All File Changes

v299_base to v300_preview (2014-04-28 to 2014-05-05) v300

• confs/hgwdev.hg.conf
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    Checking in most recent version of hgwdev hg.conf
• src/hg/altSplice/altSplice/genePredToBed.c
  • lines changed 3, context: html, text, full: html, text
    remove uncessary noise output from programs
• src/hg/altSplice/altSplice/genePredToPsl.c
  • lines changed 3, context: html, text, full: html, text
    remove uncessary noise output from programs
• src/hg/encode3/eap/eapAddStep/eapAddStep.c
  • lines changed 3, context: html, text, full: html, text
    Adjusting sum_bigWig and replicated_hotspot steps.
• src/hg/encode3/eap/eapFreen/eapFreen.c
  • lines changed 1, context: html, text, full: html, text
    Renaming longList structure and module to longToList.
• src/hg/encode3/eap/eapMetaSync/eapMetaSync.c
  • lines changed 2, context: html, text, full: html, text
    Turning uglyf to verbose, and updating out of date comment per Tim's code review.
• src/hg/encode3/eap/eapToHub/eapToHub.c
  • lines changed 1121, context: html, text, full: html, text
    Adjusting eapToHub to new location.
• src/hg/encode3/eap/eapUpdateSoftware/eapUpdateSoftware.c
  • lines changed 1, context: html, text, full: html, text
    Changing priority to an enum.
• src/hg/encode3/eap/inc/eapGraph.h
  • lines changed 3, context: html, text, full: html, text
    Renaming longList structure and module to longToList.
• src/hg/encode3/eap/lib/eapGraph.c
  • lines changed 20, context: html, text, full: html, text
    Renaming longList structure and module to longToList.
• src/hg/encode3/eap/oneShot/diffRepVsCrossEn/README
  • lines changed 6, context: html, text, full: html, text
    Adding data behind AWG presentation slide comparing IDR metrics to crossEnrichments.
  • lines changed 5, context: html, text, full: html, text
    Improving documentation in README, updating table from Anshul.
• src/hg/encode3/eap/oneShot/diffRepVsCrossEn/fromAnshul.tab
  • lines changed 1502, context: html, text, full: html, text
    Adding data behind AWG presentation slide comparing IDR metrics to crossEnrichments.
  • lines changed 2, context: html, text, full: html, text
    Improving documentation in README, updating table from Anshul.
• src/hg/encode3/eap/oneShot/diffRepVsCrossEn/fromPortal.tab
  • lines changed 1052, context: html, text, full: html, text
    Adding data behind AWG presentation slide comparing IDR metrics to crossEnrichments.
• src/hg/encode3/eap/oneShot/eapToHub/eapToHub.c
  • lines changed 1121, context: html, text, full: html, text
    Adjusting eapToHub to new location.
• src/hg/encode3/eap/oneShot/eapToHub/makefile
  • lines changed 4, context: html, text, full: html, text
    Adjusting eapToHub to new location.
• src/hg/encode3/encodeDataWarehouse/oneShot/edwFakeBiosample/edwFakeBiosample.c
  • lines changed 14, context: html, text, full: html, text
    Added -json option to aid debugging when Stanford changes output.
• src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwExpDataType/rsyncEdwExpDataType.c
  • lines changed 13, context: html, text, full: html, text
    Removing URL command line parameter since it is in source code now. Adding 'limit=all' to the URL since it's now required to get more than the first 25 experiments in response. Adding a new size range to the shortRna section.
• src/hg/encode3/encodeDataWarehouse/utils/edwBamRemoveChrom/edwBamRemoveChrom.c
  • lines changed 91, context: html, text, full: html, text
    Wrote little utility mostly to remove chrM for DNAse.
• src/hg/encode3/encodeDataWarehouse/utils/edwBamRemoveChrom/makefile
  • lines changed 3, context: html, text, full: html, text
    Wrote little utility mostly to remove chrM for DNAse.
• src/hg/encode3/encodeDataWarehouse/utils/edwBamStats/edwBamStats.c
  • lines changed 63, context: html, text, full: html, text
    Include some bam header info (if found) in the stats.ra output.
• src/hg/encode3/validateManifest/VERSION.TXT
  • lines changed 3, context: html, text, full: html, text
    vm version 1.9 begun; adding support for dm3 and ce10.
• src/hg/encode3/validateManifest/validateManifest.c
  • lines changed 3, context: html, text, full: html, text
    vm version 1.9 begun; adding support for dm3 and ce10.
