All File Changes

v309_preview to v309_preview2 (2014-11-10 to 2014-11-17) v309

• src/hg/cirm/quakeLab/djangoModelToAs/djangoModelToAs.c
  • lines changed 132, context: html, text, full: html, text
    Cut of something to convert the django models from Quake lab to .as files.
• src/hg/cirm/quakeLab/djangoModels/cellcapturemodels.py
  • lines changed 266, context: html, text, full: html, text
    Draft Django data models from Ben Passarelli.
  • lines changed 266, context: html, text, full: html, text
    Second cut, this time all in one file.
• src/hg/cirm/quakeLab/djangoModels/quantifymodels.py
  • lines changed 45, context: html, text, full: html, text
    Draft Django data models from Ben Passarelli.
  • lines changed 45, context: html, text, full: html, text
    Second cut, this time all in one file.
• src/hg/cirm/quakeLab/djangoModels/sequencemodels.py
  • lines changed 144, context: html, text, full: html, text
    Draft Django data models from Ben Passarelli.
  • lines changed 144, context: html, text, full: html, text
    Second cut, this time all in one file.
• src/hg/cirm/quakeLab/djangoModels/take1/cellcapturemodels.py
  • lines changed 266, context: html, text, full: html, text
    Second cut, this time all in one file.
• src/hg/cirm/quakeLab/djangoModels/take1/quantifymodels.py
  • lines changed 45, context: html, text, full: html, text
    Second cut, this time all in one file.
• src/hg/cirm/quakeLab/djangoModels/take1/sequencemodels.py
  • lines changed 144, context: html, text, full: html, text
    Second cut, this time all in one file.
• src/hg/cirm/quakeLab/djangoModels/take2/models.py
  • lines changed 324, context: html, text, full: html, text
    Second cut, this time all in one file.
  • lines changed 2, context: html, text, full: html, text
    Fixing misplaced newline.
• src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/sorted.bb
  • lines changed 0, context: html, text, full: html, text
    Deleting out of place binary file
• src/hg/genoPheno/fakeData/smallGeno.tab
  • lines changed 556, context: html, text, full: html, text
    Removing more unused old cruft.
• src/hg/genoPheno/gpFakeData/gpFakeData.c
  • lines changed 419, context: html, text, full: html, text
    Removing more unused old cruft.
• src/hg/genoPheno/gpFakeData/makefile
  • lines changed 14, context: html, text, full: html, text
    Removing more unused old cruft.
• src/hg/genoPheno/gpShuffleData/gpShuffleData.c
  • lines changed 159, context: html, text, full: html, text
    Removing old function that would be considered one shot these days.
• src/hg/genoPheno/gpShuffleData/makefile
  • lines changed 14, context: html, text, full: html, text
    Removing old function that would be considered one shot these days.
• src/hg/hgTables/genomeSpace.c
  • lines changed 21, context: html, text, full: html, text
    Replaced md5hash function with equivalent call to md5ForFile library function.
• src/hg/hgTracks/factorSource.c
  • lines changed 1, context: html, text, full: html, text
    catch NULL pointer #14368
• src/hg/hgTracks/hgTracks.c
  • lines changed 3, context: html, text, full: html, text
    add support for bigGenePred custom tracks. #13861
• src/hg/hgTracks/hgTracks.h
  • lines changed 3, context: html, text, full: html, text
    Add custom item name to show peptide sequence. refs #14054
• src/hg/hgTracks/makefile
  • lines changed 1, context: html, text, full: html, text
    Add custom item name to show peptide sequence. refs #14054
• src/hg/hgTracks/peptideAtlasTrack.c
  • lines changed 85, context: html, text, full: html, text
    Add custom item name to show peptide sequence. refs #14054
  • lines changed 13, context: html, text, full: html, text
    Try another translate function -- fixes apparent mem problem. refs #14054
• src/hg/hgTracks/simpleTracks.c
  • lines changed 3, context: html, text, full: html, text
    Add custom item name to show peptide sequence. refs #14054
• src/hg/hgc/hgc.c
  • lines changed 78, context: html, text, full: html, text
