All File Changes

v283_preview2 to v283_base (2013-04-30 to 2013-05-07) v283

• src/hg/autoSql/autoSql.c
  • lines changed 1, context: html, text, full: html, text
    Fixing bug for lstring in saveToDb C output.
• src/hg/encode3/encodeDataWarehouse/edwMakeEnrichments/edwMakeEnrichments.c
  • lines changed 31, context: html, text, full: html, text
    Making it so that it won't recompute enrichments it already has done.
• src/hg/encode3/encodeDataWarehouse/edwMakeReplicateQa/edwMakeReplicateQa.c
  • lines changed 25, context: html, text, full: html, text
    Making it so it won't do QA comparisons it has already done.
• src/hg/encode3/encodeDataWarehouse/edwReallyRemoveFiles/edwReallyRemoveFiles.c
  • lines changed 125, context: html, text, full: html, text
    Adding command line utility to remove files from warehouse.
• src/hg/encode3/encodeDataWarehouse/edwReallyRemoveFiles/makefile
  • lines changed 4, context: html, text, full: html, text
    Adding command line utility to remove files from warehouse.
• src/hg/encode3/encodeDataWarehouse/edwRunDaemon/edwRunDaemon.c
  • lines changed 1, context: html, text, full: html, text
    Making temp files bear our name.
• src/hg/encode3/encodeDataWarehouse/edwScriptSubmit/edwScriptSubmit.c
  • lines changed 60, context: html, text, full: html, text
    First cut of script registration and submission.
• src/hg/encode3/encodeDataWarehouse/edwScriptSubmit/makefile
  • lines changed 16, context: html, text, full: html, text
    First cut of script registration and submission.
• src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c
  • lines changed 13, context: html, text, full: html, text
    Making disk full error reporting more graceful. Removing some debugging statements.
• src/hg/encode3/encodeDataWarehouse/edwWebBrowse/edwWebBrowse.c
  • lines changed 1, context: html, text, full: html, text
    Fixing a <B> that should have been a </B>
• src/hg/encode3/encodeDataWarehouse/edwWebRegisterScript/edwWebRegisterScript.c
  • lines changed 131, context: html, text, full: html, text
    First cut of script registration and submission.
• src/hg/encode3/encodeDataWarehouse/edwWebRegisterScript/makefile
  • lines changed 16, context: html, text, full: html, text
    First cut of script registration and submission.
• src/hg/encode3/encodeDataWarehouse/edwWebSubmit/edwWebSubmit.c
  • lines changed 13, context: html, text, full: html, text
    Adding edwAddSubmitJob to library.
• src/hg/encode3/encodeDataWarehouse/inc/edwLib.h
  • lines changed 3, context: html, text, full: html, text
    Adding edwAddSubmitJob to library.
• src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h
  • lines changed 82, context: html, text, full: html, text
    Adding edwScriptRegistry table.
• src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
  • lines changed 2, context: html, text, full: html, text
    Improving a comment.
  • lines changed 19, context: html, text, full: html, text
    Adding edwAddSubmitJob to library.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as
  • lines changed 11, context: html, text, full: html, text
    Adding edwScriptRegistry table.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c
  • lines changed 205, context: html, text, full: html, text
    Adding edwScriptRegistry table.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.h
  • lines changed 1195, context: html, text, full: html, text
    Improving a comment.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql
  • lines changed 13, context: html, text, full: html, text
    Adding edwScriptRegistry table.
• src/hg/encode3/encodeDataWarehouse/lib/resetEdw
  • lines changed 8, context: html, text, full: html, text
    Adding in mm10 enrichment targets.
• src/hg/encode3/encodeDataWarehouse/makefile
  • lines changed 15, context: html, text, full: html, text
    Adding alpha target.
  • lines changed 3, context: html, text, full: html, text
    Adding new programs to higher level makefile.
• src/hg/hgGene/hgGeneData/links.ra
  • lines changed 9, context: html, text, full: html, text
    reverted change to Wikipedia links because not picked up by QA yet
• src/hg/hgGene/makefile
  • lines changed 4, context: html, text, full: html, text
    The -a0 command to rsync worked no better than -ar, so put it back.
• src/hg/hgLogin/hgLogin.c
  • lines changed 1, context: html, text, full: html, text
    redmine Bug 10709 mailViaPipe.c did not handle message body started with spaces correctly.