• src/hg/hgMirror/makefile
  • lines changed 6, context: html, text, full: html, text
    copying hiram's makefile suggestions into git, refs #11957, note 318
• src/hg/hgTracks/multiWig.c
  • lines changed 3, context: html, text, full: html, text
    fix bug where multiWigs crashed with only zero or one subtracks turnedon
    
  • lines changed 8, context: html, text, full: html, text
    check for load failures in multiWig
• src/hg/hgTracks/rmskTrack.c
  • lines changed 4, context: html, text, full: html, text
    prevent rmsk track from making map box off-screen
• src/hg/hgTracks/wigTrack.c
  • lines changed 1, context: html, text, full: html, text
    fix bug where multiWigs crashed with only zero or one subtracks turnedon
    
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 27, context: html, text, full: html, text
    making changes based on feedback from Jonathan, refs #12843
• src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html
  • lines changed 5, context: html, text, full: html, text
    first cut at documentation tweaks for stacked wiggles
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 1, context: html, text, full: html, text
    first cut at documentation tweaks for stacked wiggles
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 16, context: html, text, full: html, text
    first cut at documentation tweaks for stacked wiggles
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 29, context: html, text, full: html, text
    Adding announcement about re-release of 100way data. refs #12405 #12260
• src/hg/htdocs/images/Poecilia_reticulata.jpg
  • lines changed 0, context: html, text, full: html, text
    adding photo from Wikimedia Commons refs #13170
• src/hg/htdocs/images/phylo/rn5_13way.png
  • lines changed 0, context: html, text, full: html, text
    Adding phylo tree for rn5 13way refs #8212
• src/hg/htdocs/indexNews.html
  • lines changed 74, context: html, text, full: html, text
    Adding announcement about re-release of 100way data. refs #12405 #12260
• src/hg/js/hgTracks.js
  • lines changed 45, context: html, text, full: html, text
    Vis changes are now queued for update because quick vis changes followed by refresh wer creating a race condition. Redmine 13164.
  • lines changed 28, context: html, text, full: html, text
    Updates to handle case when both vis changes AND chrom change occurs, making certain queued updates get sent along. Redmine 13164.
  • lines changed 146, context: html, text, full: html, text
    Took this one step further: moved methods to their own cart object and now append queued cart updates to any hgTracks ajax update. This will provide greater flexibilty for future cart update queuing. Redmone #13164.
• src/hg/lib/hdb.c
  • lines changed 1, context: html, text, full: html, text
    Adding missing sqlFreeResult to hGetCtBedRange.
• src/hg/lib/hgBam.c
  • lines changed 1, context: html, text, full: html, text
    User reported in MLQ #13153 that bam reads ending just to the leftof the search region were included in hgTables output. BrianL made
    a nice test case in #13172. Turns out there was a fencepost error
    in forming a position range string to pass into samtools.
    fixes #13172, refs #13153
    
• src/hg/makeDb/doc/calMil1.txt
  • lines changed 12, context: html, text, full: html, text
    added blat server refs #12976
• src/hg/makeDb/doc/chrPic2.txt
  • lines changed 535, context: html, text, full: html, text
    running up genbank to complete assembly build refs #13166
  • lines changed 36, context: html, text, full: html, text
    add gold search rule refs #13166
• src/hg/makeDb/doc/criGri1.txt
  • lines changed 27, context: html, text, full: html, text
    add gold table search rule refs #6506
  • lines changed 1, context: html, text, full: html, text
    fixup path comment
• src/hg/makeDb/doc/danRer7.txt
  • lines changed 16, context: html, text, full: html, text
    adding cpgIslandsUnmasked track refs #334
• src/hg/makeDb/doc/dasNov3.txt
  • lines changed 14, context: html, text, full: html, text
    added cpgIslandsUnmasked track refs #7669
• src/hg/makeDb/doc/eriEur2.txt
  • lines changed 26, context: html, text, full: html, text
    add gold table search rule refs #9149
  • lines changed 1, context: html, text, full: html, text
    fixup path comment
• src/hg/makeDb/doc/sorAra2.txt
  • lines changed 1788, context: html, text, full: html, text
    finished an in pushQ 007237 refs #9348
• src/hg/makeDb/doc/taeGut2.txt
  • lines changed 26, context: html, text, full: html, text
    add gold table search rule refs #10190
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added chrPic2 refs #13166
  • lines changed 1, context: html, text, full: html, text
    Added poeRet1 refs #13170
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 17, context: html, text, full: html, text
    adding chrPic2 painted turtle refs #13166
  • lines changed 1, context: html, text, full: html, text
    adding chrPic2 painted turtle refs #13166
  • lines changed 17, context: html, text, full: html, text
    adding poeRet1 guppy refs #13170
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added chrPic2 refs #13166
  • lines changed 1, context: html, text, full: html, text
