All File Changes
v252_preview2 to v252_base (2011-05-31 to 2011-06-07) v252
- python/ucscgenomics/rafile/cv/CvFile.py
- lines changed 58, context: html, text, full: html, text
new version of cv validate
- lines changed 2, context: html, text, full: html, text
added new optional fields for antibody and mouse
- lines changed 2, context: html, text, full: html, text
added lots for human and mouse for future use
- lines changed 20, context: html, text, full: html, text
added support for multiple labs
- python/ucscgenomics/rafile/test.py
- lines changed 13, context: html, text, full: html, text
new version of cv validate
- python/ucscgenomics/rafile/testRaFile.py
- lines changed 205, context: html, text, full: html, text
new version of cv validate
- src/hg/encode/DAFs/2.0/caltechMm9Histone.daf
- lines changed 60, context: html, text, full: html, text
Added first version of DAFs for Caltech MM9 submission for Histone, TFBS and RNA-seq tracks.
- src/hg/encode/DAFs/2.0/caltechMm9RnaSeq.daf
- lines changed 87, context: html, text, full: html, text
Added first version of DAFs for Caltech MM9 submission for Histone, TFBS and RNA-seq tracks.
- src/hg/encode/DAFs/2.0/caltechMm9Tfbs.daf
- lines changed 60, context: html, text, full: html, text
Added first version of DAFs for Caltech MM9 submission for Histone, TFBS and RNA-seq tracks.
- src/hg/encode/DAFs/2.0/uncBsuProt.daf
- lines changed 1, context: html, text, full: html, text
Updated the .daf file for unc/Bsu prot. Set up the scaffolding for a .new.ra file
- src/hg/encode/antibodyWikiParser.py
- lines changed 1, context: html, text, full: html, text
Convert the tag to uppercase, for consistency with Tim's new standard
- src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes
- lines changed 3, context: html, text, full: html, text
Added support for tgz to be tracked in notes files.
- src/hg/encode/encodeMkGeoPkg/encodeAddGeoAccessions
- lines changed 2, context: html, text, full: html, text
Updated to match new format of mdbUpdate
- src/hg/encode/encodeValidate/config/fields.ra
- lines changed 6, context: html, text, full: html, text
Adding a term spikeInPool so that we can determine which pool was used
- src/hg/hgTables/gffOut.c
- lines changed 64, context: html, text, full: html, text
MLQ #4060 bugfix: user reported that Table Browser's GTF start_ and _stopcodons sometimes span introns, and we should be outputting discrete lines
for split codons instead of big intron-spanners (http://mblab.wustl.edu/GTF22.html).
Tested fix by comparing GTF dumps of hg18.refGene, hg18.knownGene and mm9.knownGene
between hgwdev and hgwdev-angie, ensuring that the only changes were to split up
too-large start_codon and stop_codon records.
- src/hg/hgTrackUi/hgTrackUi.c
- lines changed 2, context: html, text, full: html, text
Grammar tweak to OMIM trackUi.
- src/hg/hgTracks/bedTrack.c
- lines changed 4, context: html, text, full: html, text
fixing colorByStrand bug that it was not working in bed 8
- src/hg/hgTracks/hgTracks.c
- lines changed 3, context: html, text, full: html, text
Right-click view image should show nextExonArrows as per redmine 4074
- src/hg/hgTracks/imageV2.c
- lines changed 1, context: html, text, full: html, text
Drag and drop of tracks in image will now drag contiguous set of subtracks if dragging side button. Occasional wierdness when dragging too fast.
- src/hg/hgTracks/simpleTracks.c
- lines changed 24, context: html, text, full: html, text
Updated OMIM entry selection logic.
- lines changed 19, context: html, text, full: html, text
Added logic for OMIM color for Others category.
- lines changed 82, context: html, text, full: html, text
Updated OMIM entry selection/filtering logic functions and color scheme.
- lines changed 2, context: html, text, full: html, text
Removed 2 left over lines.
- lines changed 1, context: html, text, full: html, text
Use entry color instead of MG_BLACK for bedPlusLabelDrawAt().
- src/hg/hgc/hgc.c
- lines changed 4, context: html, text, full: html, text
Added phenotypeClass info after disorder description for omimLocation track.
- lines changed 6, context: html, text, full: html, text
Added logic to show phenotype class wqeven phenotypeId is not available.
- lines changed 92, context: html, text, full: html, text
Inital NumtS track support for hg19 and mm9
- src/hg/hgc/lowelab.c
- lines changed 1, context: html, text, full: html, text
comment out #define LISTUI for megablast track
- src/hg/htdocs/ENCODE/downloads.html
- lines changed 5, context: html, text, full: html, text
adding UChicago TFBS, redmine# 1665
- src/hg/htdocs/ENCODE/index.html
- src/hg/htdocs/ENCODE/search.html
- lines changed 7, context: html, text, full: html, text
making link to genome-preview conditional based on if the page is being displayed on genome-preview server or not
- src/hg/htdocs/FAQ/FAQreleases.html
- lines changed 2, context: html, text, full: html, text
Added anoCar2 to release list.
