All File Changes
v255_base to v256_preview (2011-08-08 to 2011-08-16) v256
- src/gfServer/gfServer.c
- lines changed 14, context: html, text, full: html, text
fix problem with interaction between memTracker (which is currently used only by gfServer) and errabort code which allocates perThreadVars off of the heap. The fix just makes it use errabort stuff before starting memTracker.
- src/hg/encode/DAFs/2.0/caltechMm9Histone.daf
- lines changed 13, context: html, text, full: html, text
Updated DAF to match the expected submission like TFBS track.
- src/hg/encode/DAFs/2.0/psuMm9Histone.daf
- lines changed 3, context: html, text, full: html, text
Updated DAF to accomated input's replcate and pooled data.
- src/hg/encode/DAFs/2.0/psuMm9Tfbs.daf
- lines changed 3, context: html, text, full: html, text
Updated DAF to accomated input's replcate and pooled data.
- src/hg/encode/antibodyWikiParser/antibodyWikiParser.py
- lines changed 2, context: html, text, full: html, text
Slight change in behavior for downloading antibody 'documents' that are actually split across two or more documents (e.g. the way the HAIB antibody validation has been coming in two distinct files). Assemble the list of files in a slightly cleaner way
- lines changed 28, context: html, text, full: html, text
Cleaned up the usage for both wiki scraping scripts
- src/hg/encode/antibodyWikiParser/makefile
- lines changed 4, context: html, text, full: html, text
Changing the makefiles to move a bit closer to Venkat's new makefile specification. I still need to get the rest of the specification details from Venkat
- src/hg/encode/cellTypeParser/cellTypeParser.py
- lines changed 29, context: html, text, full: html, text
Cleaned up the usage for both wiki scraping scripts
- src/hg/encode/cellTypeParser/makefile
- lines changed 4, context: html, text, full: html, text
Changing the makefiles to move a bit closer to Venkat's new makefile specification. I still need to get the rest of the specification details from Venkat
- src/hg/encode/encodeAnnounce/announceBoilerplate.html
- lines changed 10, context: html, text, full: html, text
Generate some raw material to create an ENCODE data release announcement
- src/hg/encode/encodeAnnounce/encodeAnnounce.pl
- lines changed 96, context: html, text, full: html, text
Generate some raw material to create an ENCODE data release announcement
- src/hg/encode/encodeDownloadReadme/downloadsReadmeTemplate.txt
- lines changed 3, context: html, text, full: html, text
Vanessa and Katrina's wording change
- src/hg/encode/encodeLoad/doEncodeLoad.pl
- lines changed 1, context: html, text, full: html, text
removed old comment from before we had design finalized
- lines changed 1, context: html, text, full: html, text
extra .txt extension in variable, removed from open statement
- src/hg/encode/encodeLoad/makefile
- lines changed 11, context: html, text, full: html, text
Modified makefile targets and scripts to place pipeline specific scripts and files under specific pipeline directory.
- lines changed 1, context: html, text, full: html, text
Updated make target for Development pipeline from 'pipeline' -> 'development'. This is a far more descriptive target and won't be confused with making production pipeline. Redmine #211
- src/hg/encode/encodeMkFilesList/encodeMkFilesList
- lines changed 1, context: html, text, full: html, text
an unless turned into an if, i got a little too exited with the unless statements, resulted in a logic error. Everytime a md5sum last modified date existed, it would get 0 as it's last modified date, i wanted that for files that didn't exist the last time md5sum was ran only. an unless is equivalent to if not (if !(condition));
- lines changed 2, context: html, text, full: html, text
changed verbosity level for some debugging prints\n
- lines changed 88, context: html, text, full: html, text
added functionality to put md5sum in metaDb
- lines changed 14, context: html, text, full: html, text
added in function to bot put bai in md5sum for bam if bai is missing
- lines changed 1, context: html, text, full: html, text
previous commit bot = not, this one i removed a variable i didn't use
- lines changed 303, context: html, text, full: html, text
lots of changes, more fleshed out comments, and found some bugs, namely the multiple regex match bug. added functionality to detect file bas name collisions, for table lookup purposes.
- lines changed 25, context: html, text, full: html, text
made functionality to check if there if an existing metaDb entry per file, if there is no corresponding fileName entry, it assumes orphaned, and warns you. In addition to that, I added functionality to make an inverted hash of md5sums and file names to check if there are collisions with regards to md5sums.
- src/hg/encode/encodeReport/gencodeStats
- lines changed 28, context: html, text, full: html, text
updated report to include gene stats
- src/hg/encode/encodeValidate/makefile
- lines changed 8, context: html, text, full: html, text
Modified makefile targets and scripts to place pipeline specific scripts and files under specific pipeline directory.
- lines changed 1, context: html, text, full: html, text
Updated make target for Development pipeline from 'pipeline' -> 'development'. This is a far more descriptive target and won't be confused with making production pipeline. Redmine #211
- lines changed 3, context: html, text, full: html, text
Updated the make targets for the config directory to only use files that are necessary by the pipeline. Redmine #2125, #211.
- lines changed 1, context: html, text, full: html, text
Forgot make target for make all.
- src/hg/encode/makefile
- lines changed 12, context: html, text, full: html, text
Update makefile for the pipeline to have updated targets that are specified in encodeLoad and encodeValidate. Also removed encodeStatus since this is not a pipeline dependent and added to general DIRS. Redmine #211, #2125.
- lines changed 2, context: html, text, full: html, text
Added encodeStatus to DIRS since this should always be made. Redmine #211, #2125.
- src/hg/hgFileSearch/hgFileSearch.c
- lines changed 1, context: html, text, full: html, text
Divorced simple search entry from description search entry. Cleaned up a simplified some code.
- src/hg/hgTables/hgTables.c
- lines changed 2, context: html, text, full: html, text
Bug #454 (hgTables fills the error logs with no-content errors):Removing an old debugging printf that must have been accidentally committed.
- src/hg/hgTracks/hgTracks.c
- lines changed 4, context: html, text, full: html, text
A more complete fix for 1X scrolling with packed sideLabels being in image. There should be 2 separate images: data and side, and I had to find all cases that write to the sideLabel. doLeftLabel() functions were easy and taken care of by passing the right image pointer. But some drawItem code also wrote to side labels and this needed a global hvgSide pointer to write to.
- lines changed 5, context: html, text, full: html, text
Fixed bug in rightClick 'view image' and now use css for sideLabel red line, to remove choppy look.
- lines changed 11, context: html, text, full: html, text
Some dragScroll >1x only changes, ifdef'd out. Debugging these was very helpful in finding some obscure cases in true 1x scrolling which we are intending to release soon.
- lines changed 5, context: html, text, full: html, text
Fix for rightClick chnage of vis when track is from dataHub (redmine 4881)
- lines changed 93, context: html, text, full: html, text
move measureTiming output into span's so it can be manipulated on client side; add experimental dead code for returning image via URL (redmine #4888)
- lines changed 2, context: html, text, full: html, text
This is the new patch candidate.