    Added poeRet1 refs #13170
• src/hg/makeDb/genbank/src/ccds/createTables.sql
  • lines changed 3, context: html, text, full: html, text
    ccds changed their schema
  • lines changed 1, context: html, text, full: html, text
    remove trailing comma
  • lines changed 1, context: html, text, full: html, text
    tax_id in Organzations should allow for null fields
• src/hg/makeDb/genbank/src/ccds/ncbiSql/createTables.sql
  • lines changed 2, context: html, text, full: html, text
    ccds changed their schema
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 2, context: html, text, full: html, text
    adding definition for poeRetNames refs #13170
• src/hg/makeDb/schema/all.joiner
  • lines changed 3, context: html, text, full: html, text
    adding global entry for genomicSuperDups track, removed individual entries for human/dog, refs #12831
  • lines changed 1, context: html, text, full: html, text
    RM Track #11226 (pushQ 7214)Rename table geneReviewsRefGene to geneReviewsDetail
    in identifier geneReviewsRefGeneId stanza.
    
• src/hg/makeDb/trackDb/chicken/galGal4/trackDb.chainNet.ra
  • lines changed 33, context: html, text, full: html, text
    adding taeGut2 chain net to galGal4 and melGal1 refs #10190
• src/hg/makeDb/trackDb/criGri/criGri1/gap.html
  • lines changed 2, context: html, text, full: html, text
    Made minor corrections (redmine #6506,9419,10190)
• src/hg/makeDb/trackDb/criGri/criGri1/gold.html
  • lines changed 3, context: html, text, full: html, text
    Made minor corrections (redmine #6506,9419,10190)
• src/hg/makeDb/trackDb/criGri/criGri1/trackDb.chainNet.ra
  • lines changed 2, context: html, text, full: html, text
    Made edits to display proper values for chain/net tracks (redmine #6506,9419,10190)
• src/hg/makeDb/trackDb/criGri/criGri1/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    add gold table search rule refs #6506
  • lines changed 2, context: html, text, full: html, text
    Made edits to display proper values for chain/net tracks (redmine #6506,9419,10190)
• src/hg/makeDb/trackDb/hedgehog/eriEur2/gap.html
  • lines changed 2, context: html, text, full: html, text
    Made minor corrections (redmine #6506,9419,10190)
• src/hg/makeDb/trackDb/hedgehog/eriEur2/gold.html
  • lines changed 3, context: html, text, full: html, text
    Made minor corrections (redmine #6506,9419,10190)
• src/hg/makeDb/trackDb/hedgehog/eriEur2/trackDb.chainNet.ra
  • lines changed 2, context: html, text, full: html, text
    Made edits to display proper values for chain/net tracks (redmine #6506,9419,10190)
• src/hg/makeDb/trackDb/hedgehog/eriEur2/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    add gold track search rule refs #9419
  • lines changed 2, context: html, text, full: html, text
    Made edits to display proper values for chain/net tracks (redmine #6506,9419,10190)
• src/hg/makeDb/trackDb/human/chainNetPlacental.ra
  • lines changed 17, context: html, text, full: html, text
    adding Chinese hamster chain net to hg19 placental refs #6506
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Staging EVS Variants track on beta, refs #9329
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    RM Track #11226 (pushQ 7214)After renaming geneReviewsGeneGRshortNBKidGRtitle to geneReviewsDetail,
    I forgot to change search rule of geneReviews table in human/trackDb.ra
    from
    xrefTable geneReviewsGeneGRshortNBKidGRtitle
    to
    xrefTable geneReviewsDetail
    
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding chrPic2 to the build refs #13166
  • lines changed 1, context: html, text, full: html, text
    adding poeRet1 to the build refs #13170
• src/hg/makeDb/trackDb/mouse/mm10/genomicSuperDups.html
  • lines changed 1, context: html, text, full: html, text
    Removing duplicate in mouseover found by contributor. refs #12831
  • lines changed 2, context: html, text, full: html, text
    replacing greater than signs with html names, refs #12831
• src/hg/makeDb/trackDb/poeRet/poeRet1/description.html
  • lines changed 63, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #13170
• src/hg/makeDb/trackDb/poeRet/poeRet1/gap.html
  • lines changed 31, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #13170
• src/hg/makeDb/trackDb/poeRet/poeRet1/gold.html
  • lines changed 34, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #13170
• src/hg/makeDb/trackDb/poeRet/poeRet1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #13170
  • lines changed 5, context: html, text, full: html, text
    adding gold table search rule refs #13170
• src/hg/makeDb/trackDb/rat/rn5/cons13way.ra
  • lines changed 103, context: html, text, full: html, text
    Adding initial draft of trackDb settings for new multiz13way for rat refs #8212
  • lines changed 2, context: html, text, full: html, text
    Adjusting values to match actual output of bigWigInfo for rn5 phyloP and phastCons subtracks. refs #8212
  • lines changed 1, context: html, text, full: html, text
    Tweaking values to match output of wigTableStats.sh for rn5 phyloP and phastCons subtracks. refs #8212
  • lines changed 1, context: html, text, full: html, text
    Fixing typo. refs #8212.