- src/hg/htdocs/FAQ/FAQtracks.html
- lines changed 0, context: html, text, full: html, text
Removed spaces from position format
- src/hg/htdocs/goldenPath/credits.html
- lines changed 10, context: html, text, full: html, text
adding BCM HGSC to credits for calJac1 and calJac3
- src/hg/htdocs/goldenPath/newsarch.html
- src/hg/htdocs/goldenPath/pubs.html
- lines changed 25, context: html, text, full: html, text
Added some pubs for David.
- src/hg/htdocs/style/HGStyle.css
- lines changed 4, context: html, text, full: html, text
Added rightClick 'hide highlihgted (green) set' and 'hide track (blue) set' options.
- src/hg/inc/versionInfo.h
- src/hg/js/hgTracks.js
- lines changed 54, context: html, text, full: html, text
Drag and drop of tracks in image will now drag contiguous set of subtracks if dragging side button. Occasional wierdness when dragging too fast.
- lines changed 98, context: html, text, full: html, text
Added rightClick 'hide highlihgted (green) set' and 'hide track (blue) set' options.
- lines changed 6, context: html, text, full: html, text
Make use of ne class blueButtons to make draging groups more visually intuitive.
- lines changed 23, context: html, text, full: html, text
Changed labels for right-click hide sets options.
- lines changed 14, context: html, text, full: html, text
individual track visibility options are confusing when rightClicking the sideButton and the sideButton is for more than one track. They are being removed.
- src/hg/js/jquery.tablednd.js
- lines changed 68, context: html, text, full: html, text
Drag and drop of tracks in image will now drag contiguous set of subtracks if dragging side button. Occasional wierdness when dragging too fast.
- lines changed 9, context: html, text, full: html, text
Fixed a problem where fast moves could scramble tracks not dragged.
- lines changed 74, context: html, text, full: html, text
Painful work to stop leaking subtrack rows when dragging set. Temporarily checking in commented out debug code because of the pain to get here.
- lines changed 58, context: html, text, full: html, text
Found bug that caused some sets not to budge. Caused by mix between string and number math. Cleaned up no longer needed debugging aid and extra protections that were not needed. Decided to bind mousemove only at dragStart.
- src/hg/lib/encode/openChromCombinedPeaks.as
- lines changed 25, context: html, text, full: html, text
Removed 7 table specific 'as' files which had been added to get buildTableDescriptions to understand the +10 fields of these bed 8 + tracks. Added a single 'as' file which I hope will now cover the 7 tables.
- src/hg/lib/encode/wgEncodeOpenChromSynthGm12878Pk.as
- lines changed 25, context: html, text, full: html, text
Need to add as files to get field descriptions into tableDescriptions for schema link
- lines changed 25, context: html, text, full: html, text
Removed 7 table specific 'as' files which had been added to get buildTableDescriptions to understand the +10 fields of these bed 8 + tracks. Added a single 'as' file which I hope will now cover the 7 tables.
- src/hg/lib/encode/wgEncodeOpenChromSynthH1hescPk.as
- lines changed 25, context: html, text, full: html, text
Need to add as files to get field descriptions into tableDescriptions for schema link
- lines changed 25, context: html, text, full: html, text
Removed 7 table specific 'as' files which had been added to get buildTableDescriptions to understand the +10 fields of these bed 8 + tracks. Added a single 'as' file which I hope will now cover the 7 tables.
- src/hg/lib/encode/wgEncodeOpenChromSynthHelas3Pk.as
- lines changed 25, context: html, text, full: html, text
Need to add as files to get field descriptions into tableDescriptions for schema link
- lines changed 25, context: html, text, full: html, text
Removed 7 table specific 'as' files which had been added to get buildTableDescriptions to understand the +10 fields of these bed 8 + tracks. Added a single 'as' file which I hope will now cover the 7 tables.
- src/hg/lib/encode/wgEncodeOpenChromSynthHepg2Pk.as
- lines changed 25, context: html, text, full: html, text
Need to add as files to get field descriptions into tableDescriptions for schema link
- lines changed 25, context: html, text, full: html, text
Removed 7 table specific 'as' files which had been added to get buildTableDescriptions to understand the +10 fields of these bed 8 + tracks. Added a single 'as' file which I hope will now cover the 7 tables.