    Add peptide table with sequence and other info for details page. refs #25054
• src/hg/hgc/hgc.h
  • lines changed 3, context: html, text, full: html, text
    Add peptide table with sequence and other info for details page. refs #25054
• src/hg/hgc/hgdpClick.c
  • lines changed 6, context: html, text, full: html, text
    Adding new pipelineClose() function that combines pipelineWait and pipelineFree and applying it where it makes sense, in some cases fixing non-symptomatic bugs from missing pipelineWaits
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 174, context: html, text, full: html, text
    Adding links on credits.html to hgGateway for mentioned UCSC assemblies refs #14336
  • lines changed 7, context: html, text, full: html, text
    Adding two missed mentioned databases, and removing links to droAna when it concerned sequencing, not browser. refs #14336
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 3, context: html, text, full: html, text
    Implemented 2 font changes suggested in code review. RM #14294
  • lines changed 4, context: html, text, full: html, text
    adding some target=_blank as noticed by Matt in code review #14345
  • lines changed 52, context: html, text, full: html, text
    Making it clearer that you can load local assembly hubs into the GBiB. Other small edits based on comments from Max. refs #14364
• src/hg/htdocs/goldenPath/help/wiggle.html
  • lines changed 8, context: html, text, full: html, text
    Adding some notes to wiggle.html that a definition line is needed with the delcaration line, per MLQ input refs #14362
• src/hg/htdocs/images/peptideAtlasMethods.png
  • lines changed 0, context: html, text, full: html, text
    Add graphic to description page. refs #14054
• src/hg/htdocs/indexIntro.html
  • lines changed 1, context: html, text, full: html, text
    adding some target=_blank as noticed by Matt in code review #14345
• src/hg/inc/hgFind.h
  • lines changed 1, context: html, text, full: html, text
    Added a feature to bold canonical gene names on intermediate page when the user searches an ambiguous gene name (IE foxp2).
  • lines changed 1, context: html, text, full: html, text
    Added new fields to hgPos struct, used for bolding canonical genes
• src/hg/inc/peptideAtlasPeptide.h
  • lines changed 67, context: html, text, full: html, text
    Add peptide table with sequence and other info for details page. refs #25054
• src/hg/lib/customFactory.c
  • lines changed 19, context: html, text, full: html, text
    add support for bigGenePred custom tracks. #13861
• src/hg/lib/genePred.c
  • lines changed 1, context: html, text, full: html, text
    add support for bigGenePred custom tracks. #13861
• src/hg/lib/grp.sql
  • lines changed 4, context: html, text, full: html, text
    remove the Tracks word from the labels refs #4049
• src/hg/lib/hgConfig.c
  • lines changed 3, context: html, text, full: html, text
    don't fail on missing hg.conf file when asking for conf variables.
• src/hg/lib/hgFind.c
  • lines changed 1, context: html, text, full: html, text
    Adding new pipelineClose() function that combines pipelineWait and pipelineFree and applying it where it makes sense, in some cases fixing non-symptomatic bugs from missing pipelineWaits
  • lines changed 81, context: html, text, full: html, text
    Added a feature to bold canonical gene names on intermediate page when the user searches an ambiguous gene name (IE foxp2).
  • lines changed 74, context: html, text, full: html, text
    Canonical genes are brought to the top of the search result
  • lines changed 2, context: html, text, full: html, text
    Fixed comments and removed extra code
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    add support for bigGenePred custom tracks. #13861
• src/hg/lib/liftOver.c
  • lines changed 1, context: html, text, full: html, text
    Fixed bug in liftOver where annotations that ended at the exact end ofa scaffold were not mapped.
    
