All File Changes

v295_preview2 to v295_base (2014-01-27 to 2014-02-03) v295

• src/hg/encode3/encodeDataWarehouse/edwWebXSendFile/edwWebXSendFile.c
  • lines changed 13, context: html, text, full: html, text
    ename "licenseplate" to "accession" in the query string.Add the user name (email address) as part of input to hmac(),
    for example - '2014-01-22ENCFF001RALlrowe@stanford.edu'
    
• src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwUser/makefile
  • lines changed 17, context: html, text, full: html, text
    "rsyncEdwUserTable" - Update edwUser table using user information from encodedcc.The old "rsyncEdwUser" function was removed from GIT.
    
• src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwUser/rsyncEdwUser.c
  • lines changed 79, context: html, text, full: html, text
    "rsyncEdwUserTable" - Update edwUser table using user information from encodedcc.The old "rsyncEdwUser" function was removed from GIT.
    
• src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwUserTable/makefile
  • lines changed 17, context: html, text, full: html, text
    "rsyncEdwUserTable" - Update edwUser table using user information from encodedcc.The old "rsyncEdwUser" function was removed from GIT.
    
• src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwUserTable/rsyncEdwUserTable.c
  • lines changed 135, context: html, text, full: html, text
    "rsyncEdwUserTable" - Update edwUser table using user information from encodedcc.The old "rsyncEdwUser" function was removed from GIT.
    
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 10, context: html, text, full: html, text
    Remove cell abbreviation table from configuration page. Not needed there and it's quite long
  • lines changed 8, context: html, text, full: html, text
    Add multi-select filter for factors to factorSource config page
  • lines changed 33, context: html, text, full: html, text
    Add UI checkbox to suppress display of cell abbreviations.
• src/hg/hgTracks/factorSource.c
  • lines changed 43, context: html, text, full: html, text
    Add multi-select filter for factors to factorSource config page
  • lines changed 2, context: html, text, full: html, text
    Ignore TF filter on clean cart. refs #9092
  • lines changed 11, context: html, text, full: html, text
    Add UI checkbox to suppress display of cell abbreviations.
  • lines changed 1, context: html, text, full: html, text
    Remove debug
• src/hg/hgTracks/hgTracks.c
  • lines changed 16, context: html, text, full: html, text
    Fixes #12509. Create special chrom ordering for hg38 as specified in the ticket.
  • lines changed 2, context: html, text, full: html, text
    Fixed highlight implementation (redmine #709) bug resulting in position autocomplete box being superimposed on by hgTracks image (redmine #12589).
  • lines changed 5, context: html, text, full: html, text
    Removed display of empty parentheses when showing cytoBandIdeo without p/q arm information
• src/hg/hgTracks/hgTracks.h
  • lines changed 4, context: html, text, full: html, text
    Add multi-select filter for factors to factorSource config page
• src/hg/hgTracks/simpleTracks.c
  • lines changed 2, context: html, text, full: html, text
    Add UI checkbox to suppress display of cell abbreviations.
• src/hg/hgc/hgc.c
  • lines changed 3, context: html, text, full: html, text
    Add table of Factorbook aliases for TF genes, so outside link works. Suppress link if there's no page. refs #9092
• src/hg/hgc/hgc.h
  • lines changed 4, context: html, text, full: html, text
    Add some flexibility to Motif section display. refs #9092
• src/hg/hgc/peakClusters.c