- src/hg/lib/encode/wgEncodeOpenChromSynthHuvecPk.as
- lines changed 25, context: html, text, full: html, text
Need to add as files to get field descriptions into tableDescriptions for schema link
- lines changed 25, context: html, text, full: html, text
Removed 7 table specific 'as' files which had been added to get buildTableDescriptions to understand the +10 fields of these bed 8 + tracks. Added a single 'as' file which I hope will now cover the 7 tables.
- src/hg/lib/encode/wgEncodeOpenChromSynthK562Pk.as
- lines changed 25, context: html, text, full: html, text
Need to add as files to get field descriptions into tableDescriptions for schema link
- lines changed 25, context: html, text, full: html, text
Removed 7 table specific 'as' files which had been added to get buildTableDescriptions to understand the +10 fields of these bed 8 + tracks. Added a single 'as' file which I hope will now cover the 7 tables.
- src/hg/lib/encode/wgEncodeOpenChromSynthNhekPk.as
- lines changed 25, context: html, text, full: html, text
Need to add as files to get field descriptions into tableDescriptions for schema link
- lines changed 25, context: html, text, full: html, text
Removed 7 table specific 'as' files which had been added to get buildTableDescriptions to understand the +10 fields of these bed 8 + tracks. Added a single 'as' file which I hope will now cover the 7 tables.
- src/hg/lib/fileUi.c
- lines changed 14, context: html, text, full: html, text
Integrate supplemental materials in hgFileUi CGI better.
- lines changed 37, context: html, text, full: html, text
Almost broke beta downloads page. QA would have given me grief.
- src/hg/lib/mdb.c
- src/hg/lib/omimGeneMap.as
- lines changed 10, context: html, text, full: html, text
Changed several fields from string to lstring.
- src/hg/lib/web.c
- lines changed 19, context: html, text, full: html, text
implement cgiApoptosis system
- lines changed 5, context: html, text, full: html, text
adding error message on actual apoptosis timeout exit
- lines changed 6, context: html, text, full: html, text
error message to apache error logs and polite message for user for cgiApoptosis
- lines changed 1, context: html, text, full: html, text
hgLoadBed is also a problem on the RR and needs a time out exit
- src/hg/makeDb/doc/bosTau6.txt
- lines changed 66, context: html, text, full: html, text
Cow bosTau6 vs Platypus ornAna1 LASTZ
- src/hg/makeDb/doc/caeJap4.txt
- lines changed 114, context: html, text, full: html, text
rework caeJap4 with genbank sequence and correct labeles on other cae nematodes
- src/hg/makeDb/doc/caeRem4.txt
- lines changed 1, context: html, text, full: html, text
rework caeJap4 with genbank sequence and correct labeles on other cae nematodes
- src/hg/makeDb/doc/caeSp111.txt
- lines changed 5, context: html, text, full: html, text
rework caeJap4 with genbank sequence and correct labeles on other cae nematodes
- src/hg/makeDb/doc/caeSp71.txt
- lines changed 3, context: html, text, full: html, text
rework caeJap4 with genbank sequence and correct labeles on other cae nematodes
- src/hg/makeDb/doc/caeSp91.txt
- lines changed 3, context: html, text, full: html, text
rework caeJap4 with genbank sequence and correct labeles on other cae nematodes
- src/hg/makeDb/doc/canFam2.txt
- src/hg/makeDb/doc/cb4.txt
- lines changed 3, context: html, text, full: html, text
rework caeJap4 with genbank sequence and correct labeles on other cae nematodes
- src/hg/makeDb/doc/ce10.txt
- lines changed 1, context: html, text, full: html, text
rework caeJap4 with genbank sequence and correct labeles on other cae nematodes
- src/hg/makeDb/doc/encodeDccHg18/wgEncodeBroadHmm.release1.notes
- lines changed 62, context: html, text, full: html, text
Should have been checked in long ago.
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibTfbs.release1.notes
- lines changed 4015, context: html, text, full: html, text
added notes files for HAIB TFBS release 1
- src/hg/makeDb/doc/encodeDccMm9/wgEncodeLicrHistone.release1.notes
- lines changed 356, context: html, text, full: html, text
Added release1 notes for the LICR Histone Track.
- src/hg/makeDb/doc/encodeDccMm9/wgEncodeLicrRnaSeq.release1.notes
- lines changed 224, context: html, text, full: html, text
Added release1 notes for the LICR RNA-seq Track.
- src/hg/makeDb/doc/encodeDccMm9/wgEncodeLicrTfbs.release1.notes
- lines changed 383, context: html, text, full: html, text
Added release1 notes for the LICR Tfbs Track.
- src/hg/makeDb/doc/encodeDccMm9/wgEncodeUwDnase.release1.notes
- lines changed 596, context: html, text, full: html, text
Added release1 notes for the UW DNaseI HS track.
