All File Changes
v271_base to v272_preview (2012-08-07 to 2012-08-14) v272
- python/lib/ucscGb/encode/mkChangeNotes.py
- lines changed 1, context: html, text, full: html, text
added a warning for new and revoked files at the same time
- src/hg/hgCustom/hgCustom.c
- lines changed 2, context: html, text, full: html, text
Feature #3265 (nightly cron job should build utils and cgis with various USE_* options):Tim found that build breaks with USE_BAM=0 USE_TABIX=1 USE_KNETFILE_HOOKS=1 -- fixing.
- src/hg/hgLogin/hgLogin.c
- lines changed 17, context: html, text, full: html, text
Upper case all mysql keywords in query statements.
- lines changed 1, context: html, text, full: html, text
remove include of crypt.h. It's not needed, and it's not present in MacOSX (#8746)
- src/hg/hgTracks/gencodeTracks.c
- lines changed 28, context: html, text, full: html, text
fixed breaking control over gene labels when gencode track was refactored
- src/hg/hgTracks/hgTracks.h
- lines changed 4, context: html, text, full: html, text
fixed breaking control over gene labels when gencode track was refactored
- src/hg/hgTracks/simpleTracks.c
- lines changed 19, context: html, text, full: html, text
fixed breaking control over gene labels when gencode track was refactored
- src/hg/htdocs/ENCODE/dataSummary.html
- lines changed 12, context: html, text, full: html, text
#8736: Update Experiment List pages for human and mouse, based on Jun30 quarterly reports
- src/hg/htdocs/ENCODE/dataSummaryMouse.html
- lines changed 16, context: html, text, full: html, text
#8736: Update Experiment List pages for human and mouse, based on Jun30 quarterly reports
- src/hg/htdocs/ENCODE/downloadsMouse.html
- lines changed 4, context: html, text, full: html, text
Adding link to downloads for new mouse ENCODE track PSU RNA-Seq (Release 1) RM#107
- src/hg/htdocs/ENCODE/index.html
- lines changed 3, context: html, text, full: html, text
#8736: Update Experiment List pages for human and mouse, based on Jun30 quarterly reports
- src/hg/htdocs/ENCODE/integrativeAnalysis/VM/index.html
- lines changed 10, context: html, text, full: html, text
#8740: Portal redirect to Galaxy for analysis virtual machines
- lines changed 2, context: html, text, full: html, text
Improvements to user message. Shorten and add links
- src/hg/htdocs/goldenPath/help/ftp.html
- lines changed 1, context: html, text, full: html, text
Made absolte path to relative path to style sheet, as it should be.
- src/hg/htdocs/goldenPath/help/geneSearchBox.html
- lines changed 18, context: html, text, full: html, text
rewording to match new comboBox functionality
- lines changed 1, context: html, text, full: html, text
turns out that the button is labeled 'go' in hgTracks and 'submit' in hgGateway. I decided that people would probably come to this page more often from hgGateway.
- src/hg/htdocs/goldenPath/help/mysql.html
- lines changed 2, context: html, text, full: html, text
Fixed path for two links.
- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
- lines changed 7, context: html, text, full: html, text
Filling out documentation of wgEncode setting (prompted by Redmine that Rachel will file re use on hub)
- src/hg/htdocs/images/autoselect.jpg
- lines changed 0, context: html, text, full: html, text
update image to reflect merged gene suggest
- lines changed 0, context: html, text, full: html, text
remove white-space at the bottom
- src/hg/htdocs/style/HGStyle.css
- src/hg/inc/cart.h
- lines changed 16, context: html, text, full: html, text
remove some routines used only by the proteome browser (#5740)
- src/hg/lib/cart.c
- lines changed 47, context: html, text, full: html, text
remove some routines used only by the proteome browser (#5740)
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibTfbs.release3.notes
- src/hg/makeDb/doc/encodeDccMm9/wgEncodeLicrTfbs.release3.notes
- lines changed 43, context: html, text, full: html, text
update notes file after removing the *Plac* input only file that have not been released that was revoked previously using the procedure of released dataset
- src/hg/makeDb/doc/encodeDccMm9/wgEncodeSydhHist.release2.notes
- lines changed 274, context: html, text, full: html, text
renaming file to proper composite name
- src/hg/makeDb/doc/encodeDccMm9/wgEncodeSydhHistone.release2.notes
- lines changed 274, context: html, text, full: html, text
first pass at notes for sydh histone
- lines changed 274, context: html, text, full: html, text
renaming file to proper composite name
- src/hg/makeDb/doc/geoFor1.txt
- lines changed 992, context: html, text, full: html, text
7-way done and ready for downloads
- lines changed 143, context: html, text, full: html, text
download files ready to go
- lines changed 113, context: html, text, full: html, text
done with hgPal downloads for 7-way
- lines changed 9, context: html, text, full: html, text
completed upstream maf files
- src/hg/makeDb/genbank/etc/genbank.conf
- lines changed 2, context: html, text, full: html, text
adding upstream definition to geoFor1
- src/hg/makeDb/genbank/etc/hgwbeta.dbs
- lines changed 1, context: html, text, full: html, text
Reinstating panTro1 after beginning to archive it. It is the only chimp with a BAC End Pairs track.
- src/hg/makeDb/genbank/etc/rr.dbs
- lines changed 1, context: html, text, full: html, text
Reinstating panTro1 after beginning to archive it. It is the only chimp with a BAC End Pairs track.
- src/hg/makeDb/hgTrackDb/hgTrackDb.c
- lines changed 8, context: html, text, full: html, text
It was necessary to make the warnings silent on make strict. Otherwise the current trackDbs for beta cause warnings that prevents the beta build.
- lines changed 2, context: html, text, full: html, text
Jeeeezzz it seems make strict on beta cannot survive any of the tag validation.
- src/hg/makeDb/schema/all.joiner
- lines changed 1, context: html, text, full: html, text
adding geoFor to the xenoRefGene definitions
- src/hg/makeDb/trackDb/baboon/papAnu2/description.html
- lines changed 1, context: html, text, full: html, text
Use the same picture as papHam1, since the two assemblies are both from the same animal
- src/hg/makeDb/trackDb/birds/geoFor1/cons7way.html
- lines changed 29, context: html, text, full: html, text
finalize this 7-way description document
- lines changed 1, context: html, text, full: html, text
adding Zebra finch to the list of species
- src/hg/makeDb/trackDb/birds/geoFor1/trackDb.7way.ra
- lines changed 7, context: html, text, full: html, text
default visibilities and correct range on the phyloP overall
- src/hg/makeDb/trackDb/birds/geoFor1/trackDb.ra
- lines changed 8, context: html, text, full: html, text
add correct search spec for gold table
- src/hg/makeDb/trackDb/birds/melUnd1/trackDb.ra
- lines changed 8, context: html, text, full: html, text
add gold table search rule
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 2, context: html, text, full: html, text
Shortening target for REST in CV
- lines changed 175, context: html, text, full: html, text
Adding targetClass variable to CV
- lines changed 1, context: html, text, full: html, text
Adding H1 derived neuron protocols to CV
- lines changed 12, context: html, text, full: html, text
Adding targetClass typeOfTerm to CV
- lines changed 1, context: html, text, full: html, text
Adding targetClass typeOfTerm to CV
- src/hg/makeDb/trackDb/human/hg19/hg19vertChainNet.html
- lines changed 4, context: html, text, full: html, text
add Medium ground finch to the matrix notes
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
- lines changed 4306, context: html, text, full: html, text
fixed controls naming and removed duplicate controls
- lines changed 4, context: html, text, full: html, text
didn't revoke the originals last time
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
- lines changed 1598, context: html, text, full: html, text
last metadata for open chrom chip
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
- lines changed 1820, context: html, text, full: html, text
added in last SydhTfbs tracks hg19
- lines changed 161, context: html, text, full: html, text
added in all but one ControlId
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeGisRnaPet.ra
- lines changed 43, context: html, text, full: html, text
Restaging on beta for GIS RNA PET (Release 2) RM#5942
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeCaltechRnaSeq.ra
- lines changed 1454, context: html, text, full: html, text
Releasing Caltech RNA-seq (Release 4) to the RR (redmine #8537)
- src/hg/makeDb/trackDb/human/hg19/snp137.shared.html
- lines changed 54, context: html, text, full: html, text
Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):Describe Function categories still in use in the coloring section (thx Brooke).
