All File Changes
v260_preview to v260_preview2 (2011-11-15 to 2011-11-22) v260
- python/lib/ucscgenomics/mkChangeNotes.py
- lines changed 1, context: html, text, full: html, text
fixed a mkChangenotes bug, loose was applied to alpha metaDb, but it shouldn't
- lines changed 1, context: html, text, full: html, text
for printing solo report, the gbdb path was set to release path
- src/hg/encode/DAFs/3.0/mm9/wgEncodeCshlLongRnaSeq.daf
- lines changed 67, context: html, text, full: html, text
First pass at generating a DAF. Redmine #5986.
- lines changed 2, context: html, text, full: html, text
Added localization to DAF.
- lines changed 11, context: html, text, full: html, text
Added spike-In and meta-data variable spike-in pools.
- src/hg/encode/encodeDownloadReadme/redirectTemplateIndex.html
- lines changed 31, context: html, text, full: html, text
reworked the makefiles to allow for a split pipeline
- src/hg/encode/encodeLoad/doEncodeLoad.pl
- lines changed 19, context: html, text, full: html, text
added support for using libraries in the same directory as the executable, this fundamentally changes how the pipeline works, but is needed to separate the beta pipeline and prod
- lines changed 19, context: html, text, full: html, text
this reverts f329d887708f96c02a837be3c02f479c9ad25e81
- lines changed 19, context: html, text, full: html, text
Revert "this reverts f329d887708f96c02a837be3c02f479c9ad25e81"
This reverts commit 01048282df9dd45dacc1379fce56c471a248f0d5.
- lines changed 11, context: html, text, full: html, text
changed to GB standard of doing rhe libraries live where you do thing
- lines changed 2, context: html, text, full: html, text
added switch for beta and prod assembly choices
- lines changed 2, context: html, text, full: html, text
Revert "added switch for beta and prod assembly choices"
This reverts commit fd53bd21cb46b029ddffa44ee38a9c47be116d98.
- lines changed 8, context: html, text, full: html, text
updated usage statement, and renamed variables
- lines changed 9, context: html, text, full: html, text
removed comment line that is no longer needed
- lines changed 14, context: html, text, full: html, text
changed the location of the tagging function for the pipeline submissions
- src/hg/encode/encodeLoad/doEncodeUnload.pl
- lines changed 10, context: html, text, full: html, text
added support for using libraries in the same directory as the executable, this fundamentally changes how the pipeline works, but is needed to separate the beta pipeline and prod
- lines changed 10, context: html, text, full: html, text
this reverts f329d887708f96c02a837be3c02f479c9ad25e81
- lines changed 10, context: html, text, full: html, text
Revert "this reverts f329d887708f96c02a837be3c02f479c9ad25e81"
This reverts commit 01048282df9dd45dacc1379fce56c471a248f0d5.
- lines changed 10, context: html, text, full: html, text
changed to GB standard of doing rhe libraries live where you do thing
- lines changed 1, context: html, text, full: html, text
added switch for beta and prod assembly choices
- lines changed 1, context: html, text, full: html, text
Revert "added switch for beta and prod assembly choices"
This reverts commit fd53bd21cb46b029ddffa44ee38a9c47be116d98.
- lines changed 1, context: html, text, full: html, text
removed SafePipe from libraries in unload, it's not being used
- lines changed 7, context: html, text, full: html, text
updated usage statement, and renamed variables
- lines changed 9, context: html, text, full: html, text
removed comment line that is no longer needed
- src/hg/encode/encodeLoad/makefile
- lines changed 15, context: html, text, full: html, text
reworked the makefiles to allow for a split pipeline
- src/hg/encode/encodeQaInit/encodeQaInit
- src/hg/encode/encodeQaPrepareRelease/encodeQaPrepareRelease
- lines changed 7, context: html, text, full: html, text
fleshed out an error message
- src/hg/encode/encodeRenameObj/encodeRenameObj.c
- lines changed 7, context: html, text, full: html, text
training wheels as requested: now checks that new name starts with composite name
- lines changed 130, context: html, text, full: html, text
add support for multiple files in the fileName meta data field
- lines changed 56, context: html, text, full: html, text
adding support for attic renamed replaced revoked
- src/hg/encode/encodeValidate/config/makefile
- lines changed 24, context: html, text, full: html, text
reworked the makefiles to allow for a split pipeline
- src/hg/encode/encodeValidate/config/redirectTemplateIndex.html
- lines changed 31, context: html, text, full: html, text
reworked the makefiles to allow for a split pipeline
- src/hg/encode/encodeValidate/doEncodeValidate.pl
- lines changed 12, context: html, text, full: html, text
added support for using libraries in the same directory as the executable, this fundamentally changes how the pipeline works, but is needed to separate the beta pipeline and prod
- lines changed 1, context: html, text, full: html, text
removed non-standard package
- lines changed 12, context: html, text, full: html, text
this reverts f329d887708f96c02a837be3c02f479c9ad25e81
- lines changed 12, context: html, text, full: html, text
Revert "this reverts f329d887708f96c02a837be3c02f479c9ad25e81"
This reverts commit 01048282df9dd45dacc1379fce56c471a248f0d5.
- lines changed 12, context: html, text, full: html, text
changed to GB standard of doing rhe libraries live where you do thing
- lines changed 3, context: html, text, full: html, text
added switch for beta and prod assembly choices
- lines changed 3, context: html, text, full: html, text
Revert "added switch for beta and prod assembly choices"
This reverts commit fd53bd21cb46b029ddffa44ee38a9c47be116d98.