- src/hg/makeDb/doc/hg18.txt
- lines changed 95, context: html, text, full: html, text
Added section of hg18 new OMIM tracks build.
- src/hg/makeDb/doc/hg19.txt
- lines changed 41, context: html, text, full: html, text
Updated with the steps for getting the Rfam hg19 alignments from the Rfam group
- lines changed 5, context: html, text, full: html, text
Added the missing step of building omimAvSnp table.
- lines changed 34, context: html, text, full: html, text
Inital Numts tracks for hg19 and mm9
- src/hg/makeDb/doc/melGal1.txt
- src/hg/makeDb/doc/mm9.txt
- lines changed 31, context: html, text, full: html, text
Inital Numts tracks for hg19 and mm9
- src/hg/makeDb/doc/monDom5.txt
- src/hg/makeDb/doc/ornAna1.txt
- lines changed 8, context: html, text, full: html, text
Cow bosTau6 vs Platypus ornAna1 LASTZ
- src/hg/makeDb/doc/panTro3.txt
- lines changed 25, context: html, text, full: html, text
Generate liftOver file for panTro3 to panTro2
- src/hg/makeDb/doc/rn4.txt
- src/hg/makeDb/doc/susScr2.txt
- src/hg/makeDb/genbank/etc/genbank.conf
- lines changed 19, context: html, text, full: html, text
Added caeJap4 C. japonica GCA_000147155.1
- lines changed 1, context: html, text, full: html, text
updated ccds human build number
- src/hg/makeDb/hgLoadBed/hgLoadBed.c
- lines changed 23, context: html, text, full: html, text
hgLoadBed is also a problem on the RR and needs a time out exit
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 7, context: html, text, full: html, text
Changing the Tam to OHTam as discovered it was registered as the wrong molecule by the lab
- lines changed 1, context: html, text, full: html, text
changed the term for the new OHTAM entry, the first 'O' was actually a zero.
- lines changed 360, context: html, text, full: html, text
Fixed errors found in code review when recovering 8 cell lines.
- lines changed 69, context: html, text, full: html, text
Assorted changes to get the antibodies to (mostly) pass validation (down to only 77 errors - yay)
- lines changed 422, context: html, text, full: html, text
Standardized the case of the tag for cell types
- lines changed 1, context: html, text, full: html, text
Changed age to attic in attic description
- lines changed 46, context: html, text, full: html, text
Promoted 5 cell lines to tier 2
- lines changed 3, context: html, text, full: html, text
Addressing feedback from this week's code review
- lines changed 2, context: html, text, full: html, text
added the cv validation to View
- lines changed 31, context: html, text, full: html, text
Cell Lines Reverted to Tier 3
- lines changed 1, context: html, text, full: html, text
Fixed typo in description
- lines changed 40, context: html, text, full: html, text
Removed duplicate lineage terms
- lines changed 35, context: html, text, full: html, text
Added and Fixed More Lineage Terms
- lines changed 44, context: html, text, full: html, text
Complete lineage updates to human cell lines
- lines changed 16, context: html, text, full: html, text
Accepted several provisional stanzas
- src/hg/makeDb/trackDb/dog/trackDb.chainNet.ra
- lines changed 4, context: html, text, full: html, text
Use bosTau6 for chain net label
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaChipSeq.ra
- lines changed 397, context: html, text, full: html, text
Added missing control files, as referenced in redmine 825.
- lines changed 465, context: html, text, full: html, text
changed HTB-11 to SK-N-SH
- src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeYaleChIPseq.ra
- lines changed 4378, context: html, text, full: html, text
releasing Yale TFBS, release 4, redmine# 1319
- src/hg/makeDb/trackDb/human/hg18/omimAvSnp.html
- lines changed 55, context: html, text, full: html, text
Added hg18 omimAvSnp.html.
- src/hg/makeDb/trackDb/human/hg18/omimDescriptionText.html
- lines changed 21, context: html, text, full: html, text
Added human/hg18/omimDescriptionText.html.
- src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
- lines changed 2, context: html, text, full: html, text
releasing Yale TFBS, release 4, redmine# 1319
- lines changed 2, context: html, text, full: html, text
Added new release in for updates to TFBS Haib track.
- lines changed 1, context: html, text, full: html, text
changed haibtfbs to have a .new for alpha
- src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.new.ra
- lines changed 19, context: html, text, full: html, text
changed HTB-11 to SK-N-SH
- src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseq.html
- lines changed 58, context: html, text, full: html, text
releasing Yale TFBS, release 4, redmine# 1319
- src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseq.new.ra
- lines changed 1, context: html, text, full: html, text
Changed windowing function from mean -> mean+whiskers as stated by QA in Redmine #1319.
