CVS changes by file
review to branch (2009-10-20 to 2009-10-27) v218
- src/hg/archaeStuff/data/Genome-info-meta
- 1.11 lines changed: 31, context: html, text, full: html, text
add Nymph Lake metagenome
- src/hg/archaeStuff/scripts/archaeBrowser/Blast.pm
- 1.27 lines changed: 4, context: html, text, full: html, text
change to support Nymph Lake metagenome
- src/hg/archaeStuff/scripts/archaeBrowser/ConservedDomains.pm
- 1.5 lines changed: 4, context: html, text, full: html, text
change to support Nymph Lake metagenome
- src/hg/archaeStuff/scripts/archaeBrowser/OrganismDb.pm
- 1.46 lines changed: 27, context: html, text, full: html, text
change to support Nymph Lake metagenome
- src/hg/archaeStuff/scripts/archaeBrowser/RemovePriv.pm
- 1.4 lines changed: 1, context: html, text, full: html, text
change to support Nymph Lake metagenome
- src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
- 1.20 lines changed: 1, context: html, text, full: html, text
Don't display parentTable which is actually obsolete
- src/hg/encode/encodeValidate/config/cv.ra
- 1.140 lines changed: 7, context: html, text, full: html, text
Vendor for H3K4me3 has changed.
- 1.139 lines changed: 1, context: html, text, full: html, text
Change BAFT to BATF
- 1.138 lines changed: 110, context: html, text, full: html, text
Added 10 new antibodies for Myers and one for Farnham and Myers
- src/hg/encode/encodeValidate/config/pi.ra
- 1.1 lines changed: 94, context: html, text, full: html, text
First cut of reporting script for ENCODE
- src/hg/encode/encodeValidate/doEncodeReport.pl
- 1.1 lines changed: 318, context: html, text, full: html, text
First cut of reporting script for ENCODE
- src/hg/hgGene/hgGeneData/Human/links.ra
- 1.36 lines changed: 2, context: html, text, full: html, text
Updating OMIM link to make it faster.
- src/hg/hgc/encodeClick.c
- 1.10 lines changed: 63, context: html, text, full: html, text
Details stuff for 5C tracks.
- src/hg/hgc/hgc.c
- 1.1579 lines changed: 4, context: html, text, full: html, text
Details stuff for 5C tracks.
- src/hg/hgc/hgc.h
- 1.48 lines changed: 3, context: html, text, full: html, text
Details stuff for 5C tracks.
- src/hg/inc/versionInfo.h
- 1.158 lines changed: 1, context: html, text, full: html, text
"New version number v218"
- src/hg/instinct/createDescriptionHTML/createSingleDescriptionHTML.pl
- 1.2 lines changed: 3, context: html, text, full: html, text
Printing of previous local_url bug fix
- src/hg/instinct/hgHeatmap2/hgHeatmap2.c
- 1.80 lines changed: 4, context: html, text, full: html, text
Added local url ability
- src/hg/instinct/hgHeatmap2/hgHeatmap2.h
- 1.51 lines changed: 1, context: html, text, full: html, text
Added local_url feature
- src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_etemadmoghadam2009.ra
- src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_miller2005.ra
- src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.ra
- 1.31 lines changed: 6, context: html, text, full: html, text
Fixed downsampling on new datasets
- 1.30 lines changed: 83, context: html, text, full: html, text
New datasets
- src/hg/instinct/hgHeatmap2/hgHeatmapFrontend/js/hgHeatmap.js
- 1.76 lines changed: 4, context: html, text, full: html, text
Added local url function
- src/hg/instinct/inc/hgHeatmapLib.h
- 1.38 lines changed: 1, context: html, text, full: html, text
Added local_url function
- src/hg/instinct/lib/hgHeatmapLib.c
- 1.63 lines changed: 2, context: html, text, full: html, text
Local url pointer added
- src/hg/js/hui.js
- 1.41 lines changed: 27, context: html, text, full: html, text
Added count of selected subtracks
- 1.40 lines changed: 22, context: html, text, full: html, text
Made vis changes work on 3-way matCBs
- 1.39 lines changed: 6, context: html, text, full: html, text
Temorarily readd hintOverSortableColumnHeader to avoid js errors.