- src/hg/hgTracks/hgTracks.h
- lines changed 1, context: html, text, full: html, text
A more complete fix for 1X scrolling with packed sideLabels being in image. There should be 2 separate images: data and side, and I had to find all cases that write to the sideLabel. doLeftLabel() functions were easy and taken care of by passing the right image pointer. But some drawItem code also wrote to side labels and this needed a global hvgSide pointer to write to.
- src/hg/hgTracks/imageV2.c
- lines changed 4, context: html, text, full: html, text
Fixed bug in rightClick 'view image' and now use css for sideLabel red line, to remove choppy look.
- src/hg/hgTracks/imageV2.h
- lines changed 3, context: html, text, full: html, text
Turning on dragScroll 1x, shift-dragZoom and in place update.
- src/hg/hgTracks/mainMain.c
- lines changed 2, context: html, text, full: html, text
put measureTiming stuff in spans
- src/hg/hgTracks/searchTracks.c
- lines changed 25, context: html, text, full: html, text
A version of advanced track search that lets subtracks 'inherit' descriptions from their parent.
- lines changed 199, context: html, text, full: html, text
Divorced simple search entry from description search entry. Cleaned up a simplified some code.
- src/hg/hgTracks/simpleTracks.c
- lines changed 24, context: html, text, full: html, text
A more complete fix for 1X scrolling with packed sideLabels being in image. There should be 2 separate images: data and side, and I had to find all cases that write to the sideLabel. doLeftLabel() functions were easy and taken care of by passing the right image pointer. But some drawItem code also wrote to side labels and this needed a global hvgSide pointer to write to.
- lines changed 2, context: html, text, full: html, text
fixed problem with automatic-only and manual-only filters
- lines changed 19, context: html, text, full: html, text
Some dragScroll >1x only changes, ifdef'd out. Debugging these was very helpful in finding some obscure cases in true 1x scrolling which we are intending to release soon.
- src/hg/hgTracks/variation.c
- lines changed 14, context: html, text, full: html, text
A more complete fix for 1X scrolling with packed sideLabels being in image. There should be 2 separate images: data and side, and I had to find all cases that write to the sideLabel. doLeftLabel() functions were easy and taken care of by passing the right image pointer. But some drawItem code also wrote to side labels and this needed a global hvgSide pointer to write to.
- lines changed 33, context: html, text, full: html, text
Some dragScroll >1x only changes, ifdef'd out. Debugging these was very helpful in finding some obscure cases in true 1x scrolling which we are intending to release soon.
- src/hg/hgTracks/vcfTrack.c
- lines changed 71, context: html, text, full: html, text
Feature #2823 (VCF track handler): Added UI control over height of haplotype-sorting display.
- lines changed 34, context: html, text, full: html, text
Feature #2821 (VCF parser): improved representation of alleles:parse ref and comma-sep'd alt allele string into count and array
inside record, so callers don't all have to parse the comma-sep'd
alternate allele string.
- lines changed 8, context: html, text, full: html, text
Feature #3710 (vcfTabix UI options): added checkbox to enable/disable haplotype sorting display.
- lines changed 28, context: html, text, full: html, text
Feature #3710 (vcfTabix UI options): added option to use pgSnp colors instead of blueRef/redAlt in haplotype sorting display.
- lines changed 165, context: html, text, full: html, text
Feature #3711 (vcfTabix haplotype sorting display): Draw hierarchical tree in left label area (as much as can fit there).
- lines changed 16, context: html, text, full: html, text
Feature #3711 (vcfTabix haplotype-sorting display): Limit the numberof variants close to the center variant that we use for clustering,
to prevent the clustering from timing out in large regions with large
genotype counts (e.g. 1094 genotypes from 1000 Genomes phase 1 interim).
- src/hg/hgc/gencodeClick.c
- lines changed 15, context: html, text, full: html, text
reorder basic information and user clearer labeling. include strand and fix position wrap
- src/hg/hgc/hgc.c
- lines changed 1, context: html, text, full: html, text
MLQ #4908 (genomicSuperDups strand): genomicSuperDups' strand column isalready displayed in hgc output as "Other Position Relative Orientation"
which is its real meaning (not the usual sense of the strand column).
So don't tell bedPrintPos that we have bed 6, because then it prints out
a confusing redundant "Strand:".
- src/hg/hgc/vcfClick.c
- lines changed 39, context: html, text, full: html, text
Feature #2823 (VCF track handler): Added summaries of genotype and allele freqs to details page.
- lines changed 53, context: html, text, full: html, text
Feature #2821 (VCF parser): improved representation of alleles:parse ref and comma-sep'd alt allele string into count and array
inside record, so callers don't all have to parse the comma-sep'd
alternate allele string.
- src/hg/htdocs/ENCODE/downloads.html
- lines changed 8, context: html, text, full: html, text
adding missing hg18 BU Orchid, fixed hg19 Genecode Genes V4 to state V4, removed extra 'ENCODE' at begining of one of the hg18 Broad ChromHMM long label section since that was the convention of hg18 downloads
- lines changed 5, context: html, text, full: html, text
added SUNY SwitchGear, redmine #169
- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
- lines changed 189, context: html, text, full: html, text
See redmine 4795. I made changes for Donna's code review that I did. 2 grammar corrections plus the listed html corrections. Then I just went through and cleaned up the html...a LOT. Closed open p tags, changed a long definition list <dt> to a simple <pre> tag, etc. Now passes through the w3c validator with no errors...started with almost 40 errors.
- src/hg/htdocs/style/HGStyle.css
- lines changed 4, context: html, text, full: html, text
Fixed bug in rightClick 'view image' and now use css for sideLabel red line, to remove choppy look.
- src/hg/inc/omim.h
- lines changed 4, context: html, text, full: html, text
Changed omimPhenotypeClassColName from phenotypeClass to omimPhenoMapKey.
- src/hg/inc/search.h
- lines changed 1, context: html, text, full: html, text
Divorced simple search entry from description search entry. Cleaned up a simplified some code.
- src/hg/inc/vcfUi.h
- lines changed 4, context: html, text, full: html, text
Feature #2823 (VCF track handler): Added UI control over height of haplotype-sorting display.
- lines changed 3, context: html, text, full: html, text
Feature #3710 (vcfTabix UI options): added checkbox to enable/disable haplotype sorting display.
- lines changed 4, context: html, text, full: html, text
Feature #3710 (vcfTabix UI options): added option to use pgSnp colors instead of blueRef/redAlt in haplotype sorting display.
- src/hg/js/hgTracks.js
- lines changed 74, context: html, text, full: html, text
Fixed some reentrant problems when image is dragScrolled and then ajax updated. While much of this is >1x specific, not all is. Also did some renaming to make functionality more clear.