  • lines changed 3, context: html, text, full: html, text
    Add some flexibility to Motif section display. refs #9092
  • lines changed 13, context: html, text, full: html, text
    Rearrange sections on factorSource details page and make another sectdion collapsible (motifs section better placed). refs #9092
  • lines changed 20, context: html, text, full: html, text
    1. Bug fix: need section on details page for peak clusters lacking motif. 2. Some code simplification. refs #9092
• src/hg/hgc/regMotif.c
  • lines changed 1, context: html, text, full: html, text
    Fix error check -- allow motif display without DNA sequence (as in dm2 flyReg track)
  • lines changed 24, context: html, text, full: html, text
    Add some flexibility to Motif section display. refs #9092
• src/hg/htdocs/ENCODE/index.html
  • lines changed 2, context: html, text, full: html, text
    Request to split Publications link on ENCODE portal into two (Community vs. Consortium), from John Stam, with Mike P. concurrence (prompted by input from Science editor
• src/hg/htdocs/ENCODE/pubsOther.html
  • lines changed 3, context: html, text, full: html, text
    Request to split Publications link on ENCODE portal into two (Community vs. Consortium), from John Stam, with Mike P. concurrence (prompted by input from Science editor
  • lines changed 8, context: html, text, full: html, text
    Brief additions by Mike Pazin.
• src/hg/htdocs/FAQ/FAQlink.html
  • lines changed 1, context: html, text, full: html, text
    Changed hg18->hg19 in link, per Steve's code review.
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 1, context: html, text, full: html, text
    Fixed incorrect assembly name for tarSyr1. MLQ #12999.
• src/hg/htdocs/indexNews.html
  • lines changed 3, context: html, text, full: html, text
    Moved period outside of link in 2 places.
• src/hg/inc/hdb.h
  • lines changed 22, context: html, text, full: html, text
    Fixes #12509. Create special chrom ordering for hg38 as specified in the ticket.
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v295
• src/hg/inc/web.h
  • lines changed 7, context: html, text, full: html, text
    1. Bug fix: need section on details page for peak clusters lacking motif. 2. Some code simplification. refs #9092
• src/hg/js/autocomplete.js
  • lines changed 1, context: html, text, full: html, text
    Fixed highlight implementation (redmine #709) bug resulting in position autocomplete box being superimposed on by hgTracks image (redmine #12589).
• src/hg/js/hgTracks.js
  • lines changed 7, context: html, text, full: html, text
    Fixed user reported error when refreshing image that has 'ruler' track on hide. Redmine #12553. Also cleaned up 2 cases where user action may leave the highlight outside the image boundaries. Redmine #709.
  • lines changed 21, context: html, text, full: html, text
    Fixed bug seen only on FF where vis drop-downs were disabled after back-button (redmine #12511). Also made warnBox play nice with highlight (redmine #709).
• src/hg/js/utils.js
  • lines changed 1, context: html, text, full: html, text
    Galt requested this in-comment typo be fixed in code-review (redmine #12571). No functional change here.
• src/hg/lib/hdb.c
  • lines changed 102, context: html, text, full: html, text
    Fixes #12509. Create special chrom ordering for hg38 as specified in the ticket.
• src/hg/lib/jksql.c
  • lines changed 44, context: html, text, full: html, text
    cleanup of comments, adding case of profile being null in variousmonitoring statements, fixing missing cloneString() around "db", fixing case of
    db being null in sqlConnCacheEntryDbMatch.
    