- src/hg/lib/hui.c
- 1.244 lines changed: 2, context: html, text, full: html, text
Added count of selected subtracks
- 1.243 lines changed: 56, context: html, text, full: html, text
Moved dimension Z outside of matrix. Requested by Pauline and does make things clearer
- 1.242 lines changed: 1, context: html, text, full: html, text
Remove hintOverSortableColumnHeader which does nothing
- src/hg/makeDb/doc/encodeDccHg18/broadBernstein.txt
- 1.8 lines changed: 74, context: html, text, full: html, text
I guess I was sitting on these changes rather than checking them in
- src/hg/makeDb/doc/encodeDccHg18/broadChipSeq.notes.txt
- 1.5 lines changed: 280, context: html, text, full: html, text
I guess I was sitting on these changes rather than checking them in
- src/hg/makeDb/doc/encodeDccHg18/dnctRelease2.notes.txt
- 1.1 lines changed: 819, context: html, text, full: html, text
File list for Open Chromatin release 2
- src/hg/makeDb/doc/encodeDccHg18/dukeUtaUncCrawford.txt
- 1.9 lines changed: 327, context: html, text, full: html, text
Put release2 into the pushQ
- src/hg/makeDb/doc/encodeDccHg18/yaleDavisHarvardSnyder.txt
- 1.10 lines changed: 19, context: html, text, full: html, text
More submissions for Yale (post release2)
- src/hg/makeDb/doc/hg19.txt
- 1.52 lines changed: 401, context: html, text, full: html, text
Rerun the 4D site predictions with chrX only and non-ChrX others
- 1.51 lines changed: 84, context: html, text, full: html, text
Now working on phyloP business
- 1.50 lines changed: 38, context: html, text, full: html, text
Bring the msa_split procedure up to date
- 1.49 lines changed: 670, context: html, text, full: html, text
done with phastCons runs for the 46-way
- src/hg/makeDb/doc/makeEnsembl.txt
- 1.14 lines changed: 24, context: html, text, full: html, text
Rat rn4 v56 update done
- src/hg/makeDb/hgCgiData/Human/microarrayGroups.ra
- src/hg/makeDb/trackDb/human/dgv.html
- 1.6 lines changed: 18, context: html, text, full: html, text
changed layout of color description to match SNP tracks and added color to the text
- src/hg/makeDb/trackDb/human/encodeAffyChIpHl60PvalStrict.html
- 1.5 lines changed: 2, context: html, text, full: html, text
Fixed broken links to atcc.org products.
- src/hg/makeDb/trackDb/human/encodeAffyChIpHl60SignalStrict.html
- 1.5 lines changed: 2, context: html, text, full: html, text
Fixed broken links to atcc.org products.
- src/hg/makeDb/trackDb/human/encodeAffyChIpHl60SitesStrict.html
- 1.4 lines changed: 2, context: html, text, full: html, text
Fixed broken links to atcc.org products.
- src/hg/makeDb/trackDb/human/encodeGencodeGeneMar07.html
- 1.15 lines changed: 2, context: html, text, full: html, text
Fixed broken links to atcc.org products.
- src/hg/makeDb/trackDb/human/encodeGencodeRaceFrags.html
- 1.15 lines changed: 2, context: html, text, full: html, text
Fixed broken links to atcc.org products.
- src/hg/makeDb/trackDb/human/encodeStanfordChip.html
- 1.3 lines changed: 3, context: html, text, full: html, text
Fixed broken links to atcc.org products.
- src/hg/makeDb/trackDb/human/encodeStanfordChipSmoothed.html
- 1.3 lines changed: 3, context: html, text, full: html, text
Fixed broken links to atcc.org products.
- src/hg/makeDb/trackDb/human/encodeStanfordMeth.html
- 1.5 lines changed: 8, context: html, text, full: html, text
Fixed broken links to atcc.org products.
- src/hg/makeDb/trackDb/human/encodeStanfordMethSmoothed.html
- 1.5 lines changed: 8, context: html, text, full: html, text
Fixed broken links to atcc.org products.
- src/hg/makeDb/trackDb/human/encodeStanfordPromoters.html
- 1.5 lines changed: 16, context: html, text, full: html, text
Fixed broken links to atcc.org products.
- src/hg/makeDb/trackDb/human/encodeUvaDnaRepOrigins.html
- 1.16 lines changed: 1, context: html, text, full: html, text
Fixed broken links to atcc.org products.
- src/hg/makeDb/trackDb/human/hg17/encodeNhgriDukeDnaseHs.html
- 1.11 lines changed: 4, context: html, text, full: html, text
Fixed broken links to atcc.org products.