- lines changed 25, context: html, text, full: html, text
update measureTiming output when doing in-place update; fix Number() cast based on tdreszer's code review
- lines changed 18, context: html, text, full: html, text
disable buttons while we are finishing the update; don't allow control-select as it was screwing up right-click on the mac
- src/hg/js/jquery.imgareaselect.js
- lines changed 1, context: html, text, full: html, text
disable buttons while we are finishing the update; don't allow control-select as it was screwing up right-click on the mac
- src/hg/lib/omimPhenotype.as
- lines changed 1, context: html, text, full: html, text
Changed col phenotypeClass to omimPhenoMapKey per OMIM request.
- src/hg/lib/omimPhenotype.sql
- lines changed 2, context: html, text, full: html, text
Changed col phenotypeClass to omimPhenoMapKey per OMIM request.
- src/hg/lib/pgSnp.c
- lines changed 92, context: html, text, full: html, text
Feature #2821 (VCF parser): improved representation of alleles:parse ref and comma-sep'd alt allele string into count and array
inside record, so callers don't all have to parse the comma-sep'd
alternate allele string.
- lines changed 18, context: html, text, full: html, text
Feature #3710 (vcfTabix UI options): added checkbox to enable/disable haplotype sorting display.
- src/hg/lib/search.c
- lines changed 4, context: html, text, full: html, text
Divorced simple search entry from description search entry. Cleaned up a simplified some code.
- src/hg/lib/vcfUi.c
- lines changed 25, context: html, text, full: html, text
Feature #2823 (VCF track handler): Added UI control over height of haplotype-sorting display.
- lines changed 33, context: html, text, full: html, text
Feature #3710 (vcfTabix UI options): added checkbox to enable/disable haplotype sorting display.
- lines changed 37, context: html, text, full: html, text
Feature #3710 (vcfTabix UI options): added option to use pgSnp colors instead of blueRef/redAlt in haplotype sorting display.
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeCshlLongRnaSeq.release1.notes
- lines changed 289, context: html, text, full: html, text
removed warnings about attic files
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibGenotype.release1.notes
- lines changed 2, context: html, text, full: html, text
Cleaning up the notes file
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhTfbs.release1.notes
- lines changed 2020, context: html, text, full: html, text
updated notes file for new files and name changes
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwDnase.release3.notes
- lines changed 217, context: html, text, full: html, text
updated notes file for uw dnase and uw histone
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwHistone.release2.notes
- lines changed 255, context: html, text, full: html, text
updated notes file for uw dnase and uw histone
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwTfbs.release2.notes
- lines changed 448, context: html, text, full: html, text
updated the release2 notes
- src/hg/makeDb/doc/makeEnsembl.txt
- lines changed 1050, context: html, text, full: html, text
update v63 has been run on everything
- src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
- lines changed 36, context: html, text, full: html, text
Updated the swarm timing statistics for Pfam and Scop
- src/hg/makeDb/genbank/src/dbload/gbMetaData.c
- lines changed 1, context: html, text, full: html, text
add a new molecule type, ms-rRNA, that genbank is now using
- src/hg/makeDb/genbank/src/inc/gbDefs.h
- lines changed 2, context: html, text, full: html, text
add a new molecule type, ms-rRNA, that genbank is now using
- src/hg/makeDb/genbank/src/lib/gbDefs.c
- lines changed 1, context: html, text, full: html, text
add a new molecule type, ms-rRNA, that genbank is now using
- src/hg/makeDb/genbank/src/process/gbParse.c
- lines changed 1, context: html, text, full: html, text
read /product field under CDS as a multiline field
- src/hg/makeDb/schema/all.joiner
- lines changed 38, context: html, text, full: html, text
Added related entries for rgdGene2.
- lines changed 7, context: html, text, full: html, text
adding hg19Patch5 definitions
- lines changed 1, context: html, text, full: html, text
adding anoCar2 for chain and net coverage
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 2, context: html, text, full: html, text
Adding Tims changes to objStatus
- lines changed 8, context: html, text, full: html, text
Updated Tags so that the tables wouldn't have names longer than 64 characters.
- lines changed 16, context: html, text, full: html, text
Adding approved antibodies
- lines changed 121, context: html, text, full: html, text
Registering more antibodies
- lines changed 29, context: html, text, full: html, text
Adding more antibodies, this should be it
- lines changed 7, context: html, text, full: html, text
Fixed registration of CEBPD antibody and added information for the CEBPB cell line.
- lines changed 36, context: html, text, full: html, text
commented out k562b and hepg2b
- lines changed 19, context: html, text, full: html, text
Registered Erythroblast and added protocols for erythroblast and megakaryocyte primary cells.
- lines changed 2, context: html, text, full: html, text
changed t-rex-hek293 to hek293-t-rex
- lines changed 2, context: html, text, full: html, text
changed fetalpbde to pdbefetal
- lines changed 11, context: html, text, full: html, text
Added two proteogenomics protocols
- src/hg/makeDb/trackDb/cv/beta/cv.ra
- lines changed 516, context: html, text, full: html, text
Modified several tags to adhere to the restriction that tags should be unique.< tag BCLUNGb
---
> tag BCLUNG
Typo fixed.
< description Normal Neonatal Human Microvascular Endothelial Cells (single Donor), Dermal-Derived
---
> description Normal Neonatal Human Microvascular Endothelial Cells (single Donnor), Dermal-Derived
Documented the relationship between the HEK293 and t-rex cell lines
< description Human embryonic kidney cells transformed with Adenovirus 5 DNA stably expressing tetracycline repressor, HEK293 (ATCC number CRL-1573) is the parental cell line
---
> description Human embryonic kidney cells transformed with Adenovirus 5 DNA stably expressing tetracycline repressor, ATCC number CRL-1573
Added an order URL indicating the Wold lab for something produced in the Wold lab. In
such cases, an order URL is less error-prone than a note that it's from the XYZ lab.
Nameley, it's less typo prone.
< orderUrl http://woldlab.caltech.edu/
Commenting out stanzas that are due to be removed.
< #removed per Redmine #222
< #term UW-5C-Myc-Region
< #tag UW5CMYC
< #type region
< #description Myc upstream gene desert region used in UW 5C experiments (hg19 chr8:126445818-130737929)
<
< #term UW-5C-Gene-Regions
< #tag UW5CGENE
< #type region
< #description Set of 25 regions interrogated in UW 5C gene-targeted experiments
---
> term UW-5C-Myc-Region
> tag UW5CMYC
> type region
> description Myc upstream gene desert region used in UW 5C experiments (hg19 chr8:126445818-130737929)
> term UW-5C-Gene-Regions
> tag UW5CGENE
> type region
> description Set of 25 regions interrogated in UW 5C gene-targeted experiments
A significantly-improved comment
< description Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth).
> description Contigs
Commenting out a deprecated stanza
< #FastQ is now deprecated
< #term Fastq
< #tag FASTQ
< #type view
< #label Fastq
< #description Raw sequence with Phred33 quality scores
> term Fastq
> tag FASTQ
> type view
> label Fastq
> description Raw sequence with Phred33 quality scores
A much better description for a new stanza
< label Genes De Novo
< description 'De novo' genes defined by Cufflinks with FPKM.