  • lines changed 1, context: html, text, full: html, text
    changing getter back to mysql_use_result, as it was before myJan 15 commit.
    
• src/hg/lib/web.c
  • lines changed 17, context: html, text, full: html, text
    1. Bug fix: need section on details page for peak clusters lacking motif. 2. Some code simplification. refs #9092
• src/hg/lib/wigDataStream.c
  • lines changed 2, context: html, text, full: html, text
    small changes after code review, refs #12570
• src/hg/makeDb/doc/encodeRegHg19.txt
  • lines changed 6, context: html, text, full: html, text
    Cleanup
• src/hg/makeDb/doc/galGal4.txt
  • lines changed 54, context: html, text, full: html, text
    Re-ran galGal4 snp138 pipeline with the addition of some custom-generated contig mappings. Way back at the beginning of galGal4,
    Hiram found that some contig names were >31 chars and shortened
    them, so they weren't automatically picked up by doDbSnp.pl's
    mapping of RefSeq contigs -> GenBank contigs -> chrom.sizes.
    Expanding them back allows us to get the GB contig ID, then map
    to RS contig ID. refs #12490
    
• src/hg/makeDb/doc/hg38.txt
  • lines changed 10, context: html, text, full: html, text
    load non-bridged contig locations as a track refs #11681
  • lines changed 1, context: html, text, full: html, text
    better default position centered on ABO gene refs #11681
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 1, context: html, text, full: html, text
    Add table of Factorbook aliases for TF genes, so outside link works. Suppress link if there's no page. refs #9092
  • lines changed 138, context: html, text, full: html, text
    Add multi-select filter for factors to factorSource config page
  • lines changed 2, context: html, text, full: html, text
    Bump up window size to display motifs
  • lines changed 2, context: html, text, full: html, text
    Clean up Tfbs Clusters tables
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTfbsClusteredV3.html
  • lines changed 1, context: html, text, full: html, text
    Add UI checkbox to suppress display of cell abbreviations.
• src/hg/makeDb/trackDb/human/hg38/altSequences.ra
  • lines changed 9, context: html, text, full: html, text
    better set up for the alternate mapping track refs #11681
  • lines changed 1, context: html, text, full: html, text
    trying priorities all set to zero, and start the chain net packaging early refs #11681
• src/hg/makeDb/trackDb/human/hg38/chainNetPrimate.ra
  • lines changed 215, context: html, text, full: html, text
    trying priorities all set to zero, and start the chain net packaging early refs #11681
• src/hg/makeDb/trackDb/human/hg38/contigAlignmentSegments.html
  • lines changed 5, context: html, text, full: html, text
    adding contigAlignmentSegments track refs #11681
• src/hg/makeDb/trackDb/human/hg38/cpgIslandSuper.html
  • lines changed 15, context: html, text, full: html, text
    Added paragraphs explaining the addition of the unmasked version of the track (redmine #12466)
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 50, context: html, text, full: html, text
    trying priorities all set to zero, and start the chain net packaging early refs #11681
  • lines changed 8, context: html, text, full: html, text
    adding contigAlignmentSegments track refs #11681
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    Add table of Factorbook aliases for TF genes, so outside link works. Suppress link if there's no page. refs #9092
  • lines changed 1, context: html, text, full: html, text
    Add multi-select filter for factors to factorSource config page
• src/hg/pslToBed/tests/expected/doTest1.bed
  • lines changed 285, context: html, text, full: html, text
    make pslToBed tests less bloated
• src/hg/pslToBed/tests/expected/doTest1.bed.gz
  • lines changed 0, context: html, text, full: html, text
    make pslToBed tests less bloated
• src/hg/pslToBed/tests/expected/doTest2.bed
  • lines changed 55307, context: html, text, full: html, text
    make pslToBed tests less bloated
• src/hg/pslToBed/tests/expected/doTest2.bed.gz
  • lines changed 0, context: html, text, full: html, text
    make pslToBed tests less bloated
• src/hg/pslToBed/tests/input/test1.psl
  • lines changed 285, context: html, text, full: html, text
    make pslToBed tests less bloated
• src/hg/pslToBed/tests/input/test1.psl.gz
  • lines changed 0, context: html, text, full: html, text
    make pslToBed tests less bloated
• src/hg/pslToBed/tests/input/test2.cds
  • lines changed 43689, context: html, text, full: html, text
    make pslToBed tests less bloated
• src/hg/pslToBed/tests/input/test2.cds.gz
  • lines changed 0, context: html, text, full: html, text
    make pslToBed tests less bloated
• src/hg/pslToBed/tests/input/test2.psl
  • lines changed 55307, context: html, text, full: html, text
    make pslToBed tests less bloated
• src/hg/pslToBed/tests/input/test2.psl.gz
  • lines changed 0, context: html, text, full: html, text
    make pslToBed tests less bloated
• src/hg/pslToBed/tests/makefile
  • lines changed 5, context: html, text, full: html, text
    make pslToBed tests less bloated
• src/hg/utils/automation/blastz-run-ucsc
  • lines changed 2, context: html, text, full: html, text
    fixed lavToPsl and can now use 2bit files for target bits refs #11681
• src/hg/utils/automation/doBlastzChainNet.pl
  • lines changed 9, context: html, text, full: html, text
    fixed lavToPsl and can now use 2bit files for target bits refs #11681
• src/hg/utils/automation/doDbSnp.pl
  • lines changed 2, context: html, text, full: html, text
    Re-ran galGal4 snp138 pipeline with the addition of some custom-generated contig mappings. Way back at the beginning of galGal4,
    Hiram found that some contig names were >31 chars and shortened
    them, so they weren't automatically picked up by doDbSnp.pl's
    mapping of RefSeq contigs -> GenBank contigs -> chrom.sizes.
    Expanding them back allows us to get the GB contig ID, then map
    to RS contig ID. refs #12490
    