- lines changed 7, context: html, text, full: html, text
Feature #8551: Coloring function category names according to default coloring scheme (thx Brooke).
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- lines changed 2, context: html, text, full: html, text
Releasing Caltech RNA-seq (Release 4) to the RR (redmine #8537)
- lines changed 6, context: html, text, full: html, text
Changed release tags to move new highlighting feature to beta (redmine #8634)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.release4.html
- lines changed 218, context: html, text, full: html, text
Corrected formatting of html and made appropriate grammar/content corrections (redmine #8537)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.release4.ra
- lines changed 105, context: html, text, full: html, text
Removing the maxWindows as it is not needed anymore and fixing the long labels to get rid of the parens ticket 8537
- src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliChip.release2.html
- lines changed 47, context: html, text, full: html, text
Changing the html according to code review of Steve
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV7.release3.ra
- lines changed 2, context: html, text, full: html, text
fixed problem where gencode V7 and were referencing table that were not in that release
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV9.ra
- lines changed 1, context: html, text, full: html, text
fixed problem where gencode V7 and were referencing table that were not in that release
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.release2.html
- lines changed 10, context: html, text, full: html, text
Fixing the issues in ticket 5942. Trying to add references
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.release2.ra
- lines changed 1, context: html, text, full: html, text
Fixing the issues in ticket 5942. Trying to add references
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylWgbs.html
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release3.ra
- lines changed 452, context: html, text, full: html, text
short labels first attempt
- lines changed 500, context: html, text, full: html, text
fixed controls issue in haib tfbs trackDb
- lines changed 73, context: html, text, full: html, text
added in twiers for h1neruons and fixed long and short labels
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.release2.ra
- lines changed 272, context: html, text, full: html, text
added in last open chrom chip tracks
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release3.ra
- lines changed 227, context: html, text, full: html, text
added in last SydhTfbs tracks hg19
- lines changed 26, context: html, text, full: html, text
added back tracks that were erroneously pulled out, and pulled out bad ones
- src/hg/makeDb/trackDb/mouse/mm10/cons60way.html
- lines changed 1, context: html, text, full: html, text
Removed redundant table data and row closing tags found by hgTablesTest.
- lines changed 2, context: html, text, full: html, text
Updated tables to use our nice table class. Thanks, Greg.
- lines changed 1, context: html, text, full: html, text
Removed comma that made squirrel monkey sound like two organisms.
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.60way.ra
- lines changed 3, context: html, text, full: html, text
Shortened shortLabels greater than 17 chars.