---
> label Genes DeNovo
> description Expression estimates for genes defined by Cufflinks in de novo mode in gtf format
Another much better description
< description TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions
---
> description TopHat-defined splice junctions
New stanzas
< term PeakSeqConservPeaks
< tag PSCPEAKS
< type view
< label PeakSeq Conserved Peaks
< description Regions of conserved enriched signal in experiment performed by PeakSeq
<
< term PeakSeqOptimalPeak
< tag PSOPEAKS
< type view
< label PeakSeq Optimal Peaks
< description Regions of optimal enriched signal in experiment performed by PeakSeq
<
< #snippet for UW5c's primer view
< term Primer
< tag Primer
< type view
< label Primer
< description placeholder for Uw5c's primer file, so it can be in metaDb properly
<
< term SppConservPeaks
< tag SCPPEAKS
< type view
< label Spp Conservative Peaks
< description Regions of optimal enriched signal in experiment performed by Spp
<
< term SppOptimalPeaks
< tag SOPPEAKS
< type view
< label SPP Optimal Peaks
< description Regions of conserved enriched signal in experiment performed by SPP
<
Another improved description
< description 'De novo' transcripts with FPKM produced by Cufflinks
---
> description Transcript models and expression estimates in FPKM produced by Cufflinks in de novo mode
Another new stanza
< term UniformSignal
< tag UNISIG
< type view
< label Uniform Signal by AWG
< description Uniform Signal
<
Other cases of tags renamed to make all tags will be unique.
< tag CNVdt
---
> tag CNV
< tag SANGER
---
> tag GENCODE
< tag LICRm
---
> tag LICR
< tag CALTECHm
---
> tag CALTECH
< tag UMASSm
---
> tag UMASS
< tag DUKEm
---
> tag DUKE
< tag PSUm
---
> tag PSU
< tag UWm
---
> tag UW
< tag STANFORDm
---
> tag STANFORD
< tag YALEm
---
> tag YALE
< tag CONTROLi
---
> tag CONTROL
Change in case
< validate none
> validate None
Unclear why this was added...
< labInst California Institute of Technology
9523d9481
< label Carninci - RIKEN Omics Science Center
9658c9616
- lines changed 475, context: html, text, full: html, text
Various tags were changed slightly to make all tags unique. This comment wasremoved when the tags were changed, as it's no longer accurate
< #same tag as BC_Lung_H12817N
Tags now unique
< tag BCLUNG
---
> tag BCLUNGb
The BJ cell line issue. It looks like except for the main cell line, all the
others are commented out (deprecated? set aside for now?).
< protocol Stam:BJ_Stam_protocol.pdf
---
> #protocol Stam:BJ-tert_Stam_protocol.pdf
> # JEFF: Please read and find which of these protocols is correct for BJ and label it appropriately
>
> #These terms seem to have a lot of confusion and no one is currently using these cell lines. We are commenting out until resovled see Bug#4536
> #term BJ-5ta
> #tag BJ5TA
> #type Cell Line
> #organism human
> #description BJ foreskin fibroblast transfected with the pGRN145 hTERT, expressing T antigens of SV40 virus.(PMID: 9916802)
> #tissue Skin
> #vendorName ATCC
> #vendorId CRL-4001
> #orderUrl http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=CRL-4001&Template=cellBiology
> #karyotype normal
> #termId BTO:0001255
> #termUrl http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BTO&termId=BTO%3A0001255
> #sex M
> #tier 3
> #protocol Struhl:BJ_5ta_Struhl_protocol.pdf
> #
> #term BJ-HRas
> #tag BJHRAS
> #type Cell Line
> #organism human
> #description hTERT/BJ skin fibroblasts expressing T antigens of SV40 virus and H-RasV12
> #tissue Skin
> #vendorName Struhl laboratory
> #vendorId BJ-HRas
> #orderUrl https://struhl.med.harvard.edu/
> #karyotype normal
> #termId BTO:0001255
> #termUrl http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BTO&termId=BTO%3A0001255
> #sex M
> #tier 3
> #protocol Struhl:BJ-tert-HRas_Struhl_protocol.pdf
> #
> #
> #term BJ-T
> #tag BJT
> #type Cell Line
> #organism human
> #description foreskin fibroblast
> #tissue Skin
> #vendorName Struhl laboratory
> #vendorId BJ-T
> #orderUrl https://struhl.med.harvard.edu/
> #karyotype normal
> #termId BTO:0001255
> #termUrl http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BTO&termId=BTO%3A0001255
> #sex M
> #tier 3
> #protocol Struhl:BJ-5ta_Struhl_protocol.pdf
New cell line - with issues, the vendorId should not be [1]. This comes from
taking the output of the wiki scraping script literally...
< term Colo829
< tag COLO829
< type Cell Line
< tier 3
< organism human
< description Malignant Melanoma
< lineage missing
< karyotype missing
< sex M
< tissue Skin
< vendorName
< vendorId [1]
< orderUrl http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=CRL-1974&Template=cellBiology
< lab Crawford
< protocol Crawford:Colo829_Crawford_protocol.pdf
<
More new cell lines. This one looks fine.
< term GM12866
< tag GM12866
< type Cell Line
< tier 3
< organism human
< description B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, Treatment: Epstein-Barr Virus transformed.
< lineage mesoderm
< karyotype missing
< sex M
< tissue Blood
< vendorName Coriell
< vendorId GM12866
< orderUrl http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12866&PgId=166
< termId BTO:0002062 (non-specific)
< termUrl http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BTO&termId=BTO%3A0002062&termName=B-lymphoblastoid%20cell%20line
< lab Stam
< protocol Stam:GM12866_Stam_protocol.pdf
<
This one looks fine too
< term GM12867
< tag GM12867
< type Cell Line
< tier 3
< organism human
< description B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, Treatment: Epstein-Barr Virus transformed.
< lineage mesoderm
< karyotype missing
< sex F
< tissue Blood
< vendorName Coriell
< vendorId GM12867
< orderUrl http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12867&PgId=166
< termId BTO:0002062 (non-specific)
< termUrl http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BTO&termId=BTO%3A0002062&termName=B-lymphoblastoid%20cell%20line
< lab Stam
< protocol Stam:GM12867_Stam_protocol.pdf
<
This one looks fine
< term GM12868
< tag GM12868
< type Cell Line
< tier 3
< organism human
< description B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, Treatment: Epstein-Barr Virus transformed.
< lineage mesoderm
< karyotype missing
< sex F
< tissue Blood
< vendorName Coriell
< vendorId GM12868
< orderUrl http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12868&PgId=166
< termId BTO:0002062 (non-specific)
< termUrl http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BTO&termId=BTO%3A0002062&termName=B-lymphoblastoid%20cell%20line
< lab Stam
< protocol Stam:GM12868_Stam_protocol.pdf
<
Looks fine
< term GM12869
< tag GM12869
< type Cell Line
< tier 3
< organism human
< description B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, Treatment: Epstein-Barr Virus transformed.