• src/hg/hgTracks/config.c
  • lines changed 4, context: html, text, full: html, text
    tolerate missing a freeze field in an assembly hub, and add dense mode to snakes
• src/hg/hgTracks/hgTracks.c
  • lines changed 3, context: html, text, full: html, text
    oops... fixed a problem with right-click on a single track in a hub that I introduced last week.
• src/hg/hgTracks/snakeTrack.c
  • lines changed 18, context: html, text, full: html, text
    tolerate missing a freeze field in an assembly hub, and add dense mode to snakes
• src/hg/hgTracks/wigTrack.c
  • lines changed 8, context: html, text, full: html, text
    Fixed rightClick update of wigColorBy tracks. ref #10512 On ajax single track update the whole tracklist is not generated. Therefore, the colorBy track is not in the trackHash and must be created when needed.
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    a small tweak to snake hgc links
• src/hg/hgc/retroClick.c
  • lines changed 2, context: html, text, full: html, text
    Changed retrocopy to retrogene for consistency.
  • lines changed 1, context: html, text, full: html, text
    Changed retrocopy to retrogene for consistency.
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 1, context: html, text, full: html, text
    Adding an example of how DropBox supports byte-range requests, but Google Drive does not. refs #10078
  • lines changed 1, context: html, text, full: html, text
    Removing an example of how DropBox supports byte-range requests, but Google Drive does not. refs #10078
• src/hg/htdocs/goldenPath/help/haplotypes.html
  • lines changed 266, context: html, text, full: html, text
    Added help page for Gene Haploptye Alleles hgGene section. Also fixed typos found by Angie and printf format issue with 32-bit build found by Galt
  • lines changed 37, context: html, text, full: html, text
    First pass at polishing page. Fixed typos, changed passive to active voice, changed quotes to be html-friendly.
  • lines changed 1, context: html, text, full: html, text
    Tiny change to make sentence flow better.
  • lines changed 1, context: html, text, full: html, text
    Added commas.
  • lines changed 20, context: html, text, full: html, text
    Fixed a button and added some numbers to the score definitions.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 13, context: html, text, full: html, text
    Clarified sorting on tags a bit. This was due to user confusion as seen in ref #10701.
  • lines changed 3, context: html, text, full: html, text
    Edit description of factorSource type to fix spelling & grammar errors, also to clarify
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 38, context: html, text, full: html, text
    Arranging new pubs in alphabetical order, Code Review refs #10719
• src/hg/inc/haplotypes.h
  • lines changed 1, context: html, text, full: html, text
    Added protection for massive sets of haplotypes as seen in hgGene CGI. The cutoffs are still evolving. Also fixed some comments as per Angie's review, tightened one sort to ensure deterministic order and made some minor wording changes to the HTML output.
• src/hg/inc/liftOver.h
  • lines changed 3, context: html, text, full: html, text
    Rolled back some changes to liftOver's presence in the library. If it goes into the top-level maybe it should get some design changes as well. At the moment the design is a bit stretched.
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v283
• src/hg/js/alleles.js
  • lines changed 2, context: html, text, full: html, text
    Added protection for massive sets of haplotypes as seen in hgGene CGI. The cutoffs are still evolving. Also fixed some comments as per Angie's review, tightened one sort to ensure deterministic order and made some minor wording changes to the HTML output.
• src/hg/lib/haplotypes.c
  • lines changed 15, context: html, text, full: html, text
    Added help page for Gene Haploptye Alleles hgGene section. Also fixed typos found by Angie and printf format issue with 32-bit build found by Galt
  • lines changed 53, context: html, text, full: html, text
    Added protection for massive sets of haplotypes as seen in hgGene CGI. The cutoffs are still evolving. Also fixed some comments as per Angie's review, tightened one sort to ensure deterministic order and made some minor wording changes to the HTML output.
• src/hg/lib/hubConnect.c
  • lines changed 1, context: html, text, full: html, text
    fix typo that Galt pointed out
• src/hg/lib/liftOver.c
  • lines changed 239, context: html, text, full: html, text
    Rolled back some changes to liftOver's presence in the library. If it goes into the top-level maybe it should get some design changes as well. At the moment the design is a bit stretched.
• src/hg/makeDb/doc/blastTab.txt
  • lines changed 5, context: html, text, full: html, text
    redmine 10464: Rebuilt drBlastTab table for some assemblies after ensGene v70 update.