- src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseq.ra
- lines changed 83, context: html, text, full: html, text
releasing Yale TFBS, release 4, redmine# 1319
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
- lines changed 932, context: html, text, full: html, text
Added GEO accession numbers
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
- lines changed 17, context: html, text, full: html, text
Renamed fastqs that had a V2 in them due to wrong DAF being used
- lines changed 149, context: html, text, full: html, text
Removed the dateSubmitted1 error
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
- lines changed 573, context: html, text, full: html, text
Changing the metaData as per conversation with Atif, marking as clone-free and clone-based
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
- lines changed 6, context: html, text, full: html, text
made some corrections to sydh tfbs, I had used the old term in mdb with the zero, and I changed the name on the tag in track db for tfbs, changed TAM to OHTAM in RRbs
- lines changed 177, context: html, text, full: html, text
changed HTB-11 to SK-N-SH cell line
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibRnaSeq.ra
- lines changed 381, context: html, text, full: html, text
changed HTB-11 to SK-N-SH cell line
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
- lines changed 381, context: html, text, full: html, text
added metadata for subID 4064 and added metadata and trackdb data for 4160
- lines changed 114, context: html, text, full: html, text
loaded submission id# 4163, the entire sl102 experiment, and some missing fiels from sl13 and sl144
- lines changed 705, context: html, text, full: html, text
changed HTB-11 to SK-N-SH cell line
- lines changed 93, context: html, text, full: html, text
changed long label, added in missing expId's and dcc accession's
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
- lines changed 89, context: html, text, full: html, text
Added a few missing signals, cleaned up long and short labels, started to prep this for going to QA, see note 6 of issue 2020
- lines changed 35, context: html, text, full: html, text
Renamed to not have Rep1 when there was really no replicates
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
- lines changed 12, context: html, text, full: html, text
changed the TAM treatments to OHTAM treatments, there was some misunderstanding with regards to what treatment was used where, fixed now
- lines changed 12, context: html, text, full: html, text
made some corrections to sydh tfbs, I had used the old term in mdb with the zero, and I changed the name on the tag in track db for tfbs, changed TAM to OHTAM in RRbs
- lines changed 2649, context: html, text, full: html, text
Added 120/122 missing Peaks from AWG. Redmine #3996.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra
- lines changed 5, context: html, text, full: html, text
Changed the submission directory for the resubmitted data, fixed a comma error and changed the long labels to Kates new format
- lines changed 130, context: html, text, full: html, text
Added three new displayed subtracks and five new download-only subtracks
- lines changed 19, context: html, text, full: html, text
Added one more download-only subtrack
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
- lines changed 759, context: html, text, full: html, text
Added GEO accession numbers
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
- lines changed 1, context: html, text, full: html, text
staging Duke Affy Exon, redmine #60
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeDukeAffyExon.ra
- lines changed 2369, context: html, text, full: html, text
staging Duke Affy Exon, redmine #60
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
- lines changed 1, context: html, text, full: html, text
prepping for the release of UChicago TFBS, redmine #1665
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUchicagoTfbs.ra
- lines changed 1570, context: html, text, full: html, text
prepping for the release of UChicago TFBS, redmine #1665
- src/hg/makeDb/trackDb/human/hg19/omimAvSnp.html
- lines changed 4, context: html, text, full: html, text
Whitespace changes only. Truncated lines greater than 100 characters.
- lines changed 81, context: html, text, full: html, text
Moving omim track descriptions up to the human level from the hg19 level, as per redmine 2153 (notes 117, 118, and 121).
- src/hg/makeDb/trackDb/human/hg19/omimGene2.html
- lines changed 12, context: html, text, full: html, text
Whitespace changes only. Truncated lines greater than 100 characters.
- lines changed 99, context: html, text, full: html, text
Moving omim track descriptions up to the human level from the hg19 level, as per redmine 2153 (notes 117, 118, and 121).
- src/hg/makeDb/trackDb/human/hg19/omimGeneClass3.html
- lines changed 91, context: html, text, full: html, text
Deleting omimGeneClass3, as per redmine 2153, note 123.
- src/hg/makeDb/trackDb/human/hg19/omimLocation.html
- lines changed 13, context: html, text, full: html, text
Whitespace changes only. Truncated lines greater than 100 characters.
- lines changed 98, context: html, text, full: html, text
Moving omim track descriptions up to the human level from the hg19 level, as per redmine 2153 (notes 117, 118, and 121).