< lineage mesoderm
< karyotype missing
< sex F
< tissue Blood
< vendorName Coriell
< vendorId GM12869
< orderUrl http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12869&PgId=166
< termId BTO:0002062 (non-specific)
< termUrl http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BTO&termId=BTO%3A0002062&termName=B-lymphoblastoid%20cell%20line
< lab Stam
< protocol Stam:GM12869_Stam_protocol.pdf
<
Fine
< term GM12870
< tag GM12870
< type Cell Line
< tier 3
< organism human
< description B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, Treatment: Epstein-Barr Virus transformed.
< lineage mesoderm
< karyotype missing
< sex M
< tissue Blood
< vendorName Coriell
< vendorId GM12870
< orderUrl http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12870&PgId=166
< termId BTO:0002062 (non-specific)
< termUrl http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BTO&termId=BTO%3A0002062&termName=B-lymphoblastoid%20cell%20line
< lab Stam
< protocol Stam:GM12870_Stam_protocol.pdf
<
Fine
< term GM12871
< tag GM12871
< type Cell Line
< tier 3
< organism human
< description B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, Treatment: Epstein-Barr Virus transformed.
< lineage mesoderm
< karyotype missing
< sex M
< tissue Blood
< vendorName Coriell
< vendorId GM12871
< orderUrl http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12871&PgId=166
< termId BTO:0002062 (non-specific)
< termUrl http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BTO&termId=BTO%3A0002062&termName=B-lymphoblastoid%20cell%20line
< lab Stam
< protocol Stam:GM12871_Stam_protocol.pdf
<
Another new cell line, with vendor ID issues
< term Ishikawa
< tag ISHIKAWA
< type Cell Line
< tier 3
< organism human
< description endometrial adenocarcinoma
< lineage missing
< karyotype missing
< sex F
< tissue Uterus
< vendorName
< vendorId [3]
< orderUrl http://www.sigmaaldrich.com/catalog/ProductDetail.do?D7=0&N5=SEARCH_CONCAT_PNO%7CBRAND_KEY&N4=99040201%7CSIGMA&N25=0&QS=ON&F=SPEC
< lab Crawford
< protocol Crawford:Ishikawa_Crawford_protocol.pdf
<
An improved comment had been marked as provisional
< description Human embryonic kidney cells transformed with Adenovirus 5 DNA stably expressing tetracycline repressor, HEK293 (ATCC number CRL-1573) is the parental cell line (PROVISIONAL)
---
> description Human embryonic kidney cells transformed with Adenovirus 5 DNA stably expressing tetracycline repressor, HEK293 (ATCC number CRL-1573) is the parental cell line
Lot numbers added
< lab Snyder, Myers
< lots I1010 (Myers)
---
> lab Snyder
A new antibody, with issues. The validation type should be in the validation
document label, in place of the word "missing".
< term CEBPD_(SC-636)
< tag CEBPDSC636
< type Antibody
< antibodyDescription Rabbit polyclonal IgG, epitope mapping at the C-terminus of CEBPD of human origin.
< target CEBPD
< targetDescription The protein encoded by this intronless gene is a bZIP transcription factor which can bind as a homodimer to certain DNA regulatory regions. It can also form heterodimers with the related protein CEBP-alpha. The encoded protein is important in the regulation of genes involved in immune and inflammatory responses, and may be involved in the regulation of genes associated with activation and/or differentiation of macrophages. The cytogenetic location of this locus has been reported as both 8p11 and 8q11 (provided by RefSeq).
< vendorName Santa Cruz Biotech
< vendorId sc-636
< orderUrl http://www.scbt.com/datasheet-636-c-ebp-delta-m-17-antibody.html
< lab Myers
< lots C1010
< targetId GeneCard:CEBPD
< targetUrl http://www.genecards.org/cgi-bin/carddisp.pl?gene=CEBPD
< validation CEBPD_(SC-636)(missing):human_CEBPD_SC-636_validation_Myers.pdf
<
<
A new validation document (with issues, that "missing" shouldn't be there, and
the validation type should be there instead)
< validation ELK4(missing):human_ELK4_validation_Farnham.pdf
---
> validation missing
New antibody. This one doesn't have a validation document yet, and shouldn't be
registered without one.
< term FOSL1_(sc-605)
< tag FOSL1SC605
< type Antibody
< antibodyDescription Rabbit polyclonal antibody raised against the N-terminus of FOSL1 of rat origin.
< target FOSL1
< targetDescription The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. (provided by RefSeq)
< vendorName Santa Cruz Biotech
< vendorId sc-605
< orderUrl http://www.scbt.com/datasheet-605-fra-1-r-20-antibody.html
< lab Wold
< lots G0109
< targetId Genecard:FOSL1
< targetUrl http://www.genecards.org/cgi-bin/carddisp.pl?gene=FOSL1
< validation missing
New antibody, looks fine except for the missing validation document
5620,5636d5500
< term H3ac_(06-599)
< tag H3AC06599
< type Antibody
< antibodyDescription rabbit polyclonal antibody raised against a KLH-conjugated p
< eptide corresponding to amino acids 1-20 of Tetrahymena histone H3 (ARTKQTAR[K*]
< STGG[K*]APRKQLC) where K* is acetylated
< target H3ac
< targetDescription missing
< vendorName Millipore
< vendorId 06-599
< orderUrl http://www.millipore.com/catalogue/item/06-599
< lab Wold
< lots missing
< targetId Genecard:HIST2H3C
< targetUrl http://www.genecards.org/cgi-bin/carddisp.pl?gene=HIST2H3C
< validation missing
<
Another new antibody, missing validation doc
< term H3K4me2_(ab32356)
< tag H3K4ME2AB32356
< type Antibody
< antibodyDescription Rabbit polyclonal
< target H3K4me2
< targetDescription Histone H3 (di methyl K4). Marks promoters and enhancers.
< vendorName Abcam
< vendorId ab32356
< orderUrl http://www.abcam.com/Histone-H3-di-methyl-K4-antibody-Y47-ChIP-Grade-ab32356.html
< lab Wold
< lots 870402
< targetId Genecard:HIST2H3C
< targetUrl http://www.genecards.org/cgi-bin/carddisp.pl?gene=HIST2H3C
< validation missing
<
Another missing validation
< term H3K79me2_(ab3594)
< tag H3K79ME2AB3594
< type Antibody
< antibodyDescription Rabbit polyclonal
< target H3K79me2
< targetDescription H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3)
< vendorName Abcam
< vendorId ab3594
< orderUrl http://www.abcam.com/Histone-H3-di-methyl-K79-antibody-ChIP-Grade-ab3594.html
< lab Wold
< lots 836403
< targetId Genecard:HIST2H3C
< targetUrl http://www.genecards.org/cgi-bin/carddisp.pl?gene=HIST2H3C
< validation missing
<
Same
< term H3K79me3_(ab2621)
< tag H3K79ME3AB2621
< type Antibody
< antibodyDescription Rabbit polyclonal
< target H3K79me3
< targetDescription Associated with the gene body of actively transcribed genes
< vendorName Abcam
< vendorId ab2621
< orderUrl http://www.abcam.com/Histone-H3-tri-methyl-K79-antibody-ChIP-Grade-ab26
< 21.html
< lab Wold
< lots 805949
< targetId Genecard:HIST2H3C
< targetUrl http://www.genecards.org/cgi-bin/carddisp.pl?gene=HIST2H3C
< validation missing
<
And another. I don't understand why this one is registered without its
validation document.
