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
- 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 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
- 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
- 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