- src/hg/makeDb/trackDb/human/hg17/encodeNhgriDukeDnaseHsFeb07.html
- 1.6 lines changed: 4, context: html, text, full: html, text
Fixed broken links to atcc.org products.
- src/hg/makeDb/trackDb/human/hg17/encodeYaleChipPval.html
- 1.13 lines changed: 2, context: html, text, full: html, text
Fixed broken links to atcc.org products.
- src/hg/makeDb/trackDb/human/hg17/encodeYaleChipSig.html
- 1.7 lines changed: 2, context: html, text, full: html, text
Fixed broken links to atcc.org products.
- src/hg/makeDb/trackDb/human/hg17/encodeYaleChipSignal.html
- 1.10 lines changed: 2, context: html, text, full: html, text
Fixed broken links to atcc.org products.
- src/hg/makeDb/trackDb/human/hg17/encodeYaleChipSites.html
- 1.5 lines changed: 2, context: html, text, full: html, text
Fixed broken links to atcc.org products.
- src/hg/makeDb/trackDb/human/hg18/encodeNhgriDukeDnaseHs.html
- 1.3 lines changed: 4, context: html, text, full: html, text
Fixed broken links to atcc.org products.
- src/hg/makeDb/trackDb/human/hg18/encodeUvaDnaRepSuper.html
- 1.9 lines changed: 1, context: html, text, full: html, text
Fixed broken links to atcc.org products.
- src/hg/makeDb/trackDb/human/hg18/encodeYaleChipPval.html
- 1.4 lines changed: 2, context: html, text, full: html, text
Fixed broken links to atcc.org products.
- src/hg/makeDb/trackDb/human/hg18/encodeYaleChipSig.html
- 1.4 lines changed: 2, context: html, text, full: html, text
Fixed broken links to atcc.org products.
- src/hg/makeDb/trackDb/human/hg18/encodeYaleChipSites.html
- 1.4 lines changed: 2, context: html, text, full: html, text
Fixed broken links to atcc.org products.
- src/hg/makeDb/trackDb/human/hg18/encodeYaleChipSuper.html
- 1.9 lines changed: 1, context: html, text, full: html, text
Fixed broken links to atcc.org products.
- src/hg/makeDb/trackDb/human/hg18/knownGene.html
- 1.30 lines changed: 5, context: html, text, full: html, text
fixed typo and added color to the color key
- src/hg/makeDb/trackDb/human/hg18/trackDb.instinct.ra
- src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
- 1.620 lines changed: 1, context: html, text, full: html, text
fix up controlledVocabulary trackDb setting for CSHL long rna-seq
- 1.619 lines changed: 16, context: html, text, full: html, text
Remove download files for raw signal from metadata (not posting these for download)
- 1.618 lines changed: 38, context: html, text, full: html, text
Added 2 more submissions for UwDnase
- 1.617 lines changed: 1, context: html, text, full: html, text
Restore +1 too long label, as it was already released
- 1.616 lines changed: 68, context: html, text, full: html, text
Label consistency and length, sort order consistency for CSHL Long RNA track
- 1.615 lines changed: 54, context: html, text, full: html, text
Renamed an additional 28 tables for consistency of Open Chromatin tracks
- 1.614 lines changed: 110, context: html, text, full: html, text
restoring changes I made yesterday
- 1.613 lines changed: 3, context: html, text, full: html, text
In UwChIPSeq, replaced entries for 2HepG2 with 2HEPG2.
- 1.612 lines changed: 291, context: html, text, full: html, text
Added 10 new subtracks under UwChIPSeq
- 1.611 lines changed: 24, context: html, text, full: html, text
11 more name changes
- 1.610 lines changed: 114, context: html, text, full: html, text
Renamed 3 tables in Duke
- 1.609 lines changed: 15, context: html, text, full: html, text
add bounds information to bigWig
- 1.608 lines changed: 33, context: html, text, full: html, text
some short label edits and defaults for CSHL long RNA-seq
- 1.607 lines changed: 60, context: html, text, full: html, text
take out old CSHL long RNA-seq track
- 1.606 lines changed: 17, context: html, text, full: html, text
seom fixups for the CSHL long rna track
- 1.605 lines changed: 1296, context: html, text, full: html, text
Added a bunch of new UW Chip seq tracks
- 1.604 lines changed: 47, context: html, text, full: html, text
Added V2 notes to Open Chromatin
- 1.603 lines changed: 220, context: html, text, full: html, text
add CSHL long rna back in, now with compartment and rnaExtract
- 1.602 lines changed: 33, context: html, text, full: html, text
Add TFBS validation track from Weng lab, with first dataset
- 1.601 lines changed: 170, context: html, text, full: html, text
remove CSHL long rna
- 1.600 lines changed: 32, context: html, text, full: html, text
Added one more for UwDnase
- 1.599 lines changed: 1, context: html, text, full: html, text
Fixed one longLabel
- 1.598 lines changed: 89, context: html, text, full: html, text
Added 3 UwDnase sets
- 1.597 lines changed: 4, context: html, text, full: html, text
Made the long labels for the Broad Chip Seq controls consistent with each other
- 1.596 lines changed: 21, context: html, text, full: html, text
Added Yale HeLa E2F6.