< term MyoD_(sc-32758)
< tag MYODSC32758
< type Antibody
< antibodyDescription mouse monoclonal antibody raised against recombinant MyoD of
< mouse origin with an epitope mapping to amino acids 180-189
< target MyoD
< targetDescription This gene encodes a nuclear protein that belongs to the basic
< helix-loop-helix family of transcription factors and the myogenic factors subfam
< ily. It regulates muscle cell differentiation by inducing cell cycle arrest, a p
< rerequisite for myogenic initiation. The protein is also involved in muscle rege
< neration. It activates its own transcription which may stabilize commitment to m
< yogenesis. (provided by RefSeq)
< vendorName Santa Cruz Biotech
< vendorId sc-32758
< orderUrl http://www.scbt.com/datasheet-32758-myod-5-8a-antibody.html
< lab Wold
< lots missing
< targetId Genecard:MyoD1
< targetUrl http://www.genecards.org/cgi-bin/carddisp.pl?gene=MyoD1
< validation missing
<
Same
< term Myogenin_(sc-12732)
< tag MYOGENINSC12732
< type Antibody
< antibodyDescription mouse monoclonal antibody; epitope mapping within amino acid
< s 138-158 of myogenin of rat origin
< target Myogenin
< targetDescription Myogenin is a muscle-specific transcription factor that can in
< duce myogenesis in a variety of cell types in tissue culture. It is a member of
< a large family of proteins related by sequence homology, the helix-loop-helix (H
< LH) proteins. It is essential for the development of functional skeletal muscle.
< (provided by RefSeq)
< vendorName Santa Cruz Biotech
< vendorId sc-12732
< orderUrl http://www.scbt.com/datasheet-12732-myogenin-f5d-antibody.html
< lab Wold
< lots missing
< targetId Genecard:Myog
< targetUrl http://www.genecards.org/cgi-bin/carddisp.pl?gene=Myog
< validation missing
<
< term MEF2_(sc-17785)
< tag MEF2SC17785
< type Antibody
< antibodyDescription mouse monoclonal antibody raised against amino acids 1-300 m
< apping at the N-terminus of MEF-2A of human origin; recommended for detection of
< a broad range of MEF-2 family members of mouse, rat and human origin
< target MEF2
< targetDescription The MADS box transcription enhancer factor 2 (MEF2) family of
< proteins plays a role in myogenesis.
< vendorName Santa Cruz Biotech
< vendorId sc-17785
< orderUrl http://www.scbt.com/datasheet-17785-mef-2-b-4-antibody.htmllab Wold
< lots missing
< targetId Genecard:MEF2A
< targetUrl http://www.genecards.org/cgi-bin/carddisp.pl?gene=MEF2A
< validation missing
<
A new validation document
< validation SETDB1(missing):human_SETDB1_validation_Farnham.pdf
---
> validation missing
This new antibody looks fine, yay!
< term ZNF274_(M01)
< tag ZNF274M01
< type Antibody
< antibodyDescription Mouse monoclonal antibody raised against a partial recombinant ZNF274 (corresponding to amino acids 420-531 of the human ZNF274 protein).target ZNF274targetDescription ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor and interacts with the KAP1 corepressor complex.
< vendorName Abnova ZNF74
< vendorId M01
< orderUrl http://www.abnova.com/products/products_detail.asp?Catalog_id=H00010782
< -M01
< lab Farnham
< lots 08064-4C12
< targetId GeneCards:Genecard:ZNF274
< targetUrl http://www.genecards.org/cgi-bin/carddisp.pl?gene=Genecard:ZNF274
< validation ZNF274_(M01)(missing):human_ZNF274_M01_validation_Farnham.pdf
<
Several new views.
< term Control_32bp
< tag CNTRL32B
< type control
< description This data represents a control being compared to experiments using read length of 32 bp PROVISIONAL
<
< term Control_36bp
< tag CNTRL36B
< type control
< description This data represents a control being compared to experiments using read length of 36 bp PROVISIONAL
<
< term Control_50bp
< tag CNTRL50B
< type control
< description This data represents a control being compared to experiments using read length of 50 bp PROVISIONAL
<
(unsure)
> term DIFF_7d
> tag DIFF7D
> description Grown for 7 days in differentiation medium (Wold)
> type treatment
>
Several new treatments
< term Myoblast
< tag MYB
< description Grown differentiation medium undifferediated (Wold) PROVISIONAL
< type treatment
<
< term Myocyte_24h
< tag MYC24H
< description Grown for 24 hours in differentiation medium (Wold) PROVISIONAL
< type treatment
<
< term Myocyte_60h
< tag MYC60H
< description Grown for 60 hours in differentiation medium (Wold) PROVISIONAL
< type treatment
<
< term Myocyte_5d
< tag MYC5D
< description Grown for 5 days in differentiation medium (Wold) PROVISIONAL
< type treatment
<
< term Myocyte_7d
< tag MYC7D
< description Grown for 7 days in differentiation medium (Wold) PROVISIONAL
< type treatment
<
<
<
<
Several improved descriptions
< description PROVISIONAL Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth).
---
> description Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth).
8741c8449
< description 'De novo' genes defined by Cufflinks with FPKM. PROVISIONAL
---
> description 'De novo' genes defined by Cufflinks with FPKM.
8777c8485
< description TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions PROVISIONAL
---
> description TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions
8802c8510
< description Regions of conserved enriched signal in experiment performed by PeakSeq (PROVISIONAL)
---
> description Regions of conserved enriched signal in experiment performed by PeakSeq
8808c8516
< description Regions of optimal enriched signal in experiment performed by PeakSeq (PROVISIONAL)
---
> description Regions of optimal enriched signal in experiment performed by PeakSeq
8929c8637
< description Regions of optimal enriched signal in experiment performed by Spp (PROVISIONAL)
---
> description Regions of optimal enriched signal in experiment performed by Spp
8935c8643
< description Regions of conserved enriched signal in experiment performed by SPP (PROVISIONAL)
---
> description Regions of conserved enriched signal in experiment performed by SPP
8977c8685
< description Uniform Signal (PROVISIONAL)
---
> description Uniform Signal
Tag modified to make it unique
< tag CNV
---
> tag CNVdt
New status stanzas
< ## object Status
< term revoked
< tag REVOKED
< type objStatus
< description This file has been REVOKED by the submitting laboratory for some reason. It should not be used for further research. PROVISIONAL
<
< term replaced
< tag REPLACED
< type objStatus
< description This file has been REPLACED by the submitting laboratory with an improved version. PROVISIONAL
<
Several tags modified to make them unique.