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Makefile too
• src/hg/lib/peptideAtlasPeptide.as
  • lines changed 9, context: html, text, full: html, text
    Add peptide table with sequence and other info for details page. refs #25054
• src/hg/lib/peptideAtlasPeptide.c
  • lines changed 141, context: html, text, full: html, text
    Add peptide table with sequence and other info for details page. refs #25054
• src/hg/lib/peptideAtlasPeptide.sql
  • lines changed 15, context: html, text, full: html, text
    Add peptide table with sequence and other info for details page. refs #25054
• src/hg/lib/trackHubCheck.c
  • lines changed 1, context: html, text, full: html, text
    add support for bigGenePred in hubCheck #14376
• src/hg/liftOver/tests/expected/mm3.all.bed
  • lines changed 16, context: html, text, full: html, text
    Fixed bug in liftOver where annotations that ended at the exact end ofa scaffold were not mapped.
    
• src/hg/liftOver/tests/expected/mm3.multiple.bed
  • lines changed 6, context: html, text, full: html, text
    Fixed bug in liftOver where annotations that ended at the exact end ofa scaffold were not mapped.
    
• src/hg/liftOver/tests/expected/scaffoldEndBug.gp
  • lines changed 6, context: html, text, full: html, text
    Fixed bug in liftOver where annotations that ended at the exact end ofa scaffold were not mapped.
    
• src/hg/liftOver/tests/input/scaffoldEndBug.chain
  • lines changed 8, context: html, text, full: html, text
    Fixed bug in liftOver where annotations that ended at the exact end ofa scaffold were not mapped.
    
• src/hg/liftOver/tests/input/scaffoldEndBug.gp
  • lines changed 6, context: html, text, full: html, text
    Fixed bug in liftOver where annotations that ended at the exact end ofa scaffold were not mapped.
    
• src/hg/liftOver/tests/makefile
  • lines changed 11, context: html, text, full: html, text
    Fixed bug in liftOver where annotations that ended at the exact end ofa scaffold were not mapped.
    
• src/hg/makeDb/doc/dm6.txt
  • lines changed 234, context: html, text, full: html, text
    add iRows and frames refs #13461
  • lines changed 404, context: html, text, full: html, text
    adding phastCons 27way refs #13461
  • lines changed 191, context: html, text, full: html, text
    adding phyloP 27way refs #13461
• src/hg/makeDb/doc/eboVir3/gbkToGp.pl
  • lines changed 58, context: html, text, full: html, text
    add header per code review comment refs #14300
• src/hg/makeDb/doc/eboVir3/threeBaseAATrack.pl
  • lines changed 4, context: html, text, full: html, text
    add header per code review comment refs #14300
• src/hg/makeDb/doc/hg19.txt
  • lines changed 10, context: html, text, full: html, text
    making uniprot annotations track ready for hg19, refs #13688
  • lines changed 1, context: html, text, full: html, text
    typo in makedoc
  • lines changed 13, context: html, text, full: html, text
    Add custom item name to show peptide sequence. refs #14054
  • lines changed 3, context: html, text, full: html, text
    Add peptide table with sequence and other info for details page. refs #25054
• src/hg/makeDb/hgLoadPsl/hgLoadPsl.c
  • lines changed 8, context: html, text, full: html, text
    Adding new pipelineClose() function that combines pipelineWait and pipelineFree and applying it where it makes sense, in some cases fixing non-symptomatic bugs from missing pipelineWaits
• src/hg/makeDb/outside/uwDnaseTrackHub/uwDnaseTrackHub.c
  • lines changed 36, context: html, text, full: html, text
    Fixing up sort order and adding treatment subgroup.
• src/hg/makeDb/trackDb/drosophila/dm6/cytoBand.html
  • lines changed 12, context: html, text, full: html, text
    update to correct cytoBand description page refs #4049
  • lines changed 1, context: html, text, full: html, text
    Changing link on cytoBand page, refs #4049
• src/hg/makeDb/trackDb/drosophila/dm6/flyBaseGene.ra
  • lines changed 25, context: html, text, full: html, text
    fly base genes only on hgwdev refs #4049
• src/hg/makeDb/trackDb/drosophila/dm6/gap.html
  • lines changed 41, context: html, text, full: html, text
    update to correct gap gold description pages refs #4049
• src/hg/makeDb/trackDb/drosophila/dm6/gold.html
  • lines changed 28, context: html, text, full: html, text
    update to correct gap gold description pages refs #4049
• src/hg/makeDb/trackDb/drosophila/dm6/trackDb.ra
  • lines changed 26, context: html, text, full: html, text
    fly base genes only on hgwdev refs #4049
  • lines changed 2, context: html, text, full: html, text
    Making RefSeq packed by default, refs #4049
• src/hg/makeDb/trackDb/drosophila/refGene.html
  • lines changed 16, context: html, text, full: html, text
    Adding PMID/PMCIDs to references for refGene and xenoMrna tracks, refs #4049
• src/hg/makeDb/trackDb/drosophila/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    Adding cytoBand search for dm*. If cytoBandIdeo is rebuilt to use coarserbands, we should add a search for that as well (but with no number at the
    end of regex).
    