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 77, context: html, text, full: html, text
Inital Numts tracks for hg19 and mm9
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- lines changed 3, context: html, text, full: html, text
Updated the .daf file for unc/Bsu prot. Set up the scaffolding for a .new.ra file
- lines changed 1, context: html, text, full: html, text
staging Duke Affy Exon, redmine #60
- src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.ra
- lines changed 114, context: html, text, full: html, text
Took the rep 3 and 4 back out of the attic, I never got confirmation that they should be there
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.ra
- lines changed 92, context: html, text, full: html, text
Changing the metaData as per conversation with Atif, marking as clone-free and clone-based
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.ra
- lines changed 4, context: html, text, full: html, text
made some corrections to sydh tfbs, I had used the old term in mdb with the zero, and I changed the name on the tag in track db for tfbs, changed TAM to OHTAM in RRbs
- lines changed 4, context: html, text, full: html, text
changed the sort order for treatments so that OHTAM came before None.
- lines changed 4, context: html, text, full: html, text
chamges OHTAM's tag and None to zNone
- lines changed 11, context: html, text, full: html, text
changed HTB-11 to SK-N-SH cell line
- lines changed 193, context: html, text, full: html, text
changed none to znone in the actual tracks
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.ra
- lines changed 31, context: html, text, full: html, text
changed HTB-11 to SK-N-SH cell line
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.html
- lines changed 4, context: html, text, full: html, text
fixed broken link in description of haib tfbs
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
- lines changed 26, context: html, text, full: html, text
added metadata for subID 4064 and added metadata and trackdb data for 4160
- lines changed 24, context: html, text, full: html, text
loaded submission id# 4163, the entire sl102 experiment, and some missing fiels from sl13 and sl144
- lines changed 31, context: html, text, full: html, text
changed HTB-11 to SK-N-SH cell line
- lines changed 95, context: html, text, full: html, text
changed SKNSH to SK_N_SH in long labels, changed other short and long labels to fit norm, default windowing for raw signal is mean+whiskers now
- lines changed 4, context: html, text, full: html, text
changed Pol24 to POL24 in short labels that were inconsistent
- lines changed 1, context: html, text, full: html, text
moved geo accession to be after ucsc accession
- lines changed 1, context: html, text, full: html, text
added set type and contorl id to file sort order.
- lines changed 46, context: html, text, full: html, text
changed default options for what is on, as requested by flo.
- lines changed 1, context: html, text, full: html, text
changed long label, added in missing expId's and dcc accession's
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.html
- lines changed 1, context: html, text, full: html, text
adding missing paragraph tags
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRbpSuper.html
- lines changed 91, context: html, text, full: html, text
Addressing Redmine issue #460 by removing the SUNY Switchgear track from the RNA supertrack and rewording the supertrack description page (mostly) as specified by Frank from SUNY
- lines changed 1, context: html, text, full: html, text
Fixed up a mis-represented track name
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.ra
- lines changed 763, context: html, text, full: html, text
Added a few missing signals, cleaned up long and short labels, started to prep this for going to QA, see note 6 of issue 2020
- lines changed 6, context: html, text, full: html, text
Renamed to not have Rep1 when there was really no replicates
- lines changed 16, context: html, text, full: html, text
Changing the default on off
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSunySwitchgear.ra
- lines changed 1, context: html, text, full: html, text
Addressing Redmine issue #460 by removing the SUNY Switchgear track from the RNA supertrack and rewording the supertrack description page (mostly) as specified by Frank from SUNY
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
- lines changed 5, context: html, text, full: html, text
changed the TAM treatments to OHTAM treatments, there was some misunderstanding with regards to what treatment was used where, fixed now
- lines changed 1, context: html, text, full: html, text
made some corrections to sydh tfbs, I had used the old term in mdb with the zero, and I changed the name on the tag in track db for tfbs, changed TAM to OHTAM in RRbs
- lines changed 1057, context: html, text, full: html, text
Added 120/122 missing Peaks from AWG. Redmine #3996.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.html
- lines changed 6, context: html, text, full: html, text
cleaned up credits and spelled out Ab per Katrinas code review, redmine#4086 and #1665
- lines changed 1, context: html, text, full: html, text
removed Ab per Katrinas code review, redmine# 4086
- lines changed 1, context: html, text, full: html, text
put ab back for lab since it was accidentally removed per Katrinas code review, redmine# 4086
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.new.ra
- lines changed 52, context: html, text, full: html, text
Updated the .daf file for unc/Bsu prot. Set up the scaffolding for a .new.ra file
- lines changed 31, context: html, text, full: html, text
Added several new subtracks for uncBsuProt
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.ra
- lines changed 3, context: html, text, full: html, text
Changed the submission directory for the resubmitted data, fixed a comma error and changed the long labels to Kates new format
- src/hg/makeDb/trackDb/human/omimAvSnp.html
- lines changed 81, context: html, text, full: html, text
Moving omim track descriptions up to the human level from the hg19 level, as per redmine 2153 (notes 117, 118, and 121).
- lines changed 28, context: html, text, full: html, text
Moving generic warning and description text for OMIM tracks to a new include file, omimDescriptionText.html.