• src/hg/utils/automation/doGenscan.pl
  • lines changed 4, context: html, text, full: html, text
    better to do the bigBed conversion at load time refs #11681
• src/hg/utils/automation/makePushQSql.pl
  • lines changed 1, context: html, text, full: html, text
    new default location for bbi files refs #11681
• src/hg/utils/automation/synBlastp.csh
  • lines changed 1, context: html, text, full: html, text
    add "-clientLoad" to call to hgLoadPsl in synBlastp.csh
• src/hg/utils/gff3ToPsl/makefile
  • lines changed 1, context: html, text, full: html, text
    fix up tests for gff3ToPsl in response to a code review.
• src/hg/utils/gff3ToPsl/tests/expected/patch1test.psl
  • lines changed 266, context: html, text, full: html, text
    fix up tests for gff3ToPsl in response to a code review.
• src/hg/utils/gff3ToPsl/tests/expected/patch1test.psl.gz
  • lines changed 0, context: html, text, full: html, text
    fix up tests for gff3ToPsl in response to a code review.
• src/hg/utils/gff3ToPsl/tests/input/chrom.sizes.gz
  • lines changed 0, context: html, text, full: html, text
    fix up tests for gff3ToPsl in response to a code review.
• src/hg/utils/gff3ToPsl/tests/input/haploMaps.gff
  • lines changed 269, context: html, text, full: html, text
    fix up tests for gff3ToPsl in response to a code review.
• src/hg/utils/gff3ToPsl/tests/input/haploMaps.gff.gz
  • lines changed 0, context: html, text, full: html, text
    fix up tests for gff3ToPsl in response to a code review.
• src/hg/utils/gff3ToPsl/tests/makefile
  • lines changed 2, context: html, text, full: html, text
    fix up tests for gff3ToPsl in response to a code review.
• src/inc/common.mk
  • lines changed 5, context: html, text, full: html, text
    avoid an extra leading slash when DESTDIR is empty for DESTBINDIR refs #12106
• src/lib/bbiRead.c
  • lines changed 1, context: html, text, full: html, text
    fix a problem with disappearing narrow peaks in bigWig display. See #12558
  • lines changed 1, context: html, text, full: html, text
    backing out a change I made the other day to bigWig summary levelparsing
    
• src/lib/hash.c
  • lines changed 2, context: html, text, full: html, text
    small changes after code review, refs #12570
• src/lib/tests/udcTest.c
  • lines changed 1, context: html, text, full: html, text
    small changes after code review, refs #12570
• src/product/README.requirements
  • lines changed 4, context: html, text, full: html, text
    adding gmt and ghostscript requirements to readme
• src/test/perllib/HgConf.pm
  • lines changed 1, context: html, text, full: html, text
    Fixed error where chdir failed due to final carriage return in directory name (from pwd)
• src/userApps/README
  • lines changed 6, context: html, text, full: html, text
    mention stdin,stdout,stderr for kent command arguments, the first time ever in any README in the source tree refs #9149
• src/utils/bedScore/tests/expected/asinhTest.narrowPeak
  • lines changed 1000, context: html, text, full: html, text
    Truncate tests to 1000 lines
• src/utils/bedScore/tests/expected/broadGm12878Ctcf.jan2011.asinh.narrowPeak
  • lines changed 40006, context: html, text, full: html, text
    Truncate tests to 1000 lines
• src/utils/bedScore/tests/expected/encodeRegTest.bed
  • lines changed 44159, context: html, text, full: html, text
    Truncate tests to 1000 lines
• src/utils/bedScore/tests/expected/encodeStd2Test.bed
  • lines changed 44159, context: html, text, full: html, text
    Truncate tests to 1000 lines
• src/utils/bedScore/tests/expected/encodeTfbsTest.bed
  • lines changed 31461, context: html, text, full: html, text
    Truncate tests to 1000 lines
• src/utils/bedScore/tests/expected/regTest.narrowPeak
  • lines changed 1000, context: html, text, full: html, text
    Truncate tests to 1000 lines
• src/utils/bedScore/tests/expected/std2Test.narrowPeak
  • lines changed 1000, context: html, text, full: html, text
    Truncate tests to 1000 lines
• src/utils/bedScore/tests/input/asinhTest.narrowPeak
  • lines changed 1000, context: html, text, full: html, text
    Truncate tests to 1000 lines
• src/utils/bedScore/tests/input/broadGm12878Ctcf.jan2011.asinh.narrowPeak
  • lines changed 40006, context: html, text, full: html, text
    Truncate tests to 1000 lines
• src/utils/bedScore/tests/input/encodeTfbsTest.bed
  • lines changed 30515, context: html, text, full: html, text
    Truncate tests to 1000 lines
• src/utils/bedScore/tests/input/hsmmCtcfJan2011.narrowPeak
  • lines changed 43159, context: html, text, full: html, text
    Truncate tests to 1000 lines
• src/utils/bedScore/tests/makefile
  • lines changed 11, context: html, text, full: html, text
    Truncate tests to 1000 lines
• src/utils/bigWigCat/bigWigCat.c
  • lines changed 16, context: html, text, full: html, text
    some changes from danile to make it a bit more obvious what overlappingmeans wrt bigWigCat.
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v295 final build refs #12352
• src/utils/qa/weeklybld/doNewBranch.csh
  • lines changed 1, context: html, text, full: html, text
    add steve to email list refs #12352
• src/utils/qa/weeklybld/doNewReview2.csh
  • lines changed 1, context: html, text, full: html, text
    add steve to email list refs #12352doNewBranch.csh

• lines changed: 434183
• files changed: 108