• src/hg/makeDb/doc/canFam3.txt
  • lines changed 49, context: html, text, full: html, text
    starting canFam3 panTro4 lastz run
  • lines changed 31, context: html, text, full: html, text
    run up lastz dog chimp refs #10712
• src/hg/makeDb/doc/encodeRegHg19.txt
  • lines changed 191, context: html, text, full: html, text
    Much work on TFBS Clusters V3. And some cleanup (still more needed). refs #10097
• src/hg/makeDb/doc/galGal4.txt
  • lines changed 19, context: html, text, full: html, text
    liftUnder to galGal3 completed, refs #10732
  • lines changed 100, context: html, text, full: html, text
    add ucscToEnsembl conversion table
• src/hg/makeDb/doc/hg18.txt
  • lines changed 6, context: html, text, full: html, text
    Added QA NOTE to UCSC Genes section to note mytouch of various tables whose timestamp I changed to fix joinerCheck errors
• src/hg/makeDb/doc/nomLeu3.txt
  • lines changed 1, context: html, text, full: html, text
    Missing eof line. Found while trying using as a reference to build assembly hub.
• src/hg/makeDb/doc/panTro4.txt
  • lines changed 19, context: html, text, full: html, text
    run up lastz dog chimp refs #10712
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    Changed to rn3 in kgDb group since neither rn4 nor rn5 have the knownGenes table; this fixed some joinerCheck errors related to the knownGenes table not being present in rn4
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 15, context: html, text, full: html, text
    Add typeOfTerm for antibody target so that can be included in metadata. refs #10042
  • lines changed 16, context: html, text, full: html, text
    ReAdd typeOfTerm for antibody target so that can be included in metadata. BrianL killed it in bad merge conflict resolution. refs #10042
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 16, context: html, text, full: html, text
    Copying alpha/cv.ra to beta/cv.ra, Stanza added for new TFBS Uniform track, refs #10042
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeAwgTfbsUniform.ra
  • lines changed 691, context: html, text, full: html, text
    Restaging on beta for ENCODE TFBS Uniform from AWG (release 1),Update of md5sums after adding scores to download files, ref #10042
• src/hg/makeDb/trackDb/human/hg19/numtSeqHg19.html
  • lines changed 6, context: html, text, full: html, text
    Updating ref for human - found additional html file that uses old ref (see note 42). refs #8533
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Removed nextItem arrows being on by default for ucscRetroAli5.
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Just a comment
• src/hg/makeDb/trackDb/human/hg19/ucscRetroAli4.html
  • lines changed 49, context: html, text, full: html, text
    Added a reference. Added more description of items in tables of the details pages.
  • lines changed 2, context: html, text, full: html, text
    Fixed some errors.
  • lines changed 6, context: html, text, full: html, text
    Added code so that some links open in new tabs/windows. Minor edits.
  • lines changed 16, context: html, text, full: html, text
    Added more details to the description.
• src/hg/makeDb/trackDb/human/hg19/ucscRetroAli5.html
  • lines changed 104, context: html, text, full: html, text
    Description for Retroposed Genes 5.0 track.
  • lines changed 2, context: html, text, full: html, text
    Fixed some errors.
  • lines changed 6, context: html, text, full: html, text
    Added code so that some links open in new tabs/windows. Minor edits.
  • lines changed 16, context: html, text, full: html, text
    Added more details to the description.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgTfbsUniform.html
  • lines changed 4, context: html, text, full: html, text
    Clean up overlong link labels. QA item #7. refs #10042
  • lines changed 43, context: html, text, full: html, text
    Making changes to Description page Uniform TFBS refs #10042
  • lines changed 32, context: html, text, full: html, text
    Trying to fix a merge conflict of changes to HTML AWG TFBS Uniform ref #10042
  • lines changed 37, context: html, text, full: html, text
    Making changes to Description page Uniform TFBS refs #10042
  • lines changed 5, context: html, text, full: html, text
    Making additional small changes to HTML for AWG Uniform TFBS refs #10042
  • lines changed 6, context: html, text, full: html, text
    Adding small edits to AWG TFBS html references section, refs #10042
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAwgTfbsUniform.ra
  • lines changed 6, context: html, text, full: html, text
    Fix SK-N-SH tier designation -- it was just partially set to 2.5. QA item #8. refs #10042
  • lines changed 7, context: html, text, full: html, text
    Uniquify long labels. QA item #9. refs #10042
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 37, context: html, text, full: html, text
    First cut V3 TFBS clusters. refs #10097
• src/hg/makeDb/trackDb/human/numtSeq.html
  • lines changed 5, context: html, text, full: html, text
    Updating ref as per new ref in new numt track (see note 42). refs #8533
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Removed nextItem arrows being on by default for ucscRetroAli2.