• src/hg/makeDb/trackDb/drosophila/xenoMrna.html
  • lines changed 16, context: html, text, full: html, text
    Adding PMID/PMCIDs to references for refGene and xenoMrna tracks, refs #4049
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding gEncodeAwgDnaseMasterSites.ra to the metaDb makefile (done with Kate's help) and staging the metaData to public refs# 13230
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeAwgDnaseMasterSites.ra
  • lines changed 21, context: html, text, full: html, text
    Adding gEncodeAwgDnaseMasterSites.ra to the metaDb makefile (done with Kate's help) and staging the metaData to public refs# 13230
• src/hg/makeDb/trackDb/human/hg38/trackDb.cloneEnd.ra
  • lines changed 246, context: html, text, full: html, text
    a bugfix in the new bac ends track gets more clones out of trace db
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 12, context: html, text, full: html, text
    add a test self chain track on chr1 only (per David)
  • lines changed 12, context: html, text, full: html, text
    add swapped version of test self chain on hg38.chr1 (pre david)
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    Added dm6 to DBS.
• src/hg/makeDb/trackDb/spUniprot.html
  • lines changed 66, context: html, text, full: html, text
    making uniprot annotations track ready for hg19, refs #13688
  • lines changed 9, context: html, text, full: html, text
    some changes to the uniprot details page, refs #13688
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 22, context: html, text, full: html, text
    making uniprot annotations track ready for hg19, refs #13688
  • lines changed 9, context: html, text, full: html, text
    moving pfam under uniprot, refs #13688
  • lines changed 1, context: html, text, full: html, text
    forgot line in last commit
  • lines changed 3, context: html, text, full: html, text
    trying to comply with tdbQuery -strict
• src/hg/oneShot/freen/freen.c
  • lines changed 56, context: html, text, full: html, text
    Testing pthreadDoList example usage code.
  • lines changed 39, context: html, text, full: html, text
    Replacing old md5 module with one that follows same interface (except for some things noone used) but that is implemented by calling the md5sum program in a pipe. For large files this is about 40% faster, and for small things it just adds a couple of milliseconds. Also this gets rid of the only piece of GPL licensed code in the tree, which makes the intellecual property easier to manage.
• src/hg/pslPartition/pslPartition.c
  • lines changed 2, context: html, text, full: html, text
    Adding new pipelineClose() function that combines pipelineWait and pipelineFree and applying it where it makes sense, in some cases fixing non-symptomatic bugs from missing pipelineWaits
• src/hg/utils/automation/simplePerl.pl
  • lines changed 71, context: html, text, full: html, text
    example perl programming refs #14358
• src/hg/utils/otto/clinvar/clinVarToBed
  • lines changed 55, context: html, text, full: html, text
    toughening the clinvar otto checks as requested in code review, refs #14350
• src/hg/utils/otto/clinvar/makefile
  • lines changed 1, context: html, text, full: html, text
    toughening the clinvar otto checks as requested in code review, refs #14350
• src/hg/utils/uniprotMutations/makeUniProtToHg.sh
  • lines changed 11, context: html, text, full: html, text
    making uniprot annotations track ready for hg19, refs #13688
• src/inc/md5.h
  • lines changed 24, context: html, text, full: html, text
    Replacing old md5 module with one that follows same interface (except for some things noone used) but that is implemented by calling the md5sum program in a pipe. For large files this is about 40% faster, and for small things it just adds a couple of milliseconds. Also this gets rid of the only piece of GPL licensed code in the tree, which makes the intellecual property easier to manage.