• src/hg/makeDb/trackDb/rat/rn5/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Adding initial entry/draft for new multiz. refs #8212
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 51, context: html, text, full: html, text
    adding Chinese hamster chain net to hg19 placental refs #6506
  • lines changed 50, context: html, text, full: html, text
    adding taeGut2 chain net to galGal4 and melGal1 refs #10190
• src/hg/makeDb/trackDb/turkey/melGal1/trackDb.chainNet.ra
  • lines changed 5, context: html, text, full: html, text
    adding taeGut2 chain net to galGal4 and melGal1 refs #10190
• src/hg/makeDb/trackDb/turkey/melGal1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    adding taeGut2 chain net to galGal4 and melGal1 refs #10190
• src/hg/makeDb/trackDb/turtle/chrPic2/description.html
  • lines changed 63, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #13166
• src/hg/makeDb/trackDb/turtle/chrPic2/gap.html
  • lines changed 32, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #13166
• src/hg/makeDb/trackDb/turtle/chrPic2/gold.html
  • lines changed 34, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #13166
• src/hg/makeDb/trackDb/turtle/chrPic2/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial files from makeGenomeDb.pl refs #13166
  • lines changed 6, context: html, text, full: html, text
    add gold table search rule refs #13166
• src/hg/makeDb/trackDb/zebraFinch/taeGut2/gap.html
  • lines changed 2, context: html, text, full: html, text
    Made minor corrections (redmine #6506,9419,10190)
• src/hg/makeDb/trackDb/zebraFinch/taeGut2/gold.html
  • lines changed 3, context: html, text, full: html, text
    Made minor corrections (redmine #6506,9419,10190)
• src/hg/makeDb/trackDb/zebraFinch/taeGut2/trackDb.chainNet.ra
  • lines changed 2, context: html, text, full: html, text
    Made edits to display proper values for chain/net tracks (redmine #6506,9419,10190)
• src/hg/makeDb/trackDb/zebraFinch/taeGut2/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    add gold table table search rule refs #10190
• src/hg/makefile
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    run uniprot databases tests as part of standard test run
• src/hg/protein/makefile
  • lines changed 8, context: html, text, full: html, text
    in uniprot database, flag primary gene name to distingiush it from synonyms
• src/hg/protein/spToDb/expected/test1/gene.txt
  • lines changed 12, context: html, text, full: html, text
    in uniprot database, flag primary gene name to distingiush it from synonyms
• src/hg/protein/spToDb/spDb.sql
  • lines changed 1, context: html, text, full: html, text
    in uniprot database, flag primary gene name to distingiush it from synonyms
• src/hg/protein/spToDb/spDbTables.as
  • lines changed 1, context: html, text, full: html, text
    in uniprot database, flag primary gene name to distingiush it from synonyms
• src/hg/protein/spToDb/spToDb.c
  • lines changed 3, context: html, text, full: html, text
    in uniprot database, flag primary gene name to distingiush it from synonyms
• src/hg/utils/phyloTrees/126way.commonNames.nh
  • lines changed 126, context: html, text, full: html, text
    adding Poecilia reticulata guppy fish and 126way for genomes on hand at UCSC refs #10272
• src/hg/utils/phyloTrees/126way.nh
  • lines changed 126, context: html, text, full: html, text
    adding Poecilia reticulata guppy fish and 126way for genomes on hand at UCSC refs #10272
• src/hg/utils/phyloTrees/126way.scientificNames.nh
  • lines changed 126, context: html, text, full: html, text
    adding Poecilia reticulata guppy fish and 126way for genomes on hand at UCSC refs #10272
• src/hg/utils/phyloTrees/130way.commonNames.nh
  • lines changed 130, context: html, text, full: html, text
    adding Poecilia reticulata guppy fish and 126way for genomes on hand at UCSC refs #10272
• src/hg/utils/phyloTrees/130way.nh
  • lines changed 130, context: html, text, full: html, text