• src/hg/makeDb/trackDb/mouse/mm10/ucscRetroAli2.html
  • lines changed 104, context: html, text, full: html, text
    Description page for mouse mm10 Retroposed Genes 2.0.
  • lines changed 2, context: html, text, full: html, text
    Fixed some errors.
  • lines changed 8, context: html, text, full: html, text
    Added code so that some links open in new tabs/windows. Minor edits.
  • lines changed 17, context: html, text, full: html, text
    Added more details to the description.
• src/hg/makeDb/trackDb/mouse/mm9/numtSeqMm9.html
  • lines changed 6, context: html, text, full: html, text
    Updating ref as per new ref in new numt track (see note 42). refs #8533
• src/hg/oneShot/freen/freen.c
  • lines changed 23, context: html, text, full: html, text
    Figuring out how to find free space on a file system.
  • lines changed 15, context: html, text, full: html, text
    Testing cgiEncode.
• src/hg/regulate/regClusterBedExpCfg/regClusterBedExpCfg.c
  • lines changed 73, context: html, text, full: html, text
    Add useTarget, noLetterOk, and noNormalize options to support 2012 TF clustering. refs #10097
• src/hg/utils/automation/EnsGeneAutomate.pm
  • lines changed 197, context: html, text, full: html, text
    adding Ensembl version 71 definitions, refs #10636
• src/inc/bits.h
  • lines changed 4, context: html, text, full: html, text
    Clarified some comments based upon Angie's feedback. Thanks.
• src/inc/liftOverCore.h
  • lines changed 39, context: html, text, full: html, text
    Rolled back some changes to liftOver's presence in the library. If it goes into the top-level maybe it should get some design changes as well. At the moment the design is a bit stretched.
• src/inc/net.h
  • lines changed 1, context: html, text, full: html, text
    Improving comment for netWaitForData.
• src/inc/portable.h
  • lines changed 5, context: html, text, full: html, text
    Adding freeSpaceOnFileSystem library function.
• src/inc/userApp.mk
  • lines changed 3, context: html, text, full: html, text
    add dependency on the libraries to avoid rebuilding when nothing is changing, refs #9104
  • lines changed 8, context: html, text, full: html, text
    clearer use of DEPLIBS and separate from LINKLIBS refs #9104
• src/inc/vcfBits.h
  • lines changed 4, context: html, text, full: html, text
    Clarified some comments based upon Angie's feedback. Thanks.
• src/lib/bits.c
  • lines changed 3, context: html, text, full: html, text
    Clarified some comments based upon Angie's feedback. Thanks.
• src/lib/common.c
  • lines changed 7, context: html, text, full: html, text
    Improving error reporting in mustWriteFd.
• src/lib/liftOverCore.c
  • lines changed 246, context: html, text, full: html, text
    Rolled back some changes to liftOver's presence in the library. If it goes into the top-level maybe it should get some design changes as well. At the moment the design is a bit stretched.
• src/lib/mailViaPipe.c
  • lines changed 1, context: html, text, full: html, text
    redmine Bug 10709 mailViaPipe.c did not handle message body started with spaces correctly.
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Rolled back some changes to liftOver's presence in the library. If it goes into the top-level maybe it should get some design changes as well. At the moment the design is a bit stretched.
• src/lib/memgfx.c
  • lines changed 3, context: html, text, full: html, text
    fix clipping error in anti-aliased lines refs #10744
• src/lib/net.c
  • lines changed 1, context: html, text, full: html, text
    Improving comment for netWaitForData.
• src/lib/osunix.c
  • lines changed 12, context: html, text, full: html, text
    Adding freeSpaceOnFileSystem library function.
• src/lib/vcfBits.c
  • lines changed 5, context: html, text, full: html, text
    Clarified some comments based upon Angie's feedback. Thanks.
• src/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding a few directories to tags.
• src/parasol/paraHub/sockSuck.c
  • lines changed 1, context: html, text, full: html, text
    Fix stricter-compiler warning about lack of return statement in function that is declared to return some kind of value.
• src/parasol/paraNode/paraNode.c
  • lines changed 2, context: html, text, full: html, text
    fix warning from newer compiler
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v283 final build

• lines changed: 5088
• files changed: 117