• src/inc/pipeline.h
  • lines changed 8, context: html, text, full: html, text
    Adding new pipelineClose() function that combines pipelineWait and pipelineFree and applying it where it makes sense, in some cases fixing non-symptomatic bugs from missing pipelineWaits
• src/inc/synQueue.h
  • lines changed 4, context: html, text, full: html, text
    Adding synQueuePutUnprotected, a minor optimization.
• src/inc/trix.h
  • lines changed 3, context: html, text, full: html, text
    Adding trixSearchCmp function to header file and fixed documentation.
• src/lib/bPlusTree.c
  • lines changed 3, context: html, text, full: html, text
    fix variable size problem #14373
• src/lib/linefile.c
  • lines changed 2, context: html, text, full: html, text
    Adding new pipelineClose() function that combines pipelineWait and pipelineFree and applying it where it makes sense, in some cases fixing non-symptomatic bugs from missing pipelineWaits
• src/lib/mailViaPipe.c
  • lines changed 4, context: html, text, full: html, text
    Adding new pipelineClose() function that combines pipelineWait and pipelineFree and applying it where it makes sense, in some cases fixing non-symptomatic bugs from missing pipelineWaits
• src/lib/md5.c
  • lines changed 338, context: html, text, full: html, text
    Replacing old md5 module with one that follows same interface (except for some things noone used) but that is implemented by calling the md5sum program in a pipe. For large files this is about 40% faster, and for small things it just adds a couple of milliseconds. Also this gets rid of the only piece of GPL licensed code in the tree, which makes the intellecual property easier to manage.
• src/lib/pipeline.c
  • lines changed 14, context: html, text, full: html, text
    Adding new pipelineClose() function that combines pipelineWait and pipelineFree and applying it where it makes sense, in some cases fixing non-symptomatic bugs from missing pipelineWaits
• src/lib/pthreadDoList.c
  • lines changed 37, context: html, text, full: html, text
    Simplifying logic
• src/lib/synQueue.c
  • lines changed 7, context: html, text, full: html, text
    Adding synQueuePutUnprotected, a minor optimization.
• src/lib/textOut.c
  • lines changed 2, context: html, text, full: html, text
    Adding new pipelineClose() function that combines pipelineWait and pipelineFree and applying it where it makes sense, in some cases fixing non-symptomatic bugs from missing pipelineWaits
• src/lib/trix.c
  • lines changed 1, context: html, text, full: html, text
    Adding trixSearchCmp function to header file and fixed documentation.
• src/parasol/broadHub/broadHub.c
  • lines changed 750, context: html, text, full: html, text
    Removing more unused old cruft.
• src/parasol/broadHub/makefile
  • lines changed 14, context: html, text, full: html, text
    Removing more unused old cruft.
• src/parasol/broadNode/broadNode.c
  • lines changed 473, context: html, text, full: html, text
    Removing more unused old cruft.
• src/parasol/broadNode/makefile
  • lines changed 14, context: html, text, full: html, text
    Removing more unused old cruft.
• src/parasol/broadNodeStart/broadNodeStart.c
  • lines changed 54, context: html, text, full: html, text
    Removing more unused old cruft.
• src/parasol/broadNodeStart/makefile
  • lines changed 14, context: html, text, full: html, text
    Removing more unused old cruft.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v309 preview2 refs #14342
• src/utils/uniprotLift
  • lines changed 38, context: html, text, full: html, text
    making uniprot annotations track ready for hg19, refs #13688

• lines changed: 7507
• files changed: 122