- src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeq.html
- 1.20 lines changed: 23, context: html, text, full: html, text
Added Mapability reference to Broad
- src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMap.html
- 1.24 lines changed: 76, context: html, text, full: html, text
Added release 2 notes
- src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlLongRnaSeq.html
- 1.3 lines changed: 4, context: html, text, full: html, text
more text
- 1.2 lines changed: 124, context: html, text, full: html, text
more text
- 1.1 lines changed: 8, context: html, text, full: html, text
first pass
- src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDGF.html
- 1.4 lines changed: 50, context: html, text, full: html, text
Reorganized the wording on the page to make the description a bit nicer.
- src/hg/makeDb/trackDb/human/hg18/wgEncodeYalePolIISignal.html
- 1.4 lines changed: 1, context: html, text, full: html, text
Fixed broken links to atcc.org products.
- src/hg/makeDb/trackDb/human/hg18/wgEncodeYalePolIISites.html
- 1.4 lines changed: 1, context: html, text, full: html, text
Fixed broken links to atcc.org products.
- src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleStat1Signal.html
- 1.4 lines changed: 1, context: html, text, full: html, text
Fixed broken links to atcc.org products.
- src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleStat1Sites.html
- 1.4 lines changed: 1, context: html, text, full: html, text
Fixed broken links to atcc.org products.
- src/hg/makeDb/trackDb/human/hg19/knownGene.html
- 1.2 lines changed: 5, context: html, text, full: html, text
fixed typo and added color to the color key
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- 1.55 lines changed: 2, context: html, text, full: html, text
Get the other phastCons46way tracks set to bigWig
- src/hg/makeDb/trackDb/lowelab/nympLake0708_PGA2009_1/multizSulfolobales.html
- 1.1 lines changed: 161, context: html, text, full: html, text
Details page for multiz track
- src/hg/makeDb/trackDb/lowelab/nympLake0708_PGA2009_1/trackDb.ra
- 1.1 lines changed: 30, context: html, text, full: html, text
Update multiz track
- src/hg/utils/automation/Encode.pm
- 1.48 lines changed: 27, context: html, text, full: html, text
Add functions used by reporting script
- src/hg/utils/automation/EnsGeneAutomate.pm
- 1.20 lines changed: 172, context: html, text, full: html, text
Adding version 56 definitions
- src/hg/utils/automation/doBlastzChainNet.pl
- 1.30 lines changed: 3, context: html, text, full: html, text
Add the removal of the /err/ parasol directories during cleanUp
- src/hg/utils/automation/doEnsGeneUpdate.pl
- 1.19 lines changed: 4, context: html, text, full: html, text
fixup password string given to FTP server to be correct
- src/hg/utils/fiveCToBed/exampleFiveC.txt
- 1.1 lines changed: 3, context: html, text, full: html, text
Added a little converter for 5C data.
- src/hg/utils/fiveCToBed/fiveCToBed.c
- 1.1 lines changed: 141, context: html, text, full: html, text
Added a little converter for 5C data.
- src/hg/utils/fiveCToBed/makefile
- 1.1 lines changed: 21, context: html, text, full: html, text
Added a little converter for 5C data.
- src/hg/visiGene/vgProbeTrack/vgProbeTrack.c
- src/utils/faRenameRecords/faRenameRecords.c
- 1.1 lines changed: 57, context: html, text, full: html, text
New utility to do renaming of all sequences in fasta file seems to work.
- src/utils/faRenameRecords/makefile
- 1.1 lines changed: 18, context: html, text, full: html, text
New utility to do renaming of all sequences in fasta file seems to work.
- src/utils/qa/weeklybld/buildEnv.csh
- 1.85 lines changed: 5, context: html, text, full: html, text
Starting build v218
- lines changed: 7640
- files changed: 83