeDb/trackDb/sheep/oviAri3/gold.html
  • lines changed 2, context: html, text, full: html, text
    Removing period from html link in gold description, refs #9409
  • lines changed 3, context: html, text, full: html, text
    Moved message about dense mode to clarify when gold/brown coloration is used refs #9409
• src/hg/visiGene/vgGetText/makefile
  • lines changed 5, context: html, text, full: html, text
    add beta target to vgGetText makefile
• src/inc/cheapcgi.h
  • lines changed 5, context: html, text, full: html, text
    Making new edwCorrectFileTags utility to correct file tags after upload. Moving stuff from edwChangeFormat to library to reuse in this context.
• src/inc/genomeRangeTree.h
  • lines changed 2, context: html, text, full: html, text
    Adding functions to sum up size of all ranges in tree.
• src/inc/pipeline.h
  • lines changed 3, context: html, text, full: html, text
    enable SIGPIPE on linefile gzip subprocesses to allow closing the reading of compressed files before EOF is reached
• src/inc/rangeTree.h
  • lines changed 7, context: html, text, full: html, text
    Adding functions to sum up size of all ranges in tree.
• src/lib/cheapcgi.c
  • lines changed 26, context: html, text, full: html, text
    Making new edwCorrectFileTags utility to correct file tags after upload. Moving stuff from edwChangeFormat to library to reuse in this context.
• src/lib/genomeRangeTree.c
  • lines changed 11, context: html, text, full: html, text
    Adding functions to sum up size of all ranges in tree.
• src/lib/linefile.c
  • lines changed 3, context: html, text, full: html, text
    enable SIGPIPE on linefile gzip subprocesses to allow closing the reading of compressed files before EOF is reached
• src/lib/pipeline.c
  • lines changed 35, context: html, text, full: html, text
    enable SIGPIPE on linefile gzip subprocesses to allow closing the reading of compressed files before EOF is reached
• src/lib/rangeTree.c
  • lines changed 18, context: html, text, full: html, text
    Adding functions to sum up size of all ranges in tree.
• src/lib/tests/makefile
  • lines changed 6, context: html, text, full: html, text
    enable SIGPIPE on linefile gzip subprocesses to allow closing the reading of compressed files before EOF is reached
• src/lib/tests/pipelineTester.c
  • lines changed 17, context: html, text, full: html, text
    enable SIGPIPE on linefile gzip subprocesses to allow closing the reading of compressed files before EOF is reached
• src/utils/qa/realTime.csh
  • lines changed 3, context: html, text, full: html, text
    realTime.csh now checks hgw6 instead of 8, since 8 is going away refs #8132
• src/utils/qa/weeklybld/buildBeta.csh
  • lines changed 16, context: html, text, full: html, text
    changes necessary to move the build to hgwdev
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 11, context: html, text, full: html, text
    changes necessary to move the build to hgwdev
  • lines changed 3, context: html, text, full: html, text
    v287 final build
• src/utils/qa/weeklybld/buildHgCentralSql.csh
  • lines changed 4, context: html, text, full: html, text
    using --order-by-primary in hgcentral dump build so that rows are returned in a stable order if there is an index (the primary if found)
• src/utils/qa/weeklybld/buildUtils.csh
  • lines changed 6, context: html, text, full: html, text
    changes necessary to move the build to hgwdev
• src/utils/qa/weeklybld/cherryPickCommits.csh
  • lines changed 5, context: html, text, full: html, text
    changes necessary to move the build to hgwdev
• src/utils/qa/weeklybld/coBranch.csh
  • lines changed 6, context: html, text, full: html, text
    changes necessary to move the build to hgwdev
• src/utils/qa/weeklybld/configureSandbox.csh
  • lines changed 8, context: html, text, full: html, text
    changes necessary to move the build to hgwdev
• src/utils/qa/weeklybld/doHgNearTestRobot.csh
  • lines changed 4, context: html, text, full: html, text
    changes necessary to move the build to hgwdev
• src/utils/qa/weeklybld/doHgTablesTestRobot.csh
  • lines changed 4, context: html, text, full: html, text
    changes necessary to move the build to hgwdev
• src/utils/qa/weeklybld/doNewBranch.csh
  • lines changed 4, context: html, text, full: html, text
    changes necessary to move the build to hgwdev
• src/utils/qa/weeklybld/doNewReview2.csh
  • lines changed 5, context: html, text, full: html, text
    fix up scripts for preview2 to not require hgwbeta
• src/utils/qa/weeklybld/doRobots.csh
  • lines changed 4, context: html, text, full: html, text
    changes necessary to move the build to hgwdev
• src/utils/qa/weeklybld/makeStrictBeta.csh
  • lines changed 5, context: html, text, full: html, text
    changes necessary to move the build to hgwdev
• src/utils/qa/weeklybld/tagNewBranch.csh
  • lines changed 5, context: html, text, full: html, text
    changes necessary to move the build to hgwdev
• src/utils/qa/weeklybld/tagPreview2.csh
  • lines changed 4, context: html, text, full: html, text
    fix up scripts for preview2 to not require hgwbeta
• src/utils/qa/weeklybld/updateCgiVersion.csh
  • lines changed 5, context: html, text, full: html, text
    changes necessary to move the build to hgwdev

• lines changed: 2974
• files changed: 95