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.vertebrateChainNet.ra
- lines changed 19, context: html, text, full: html, text
adding geoFor1 to the Vertebrate chain net grouping
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
- lines changed 2, context: html, text, full: html, text
set revoke status to two CH12 entries missed earlier
- lines changed 25, context: html, text, full: html, text
set controlId for those V2 datasets
- lines changed 71, context: html, text, full: html, text
update expId for V2 datasets
- lines changed 6, context: html, text, full: html, text
add revoke status to the input only dataset (Plac)
- lines changed 301, context: html, text, full: html, text
delete input only datasets
- lines changed 25, context: html, text, full: html, text
modified V2 statement based on Steve's input, note 83, #7502
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHist.ra
- lines changed 169, context: html, text, full: html, text
added in last sydh histone mouse track
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
- lines changed 1585, context: html, text, full: html, text
update new datasets submitted before the freeze
- lines changed 273, context: html, text, full: html, text
adding md5sums and restoring some stanzas
- lines changed 147, context: html, text, full: html, text
added in last metadata for mm9 sydh tfbs
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
- lines changed 1304, context: html, text, full: html, text
update the new datasets submitted before the freeze
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/makefile
- lines changed 1, context: html, text, full: html, text
Staging on beta mm9 PSU RNA-Seq (Release 1/Final) RM#107
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeLicrTfbs.ra
- lines changed 998, context: html, text, full: html, text
Staging LICR TFBS (Release 3) on beta (redmine #7502)
- lines changed 25, context: html, text, full: html, text
Ruihua made some corrections to the metadata (redmine #7502)
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodePsuRnaSeq.ra
- lines changed 4301, context: html, text, full: html, text
Staging on beta mm9 PSU RNA-Seq (Release 1/Final) RM#107
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodePsuTfbs.ra
- lines changed 1810, context: html, text, full: html, text
Staging on beta PSU TFBS mm9 (Release 2) RM#7516
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/makefile
- lines changed 1, context: html, text, full: html, text
Staging on public, PSU RNA-Seq (Release 1) RM#107
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeLicrTfbs.ra
- lines changed 998, context: html, text, full: html, text
Releasing LICR TFBS (Release 3) to the RR (redmine #7502)
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodePsuRnaSeq.ra
- lines changed 4301, context: html, text, full: html, text
Staging on public, PSU RNA-Seq (Release 1) RM#107
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodePsuTfbs.ra
- lines changed 1810, context: html, text, full: html, text
Staging on Public PSU TFBS mm9 (Release 2) RM#7516
- src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
- lines changed 2, context: html, text, full: html, text
Staging on beta PSU TFBS mm9 (Release 2) RM#7516
- lines changed 2, context: html, text, full: html, text
Staging on Public PSU TFBS mm9 (Release 2) RM#7516
- lines changed 2, context: html, text, full: html, text
Staging LICR TFBS (Release 3) on beta (redmine #7502)
- lines changed 2, context: html, text, full: html, text
Releasing LICR TFBS (Release 3) to the RR (redmine #7502)
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.release3.html
- lines changed 2, context: html, text, full: html, text
add TFBS and LICR in the text
- lines changed 3, context: html, text, full: html, text
Added link to Bowtie (redmine #7502)
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.release3.ra
- lines changed 22, context: html, text, full: html, text
comment out stanzas whose datasets are revoked
- lines changed 77, context: html, text, full: html, text
remove the digit that appearred in the beginning of age and celltype
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuRnaSeq.html
- lines changed 2, context: html, text, full: html, text
Redmine #107. Q5. Added missing parethesis and removed extra ones.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuRnaSeq.ra
- lines changed 0, context: html, text, full: html, text
Fixed typo found in code review. Redmine #8720.
- lines changed 2, context: html, text, full: html, text
Redmine #107. Q1. Fixed long and short labels to reflect label convention.
- lines changed 1, context: html, text, full: html, text
Fixed alphabetical ordering. Redmine #107.
- lines changed 1, context: html, text, full: html, text
Redmine #107. Q4. Fixed typo in shortLabel using O instead of 0.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.release2.html
- lines changed 1, context: html, text, full: html, text
Fixes for Redmine #7516. Q3. Added period at end of sentence in Release Notes 2nd paragraph.
- lines changed 122, context: html, text, full: html, text
Redmine #7516. Q5. Fixed references to link to pubmed.