- src/hg/makeDb/trackDb/human/omimDescriptionText.html
- lines changed 29, context: html, text, full: html, text
Moving generic warning and description text for OMIM tracks to a new include file, omimDescriptionText.html.
- lines changed 10, context: html, text, full: html, text
Removed paragraph about UCSC Genes now that omim relies on RefSeq Genes. Redmine #2153, note 131.
- src/hg/makeDb/trackDb/human/omimGene2.html
- lines changed 99, context: html, text, full: html, text
Moving omim track descriptions up to the human level from the hg19 level, as per redmine 2153 (notes 117, 118, and 121).
- lines changed 28, context: html, text, full: html, text
Moving generic warning and description text for OMIM tracks to a new include file, omimDescriptionText.html.
- lines changed 5, context: html, text, full: html, text
Made colors match the actual track entries (redmine 2153, note 126).
- lines changed 40, context: html, text, full: html, text
Changed methods section to use past tense consistently, reworded many places, put references in alphabetical order, added links.
- src/hg/makeDb/trackDb/human/omimLocation.html
- lines changed 98, context: html, text, full: html, text
Moving omim track descriptions up to the human level from the hg19 level, as per redmine 2153 (notes 117, 118, and 121).
- lines changed 28, context: html, text, full: html, text
Moving generic warning and description text for OMIM tracks to a new include file, omimDescriptionText.html.
- lines changed 5, context: html, text, full: html, text
Made colors match the actual track entries (redmine 2153, note 126).
- src/hg/makeDb/trackDb/human/trackDb.chainNet.ra
- lines changed 6, context: html, text, full: html, text
Use bosTau6 for chain net label
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 3, context: html, text, full: html, text
Updated default color for OMIM tracks.
- src/hg/makeDb/trackDb/initTableList
- lines changed 10, context: html, text, full: html, text
move makeTableList code into a c-executable
- src/hg/makeDb/trackDb/lizard/anoCar2/description.html
- lines changed 1, context: html, text, full: html, text
Removed reference to chrLGe (does not exist)
- src/hg/makeDb/trackDb/makeTableList
- lines changed 27, context: html, text, full: html, text
move makeTableList code into a c-executable
- src/hg/makeDb/trackDb/makefile
- lines changed 1, context: html, text, full: html, text
adding caeAng1 to the build
- lines changed 8, context: html, text, full: html, text
move makeTableList code into a c-executable
- src/hg/makeDb/trackDb/marmoset/calJac1/description.html
- lines changed 8, context: html, text, full: html, text
adding BCM HGSC to credits for calJac1 and calJac3
- src/hg/makeDb/trackDb/marmoset/calJac3/description.html
- lines changed 9, context: html, text, full: html, text
adding BCM HGSC to credits for calJac1 and calJac3
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrRnaSeq.ra
- lines changed 6, context: html, text, full: html, text
Added experimet defining variables.
- src/hg/makeDb/trackDb/mouse/mm9/numtSeqMm9.html
- lines changed 77, context: html, text, full: html, text
Initial hg19 and mm9 NumtS tarck
- src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
- lines changed 74, context: html, text, full: html, text
Inital Numts tracks for hg19 and mm9
- src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
- lines changed 1, context: html, text, full: html, text
Fixed the naming of Signal table for Liver Replicate 2 to be wgEncodeUwDnaseLiverC57bl6MAdult8wksSigRep2 to match new file name. Also added commented out release tag for release 2 of UwDnase data that include Heart and TReg with only 1 replicate.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.ra
- lines changed 97, context: html, text, full: html, text
Updated coloring and short labels for track. (First pass)
- lines changed 12, context: html, text, full: html, text
Abbreviated Bone Marrow and Cerebellum for short labels.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.html
- lines changed 2, context: html, text, full: html, text
Removed first person narrative in track description. Added space to polA+RNA. Updated subGroup labels for longPolyA+ -> PolyA+, cell -> Whole Cell to match Human track labeling standards.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.ra
- lines changed 103, context: html, text, full: html, text
Updated notes and short and long labels for track. (First pass)
- lines changed 36, context: html, text, full: html, text
Updated coloring. Redmine 3990
- lines changed 10, context: html, text, full: html, text
Abbreviated Bone Marrow and Cerebellum for short labels.
- lines changed 2, context: html, text, full: html, text
Removed first person narrative in track description. Added space to polA+RNA. Updated subGroup labels for longPolyA+ -> PolyA+, cell -> Whole Cell to match Human track labeling standards.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.ra
- lines changed 103, context: html, text, full: html, text
Updated coloring and short labels for track.