< tag GENCODE
---
> tag SANGER
9961c9658
< tag LICR
---
> tag LICRm
9972c9669
< tag CALTECH
---
> tag CALTECHm
9983c9680
< tag UMASS
---
> tag UMASSm
9994c9691
< tag DUKE
---
> tag DUKEm
10005c9702
< tag PSU
---
> tag PSUm
10017c9714
< tag UW
---
> tag UWm
10028c9725
< tag STANFORD
---
> tag STANFORDm
10039c9736
< tag YALE
---
> tag YALEm
10278d9974
< hidden yes
Various priorities modified by Cricket
< priority 590
---
> priority 500
10333c10029
< priority 415
---
> priority 500
10342d10037
< hidden yes
10344c10039
< priority 470
---
> priority 991
10354c10049
< priority 110
---
> priority 120
More tags modified to make them unique
< tag CONTROL
---
> tag CONTROLi
More priorities modified by Cricket
< priority 325
---
> priority 235
10519c10214
< priority 590
---
> priority 500
10533c10228
< priority 590
---
> priority 500
10574c10269
< priority 166
---
> priority 500
10625c10320
< priority 590
---
> priority 500
10635c10330
< priority 150
---
> priority 160
10645c10340
< priority 430
---
> priority 500
10656,10667c10351
< priority 999
<
New stanza
< term objStatus
< tag OBJSTAT
< type typeOfTerm
< label Object Status
< description The status of the file or table object (revoked, replaced, etc) PROVISIONAL
< searchable no
< hidden no
< cvDefined yes
< validate cv
< priority 1
---
> priority 500
More new priorities.
< priority 242
---
> priority 460
10753c10437
< priority 165
---
> priority 500
10794c10478
< priority 160
---
> priority 150
10814c10498
< priority 430
---
> priority 500
10875c10559
< priority 430
---
> priority 921
10885c10569
< priority 120
---
> priority 110
10959c10643
< priority 590
---
> priority 500
- src/hg/makeDb/trackDb/fishClones.html
- lines changed 1, context: html, text, full: html, text
fixed URL to new clone registry (the old one was being redirected
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
- lines changed 15, context: html, text, full: html, text
Cleaning up view names for metaData, Fastq-> RawData, AllRawSig -> RawSignal
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
- lines changed 5, context: html, text, full: html, text
Cleaning up view names for metaData, Fastq-> RawData, AllRawSig -> RawSignal
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeGisPet.ra
- lines changed 2, context: html, text, full: html, text
Cleaning up view names for metaData, Fastq-> RawData, AllRawSig -> RawSignal
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeGisRnaSeq.ra
- lines changed 6, context: html, text, full: html, text
Cleaning up view names for metaData, Fastq-> RawData, AllRawSig -> RawSignal
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeRikenCage.ra
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwChIPSeq.ra
- src/hg/makeDb/trackDb/human/hg18/wgEncodeSangerGencode.html
- lines changed 2, context: html, text, full: html, text
cleaned up gencode's references
- src/hg/makeDb/trackDb/human/hg19/evoCpg.html
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAffyRnaChip.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHmm.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
- lines changed 14, context: html, text, full: html, text
Changing view Fastq to view RawData
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeDukeAffyExon.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencode.ra
- lines changed 55, context: html, text, full: html, text
renamed wgEncodeGencode.ra to wgEncodeGencodeV3.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV3.ra
- lines changed 55, context: html, text, full: html, text
renamed wgEncodeGencode.ra to wgEncodeGencodeV3.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV4.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV7.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisChiaPet.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisDnaPet.ra
- lines changed 7, context: html, text, full: html, text
updated md5sums for colliding file names
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
- lines changed 2, context: html, text, full: html, text
corrected some md5 errors, there were colliding file names
- lines changed 6, context: html, text, full: html, text
Trying to make the inventory match up
- lines changed 62, context: html, text, full: html, text
updated md5sums for colliding file names
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaSeq.ra
- lines changed 5, context: html, text, full: html, text
updated md5sums for colliding file names
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibGenotype.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethyl450.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylArray.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylSeq.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibRnaSeq.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeMapability.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromSynth.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyAlbanyTiling.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyRipSeq.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunySwitchgear.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhNsome.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhRnaSeq.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
- lines changed 129, context: html, text, full: html, text
changed sc582 > sc584, and added in new objects
- lines changed 257, context: html, text, full: html, text
loaded last bits of sydh tfbs
- lines changed 873, context: html, text, full: html, text
changed t-rex-hek293 > hek293-t-rex and fetalpbde > pbdefetal
- lines changed 19, context: html, text, full: html, text
inserted md5sums for new files
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUchicagoTfbs.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUmassDekker5C.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra
- lines changed 11, context: html, text, full: html, text
Removed orgiAssembly, added md5sum to fileSortOrder, removed Signal stanza
- lines changed 12, context: html, text, full: html, text
Added a protocol SDS-Page declaration for the current data, so that when the FASP data is added, it will be easier and clearer to integrate
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUw5C.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwAffyExonArray.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
- lines changed 1, context: html, text, full: html, text
added treatment as an expvar
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
- lines changed 73, context: html, text, full: html, text
added one more submission 4696
- lines changed 1, context: html, text, full: html, text
added treatment as an expvar
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeHaibGenotype.ra
- lines changed 92, context: html, text, full: html, text
copying over a fix Cricket did, redmine#1708, note# 85
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSunySwitchgear.ra
- lines changed 3, context: html, text, full: html, text
preparing metadata for release, redmine #169
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
- lines changed 1, context: html, text, full: html, text
preparing metadata for release, redmine #169
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeSunySwitchgear.ra
- lines changed 48, context: html, text, full: html, text
preparing metadata for release, redmine #169
- src/hg/makeDb/trackDb/human/hg19/numtSeqHg19.html
- lines changed 1, context: html, text, full: html, text
changed placement of word, here.