    adding Poecilia reticulata guppy fish and 126way for genomes on hand at UCSC refs #10272
• src/hg/utils/phyloTrees/130way.scientificNames.nh
  • lines changed 130, context: html, text, full: html, text
    adding Poecilia reticulata guppy fish and 126way for genomes on hand at UCSC refs #10272
• src/hg/utils/phyloTrees/commonNames.sh
  • lines changed 1, context: html, text, full: html, text
    adding Poecilia reticulata guppy fish and 126way for genomes on hand at UCSC refs #10272
• src/hg/utils/phyloTrees/dbCommonScientificCladeOrderkey.tab
  • lines changed 3, context: html, text, full: html, text
    adding Poecilia reticulata guppy fish and 126way for genomes on hand at UCSC refs #10272
• src/hg/utils/phyloTrees/makefile
  • lines changed 14, context: html, text, full: html, text
    adding Poecilia reticulata guppy fish and 126way for genomes on hand at UCSC refs #10272
• src/hg/utils/phyloTrees/scientificNames.sh
  • lines changed 1, context: html, text, full: html, text
    adding Poecilia reticulata guppy fish and 126way for genomes on hand at UCSC refs #10272
• src/hg/utils/phyloTrees/vertebrates.txt
  • lines changed 4, context: html, text, full: html, text
    adding Poecilia reticulata guppy fish and 126way for genomes on hand at UCSC refs #10272
• src/hg/utils/pslMap/pslMap.c
  • lines changed 39, context: html, text, full: html, text
    added pslMap option to limit mapping alignments to those prefixed with the cooresponding input qName
• src/hg/utils/pslMap/tests/expected/testMapFileWithInQName.psl
  • lines changed 17, context: html, text, full: html, text
    added pslMap option to limit mapping alignments to those prefixed with the cooresponding input qName
• src/hg/utils/pslMap/tests/input/gencode.blocks.qName-psl
  • lines changed 17, context: html, text, full: html, text
    added pslMap option to limit mapping alignments to those prefixed with the cooresponding input qName
• src/hg/utils/pslMap/tests/input/gencode.src.psl
  • lines changed 5, context: html, text, full: html, text
    added pslMap option to limit mapping alignments to those prefixed with the cooresponding input qName
• src/hg/utils/pslMap/tests/makefile
  • lines changed 7, context: html, text, full: html, text
    added pslMap option to limit mapping alignments to those prefixed with the cooresponding input qName
• src/hg/utils/pslMap/usage.txt
  • lines changed 3, context: html, text, full: html, text
    added pslMap option to limit mapping alignments to those prefixed with the cooresponding input qName
• src/inc/common.mk
  • lines changed 4, context: html, text, full: html, text
    correcting too many ifs after code review, refs #13154
• src/inc/longList.h
  • lines changed 52, context: html, text, full: html, text
    Renaming longList structure and module to longToList.
• src/inc/longToList.h
  • lines changed 52, context: html, text, full: html, text
    Renaming longList structure and module to longToList.
• src/lib/jsonWrite.c
  • lines changed 6, context: html, text, full: html, text
    Removed out of date part of comment.
• src/lib/longList.c
  • lines changed 100, context: html, text, full: html, text
    Renaming longList structure and module to longToList.
• src/lib/longToList.c
  • lines changed 100, context: html, text, full: html, text
    Renaming longList structure and module to longToList.
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Renaming longList to longToList.
• src/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding parasol libraries to those made with make libs.
• src/utils/qa/weeklybld/buildEnv.csh
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    v300 preview1
• src/utils/qa/weeklybld/doHgNearTestRobot.csh
  • lines changed 1, context: html, text, full: html, text
    Fixed variable assignment so spacing is preserved, allowing the test for errors to work properly

• lines changed: 9795
• files changed: 141