- lines changed 1, context: html, text, full: html, text
Fixed link that was going to the wrong track.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.release2.ra
- lines changed 1, context: html, text, full: html, text
Redmine #7516. Q2. Fixed Treatment cv linkage.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHist.release2.ra
- lines changed 18, context: html, text, full: html, text
added in last sydh histone mouse track
- lines changed 36, context: html, text, full: html, text
long ahd short labels fix
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.release3.ra
- lines changed 199, context: html, text, full: html, text
update new datasets submitted before the freeze
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDgf.ra
- lines changed 92, context: html, text, full: html, text
added age to long labels
- lines changed 23, context: html, text, full: html, text
added Signal to Raw which suppose to be Raw Signal
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.release2.ra
- lines changed 300, context: html, text, full: html, text
update the new datasets submitted before the freeze
- lines changed 1, context: html, text, full: html, text
changed a129=129 to S129=129 where S129 is listed as the tag for term 129 in cv
- lines changed 5, context: html, text, full: html, text
add a letter a in front of strain 129DLCR which started with digit
- lines changed 4, context: html, text, full: html, text
changed S129=129 back to a129=129, otherwise it would be messy to try to get right sort order with those strains share 129 prefix, I think the tag S129 for the term 129 should be changed to 129
- src/hg/makeDb/trackDb/snp131.html
- lines changed 3, context: html, text, full: html, text
Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):Fixing copy-paste error found by Brooke (snp130-specific statement in snp131, snp132).
Also adding caveat about similar situation in snp135.
- src/hg/makeDb/trackDb/snp132.shared.html
- lines changed 3, context: html, text, full: html, text
Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):Fixing copy-paste error found by Brooke (snp130-specific statement in snp131, snp132).
Also adding caveat about similar situation in snp135.
- src/hg/makeDb/trackDb/snp135.shared.html
- lines changed 5, context: html, text, full: html, text
Feature #8551 (Sequence Ontology terms for predicted functional effects on SNP details pages):Fixing copy-paste error found by Brooke (snp130-specific statement in snp131, snp132).
Also adding caveat about similar situation in snp135.
- src/hg/makeDb/trackDb/worm/ce10/description.html
- src/hg/makeDb/trackDb/worm/ce4/description.html
- src/hg/makeDb/trackDb/worm/ce6/description.html
- src/hg/utils/automation/EnsGeneAutomate.pm
- lines changed 189, context: html, text, full: html, text
Put v67 definitions back into EnsGeneAutomate.pm.
- src/inc/dsPrint.h
- lines changed 77, context: html, text, full: html, text
rewrote/renamed some dsPrint functions based upon Angie's advice in code review. Also added support for some print buffer surgery. However, the regex version is ifdef'd out for now, as I am not sure it is a good idea to check in a requirement for including <regex.h> into src/lib.
- src/lib/dsPrint.c
- lines changed 7, context: html, text, full: html, text
The casting failed in the 32bit build, due to pointer size issues. This version works in both 32 and 64 bit compiles and functionally changes nothing. Since this is a patch request, let me be clear that no checked in code yet calls any of these functions in this new module. The only affect this change has is that the 32bit build should now complete.
- lines changed 213, context: html, text, full: html, text
rewrote/renamed some dsPrint functions based upon Angie's advice in code review. Also added support for some print buffer surgery. However, the regex version is ifdef'd out for now, as I am not sure it is a good idea to check in a requirement for including <regex.h> into src/lib.
- src/lib/knetUdc.c
- lines changed 2, context: html, text, full: html, text
Feature #3265 (nightly cron job should build utils and cgis with various USE_* options):Tim found that build breaks with USE_BAM=0 USE_TABIX=1 USE_KNETFILE_HOOKS=1 -- fixing.
- src/lib/linefile.c
- lines changed 6, context: html, text, full: html, text
oops - some sort of editing error left sizes/types incorrect - easily fixed here.
- src/utils/bedToBigBed/bedToBigBed.c
- lines changed 1, context: html, text, full: html, text
incrementing version # because of bugfix to integer parsing routines in linefile.c
- src/utils/qa/makefile
- lines changed 2, context: html, text, full: html, text
trying to remove git pull from makefiles
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed: 44234
- files changed: 167