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- lines changed 2, context: html, text, full: html, text
Separating GencodeV3 from GencodeV4, using the old V3 html file
- src/hg/makeDb/trackDb/human/hg19/wgEncodeAffyRnaChip.new.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.html
- lines changed 4, context: html, text, full: html, text
adding up to 10 authors before et al, removing extra period, adding missing periods
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.html
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.ra
- lines changed 1, context: html, text, full: html, text
Changed default to dense as Jacob requested
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.html
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra
- lines changed 564, context: html, text, full: html, text
Added whole cell instead of cell where misisng, removed the transcript tables we are not going to display them.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.new.html
- lines changed 13, context: html, text, full: html, text
Updating the track description according the lab requests
- lines changed 40, context: html, text, full: html, text
Adds and edits to track descriptioin for CSHL short
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV3.html
- lines changed 217, context: html, text, full: html, text
Separating GencodeV3 from GencodeV4, using the old V3 html file
- lines changed 1, context: html, text, full: html, text
changing 'Release Notes' to 'Description' to fit our standards
- lines changed 9, context: html, text, full: html, text
cleaned up references for gencode hg19
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV3.ra
- lines changed 8, context: html, text, full: html, text
Separating GencodeV3 from GencodeV4, using the old V3 html file
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV4.html
- lines changed 198, context: html, text, full: html, text
Moving the track Description to have the name of the composite
- lines changed 1, context: html, text, full: html, text
changing 'Release Notes' to 'Description' to fit our standards
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV4.new.ra
- lines changed 130, context: html, text, full: html, text
Separating GencodeV3 from GencodeV4, using the old V3 html file
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV4.ra
- lines changed 1, context: html, text, full: html, text
Using the new wgEncodeGencodeV4.html file
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisDnaPet.new.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.ra
- lines changed 355, context: html, text, full: html, text
Trying to add replacement tracks
- lines changed 129, context: html, text, full: html, text
Cleaning up track names for resubmitted data
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.new.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.html
- lines changed 2, context: html, text, full: html, text
fixed a typo, fix links so they aren't hgwdev, and made one link relative, redmine #1708
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.ra
- lines changed 1, context: html, text, full: html, text
Adding back fileSortOrder
- lines changed 1, context: html, text, full: html, text
Explicitly remove 'scoreFilter' with 'noScoreFilter .'. Here we have a confusing case where 'bed n +' tracks have implicit score filtering, but other tracks must request score filtering with settings.
- lines changed 1, context: html, text, full: html, text
Removed view and origAssembly from the fileSortOrder
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.html
- lines changed 2, context: html, text, full: html, text
commented out multi view section
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.ra
- lines changed 417, context: html, text, full: html, text
Removed view since there was only one view
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeProtGenoSuper.html
- lines changed 72, context: html, text, full: html, text
Added appropriate text to the ENCODE Proteogenomics supertrack page
- lines changed 1, context: html, text, full: html, text
Fixed an incorrect page title
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSunySwitchgear.html
- lines changed 11, context: html, text, full: html, text
minor edits: taking period out of hyperlink, adding spaces between value & units, removing spaces before period, redmine #169
- lines changed 0, context: html, text, full: html, text
minor edit: adding space between value & units, redmine #169
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhNsome.html
- lines changed 1, context: html, text, full: html, text
changed milli liters to microliters
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.html
- lines changed 5, context: html, text, full: html, text
sydh tfbs html fixes at QA's request
- lines changed 1, context: html, text, full: html, text
forgot snyder is part of stanford now
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
- lines changed 25, context: html, text, full: html, text
changed sc582 > sc584, and added in new objects
- lines changed 177, context: html, text, full: html, text
loaded last bits of sydh tfbs
- lines changed 1, context: html, text, full: html, text
changed windowsing function to mean+whiskers
- lines changed 31, context: html, text, full: html, text
changed t-rex-hek293 > hek293-t-rex and fetalpbde > pbdefetal
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.html
- lines changed 9, context: html, text, full: html, text
Renumbered the references so that ref [2] appears in the text before ref [3]
- lines changed 10, context: html, text, full: html, text
corrected some pre-QA errors
- lines changed 49, context: html, text, full: html, text
fixed html stuff and removed view settings from trackDb
- lines changed 0, context: html, text, full: html, text
html correction per QA request
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.ra
- lines changed 1, context: html, text, full: html, text
corrected some pre-QA errors
- lines changed 7, context: html, text, full: html, text
fixed html stuff and removed view settings from trackDb
- lines changed 14, context: html, text, full: html, text
Removed orgiAssembly, added md5sum to fileSortOrder, removed Signal stanza
- lines changed 1, context: html, text, full: html, text
Added the UNC/BSU ProtGeno track to the new ProtGeno supertrack
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra
- lines changed 2, context: html, text, full: html, text
one of the rows was missing treatment
- lines changed 2, context: html, text, full: html, text
more treatment correction errors
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.ra
- lines changed 9, context: html, text, full: html, text
added one more submission 4696
- lines changed 324, context: html, text, full: html, text
something went wrong on the add last time
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 1, context: html, text, full: html, text
Updated URL for pseudoYale60 track.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrRnaSeq.ra
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuHistone.ra
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHistone.ra
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhRnaSeq.ra
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwRnaSeq.ra
- src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
- lines changed 1, context: html, text, full: html, text
Updated URL for pseudoYale60 track.
- src/hg/oneShot/doEvoFoldV2/makefile
- lines changed 11, context: html, text, full: html, text
Updated makefile using what is generated by newProg.
- src/hg/utils/automation/EnsGeneAutomate.pm
- lines changed 173, context: html, text, full: html, text
adding v63 definitions new versions for myoLuc2 and sacCer3
- src/inc/vcf.h
- lines changed 2, context: html, text, full: html, text
Feature #2821 (VCF parser): improved representation of alleles:parse ref and comma-sep'd alt allele string into count and array
inside record, so callers don't all have to parse the comma-sep'd
alternate allele string.
- src/lib/common.c
- lines changed 2, context: html, text, full: html, text
put span's around uglyTime's so we can manipulate them client side
- src/lib/tests/vcfParseTest.c
- lines changed 1, context: html, text, full: html, text
Feature #2821 (VCF parser): improved representation of alleles:parse ref and comma-sep'd alt allele string into count and array
inside record, so callers don't all have to parse the comma-sep'd
alternate allele string.
- src/lib/udc.c
- lines changed 1, context: html, text, full: html, text
oops saveEnd should be bits64
- lines changed 1, context: html, text, full: html, text
Revert "oops saveEnd should be bits64"
This reverts commit d45d8804be0b9778fff7acb9a400b861ebcc7df4.
- lines changed 67, context: html, text, full: html, text
Revert "adding 4k readAhead buffer for sparseData reduces thousands of reads down to a dozen"
This reverts commit 5a4c9d70e2416f53241781d17549445b2bc80d42.
- lines changed 69, context: html, text, full: html, text
fixed adding 4k readAhead buffer for sparseData reduces thousands of reads down to a dozen
- src/lib/vcf.c
- lines changed 22, context: html, text, full: html, text
Feature #2821 (VCF parser): improved representation of alleles:parse ref and comma-sep'd alt allele string into count and array
inside record, so callers don't all have to parse the comma-sep'd
alternate allele string.
- src/utils/qa/alertBqueue.csh
- lines changed 10, context: html, text, full: html, text
added logic to detect rare empty B-queue and quit
- lines changed 2, context: html, text, full: html, text
dropping kuhn from output now that it is running as qateam. it was always supposed to go only to those involved
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed: 29105
- files changed: 276