- lines changed 12, context: html, text, full: html, text
Abbreviated Bone Marrow and Cerebellum for short labels.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.new.ra
- lines changed 1725, context: html, text, full: html, text
Removed replicate 1's of Heart and TReg experiments, as per advisment of Mouse ENCODE group. Only experiments with 2 replicates will be released. Made new.ra to house Heart and TReg replicate 1 for release 2.
- lines changed 2, context: html, text, full: html, text
Fixed the naming of Signal table for Liver Replicate 2 to be wgEncodeUwDnaseLiverC57bl6MAdult8wksSigRep2 to match new file name. Also added commented out release tag for release 2 of UwDnase data that include Heart and TReg with only 1 replicate.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.ra
- lines changed 297, context: html, text, full: html, text
Updated track settings. Update long and short labels to provide the most information. First pass at labels.
- lines changed 81, context: html, text, full: html, text
Updated color schema to organ systems.
- lines changed 20, context: html, text, full: html, text
Updated default tracks on to be replicate 1 and added cell line 3134. Also update windowing function from maximum -> mean+whiskers.
- lines changed 7, context: html, text, full: html, text
Abbreviated Bone Marrow and Cerebellum for short labels.
- lines changed 56, context: html, text, full: html, text
Removed replicate 1's of Heart and TReg experiments, as per advisment of Mouse ENCODE group. Only experiments with 2 replicates will be released. Made new.ra to house Heart and TReg replicate 1 for release 2.
- lines changed 2, context: html, text, full: html, text
Fixed the naming of Signal table for Liver Replicate 2 to be wgEncodeUwDnaseLiverC57bl6MAdult8wksSigRep2 to match new file name. Also added commented out release tag for release 2 of UwDnase data that include Heart and TReg with only 1 replicate.
- src/hg/makeDb/trackDb/mouse/trackDb.chainNet.ra
- lines changed 4, context: html, text, full: html, text
Use bosTau6 for chain net label
- src/hg/makeDb/trackDb/opossum/monDom5/trackDb.chainNet.ra
- lines changed 8, context: html, text, full: html, text
Use bosTau6 for chain net label
- src/hg/makeDb/trackDb/pig/trackDb.chainNet.ra
- lines changed 4, context: html, text, full: html, text
Use bosTau6 for chain net label
- src/hg/makeDb/trackDb/platypus/trackDb.chainNet.ra
- lines changed 7, context: html, text, full: html, text
Use bosTau6 for chain net label
- src/hg/makeDb/trackDb/rat/trackDb.chainNet.ra
- lines changed 4, context: html, text, full: html, text
Use bosTau6 for chain net label
- src/hg/makeDb/trackDb/sacCer/sacCer2/description.html
- lines changed 9, context: html, text, full: html, text
adding a note to appease the folks at SGD
- src/hg/makeDb/trackDb/worm/caeAng1/description.html
- lines changed 129, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/worm/caeAng1/gap.html
- lines changed 64, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/worm/caeAng1/gold.html
- lines changed 23, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/worm/caeAng1/trackDb.ra
- lines changed 40, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makefile
- lines changed 1, context: html, text, full: html, text
change LOWELAB BROWSER_DIRS definition
- src/hg/oneShot/doOmimLocation/doOmimLocation.c
- lines changed 10, context: html, text, full: html, text
Updated so that we can process hg18 data as well.
- src/hg/perf/hgTracksRandom.c
- lines changed 26, context: html, text, full: html, text
add selfApoptosis here too now it needs to become a library function
- src/hg/perf/rangeQuery.c
- lines changed 1, context: html, text, full: html, text
eliminate unused variable row
- src/hg/qaPushQ/qaPushQ.c
- src/hg/utils/makeTableList/makeTableList.c
- lines changed 111, context: html, text, full: html, text
see redmine 3780; obsoletes makeTableList and initTableList bash scripts
- src/hg/utils/makeTableList/makefile
- lines changed 18, context: html, text, full: html, text
see redmine 3780; obsoletes makeTableList and initTableList bash scripts
- src/lib/https.c
- lines changed 54, context: html, text, full: html, text
https:adding ability to wait on sockets of both sides of the conversation, in particular this enables using PUT to upload a large file e.g. Amazon Storage
- lines changed 186, context: html, text, full: html, text
fixing various problems with https, including using non-blocking, select, and timeout, deal with harvards messed up servers that often hang; avoiding errAbort makes go away bogus messages about lost connection to database
- src/makefile
- lines changed 1, context: html, text, full: html, text
add makeTableList to HG_UTILS_APPLIST
- src/product/ex.hg.conf
- lines changed 6, context: html, text, full: html, text
add description of browser.cgiExpireMinutes
- src/utils/qa/bigPush.csh
- lines changed 28, context: html, text, full: html, text
giving bigPush.csh better warning messages http://redmine.soe.ucsc.edu/issues/4010
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed: 36246
- files changed: 272