- lines changed 7, context: html, text, full: html, text
updated usage statement, and renamed variables
- lines changed 11, context: html, text, full: html, text
removed comment line that is no longer needed
- lines changed 4, context: html, text, full: html, text
changed the location of the tagging function for the pipeline submissions
- lines changed 5, context: html, text, full: html, text
put a check to get pwd if you run from the firectory itself (for appending submission dir to table name for camand line runs or validate
- lines changed 5, context: html, text, full: html, text
Revert "put a check to get pwd if you run from the firectory itself (for appending submission dir to table name for camand line runs or validate"
This reverts commit dadaf46d634bad2f66b8391d7567f58de974fc26.
- lines changed 2, context: html, text, full: html, text
redid how the previous commit handled things, it turns out at that point in the code, validate has chdired into the submit directory
- src/hg/encode/encodeValidate/doc/errors.txt
- src/hg/encode/encodeValidate/makefile
- lines changed 40, context: html, text, full: html, text
reworked the makefiles to allow for a split pipeline
- src/hg/encode/encodeValidate/newtest/doEncodeValidate.pl
- lines changed 2409, context: html, text, full: html, text
removed doEncodeValidate from the testing suite, changed how it worked.
- src/hg/encode/encodeValidate/obsolete/doc/errors.txt
- src/hg/encode/encodeValidate/obsolete/tagAlignSanityCheck.pl
- src/hg/encode/encodeValidate/tagAlignSanityCheck.pl
- src/hg/encode/inc/encodePatchTdb.h
- lines changed 2, context: html, text, full: html, text
adding support for attic renamed replaced revoked
- src/hg/encode/lib/encodePatchTdb.c
- lines changed 3, context: html, text, full: html, text
adding support for attic renamed replaced revoked
- src/hg/encode/makefile
- lines changed 3, context: html, text, full: html, text
reworked the makefiles to allow for a split pipeline
- src/hg/encode/metaCheck/makefile
- lines changed 1, context: html, text, full: html, text
adding support for attic renamed replaced revoked
- src/hg/encode/metaCheck/metaCheck.c
- lines changed 409, context: html, text, full: html, text
adding support for attic renamed replaced revoked
- src/hg/hgTables/schema.c
- lines changed 42, context: html, text, full: html, text
Since hgTables sometimes displays a schema for a table that is not a track, I had to bring back the earlier code that does not require a tdb. This fixes redmine 5990.
- src/hg/hgTrackUi/hgTrackUi.c
- lines changed 12, context: html, text, full: html, text
display code for publications (t2g) track, most of them by larrym
- src/hg/hgTracks/hgTracks.c
- lines changed 13, context: html, text, full: html, text
Adding back in the routine to give subtracks a pointer to their group. This is the more thorough fix for 5992 which was rolled back to do a very simple patch.
- lines changed 20, context: html, text, full: html, text
work on merging gene suggest into position search (#5933); currently only on in larrym's tree
- src/hg/hgTracks/imageV2.c
- lines changed 15, context: html, text, full: html, text
At Angie's request, adding ability to have map items with mouse-over title but no actual link
- lines changed 8, context: html, text, full: html, text
use attributeEncode instead of htmlEncode in title attributes (e.g. allow encoded unicode)
- src/hg/hgTracks/imageV2.h
- lines changed 3, context: html, text, full: html, text
At Angie's request, adding ability to have map items with mouse-over title but no actual link
- src/hg/hgTracks/simpleTracks.c
- lines changed 105, context: html, text, full: html, text
display code for publications (t2g) track, most of them by larrym
- src/hg/hgTracks/vcfTrack.c
- lines changed 23, context: html, text, full: html, text
Feature #3711 (VCF haplotype-sorting display): Reverting to the originalstyle of drawing the hap-cluster tree (clustering-tool style instead of
phylogenetic-ish style).
This reverts commit 5770f49f480bbfe5d920ece22f96961954e43116.
- lines changed 5, context: html, text, full: html, text
Feature #3711 (VCF haplotype-sorting display): suggestion from David:draw boundaries of leaf clusters in purple.
- lines changed 181, context: html, text, full: html, text
Feature #3711 (VCF haplotype-sorting display): Added mouseover titles forclusters in left label area. Thanks Tim for adding the capability to
make a mouseover title with no link!
Also fixed mapBox for center variant: it needs to be created *before*
the other variants are drawn and mapped; this is the opposite of
drawing (center variant is drawn last so it appears on top).
Also added variant name (if not "." placeholder) to variant mouseover.
- src/hg/hgc/hgc.c
- lines changed 4, context: html, text, full: html, text
Add a <BR> if there is no description of an OMIM Gene.
- lines changed 1, context: html, text, full: html, text
display code for publications (t2g) track, most of them by larrym
- src/hg/hgc/t2g.c
- lines changed 225, context: html, text, full: html, text
display code for publications (t2g) track, most of them by larrym
- lines changed 4, context: html, text, full: html, text
Fixes for stricter -Wall warnings: use puts instead of printf if there's noformat argument, and use TRUE & FALSE instead of true & false.
- src/hg/htdocs/ENCODE/pubs.html
- lines changed 1, context: html, text, full: html, text
fixed erronous entry as reported by issue 5916
- src/hg/htdocs/goldenPath/credits.html
- lines changed 14, context: html, text, full: html, text
Fixed up the cow credits a bit.
- lines changed 2, context: html, text, full: html, text
Removed comment around microbat link.
- src/hg/htdocs/goldenPath/help/bam.html
- lines changed 2, context: html, text, full: html, text
Doc #5964 (document some trackDb variables): added BAM-specificsettings showNames and noColorTag to trackDb/README. noColorTag
is internal-use-only, and I'm considering dropping it and just
not offering the bamColorTag UI option if the bamColorTag setting
is not present. So I added only showNames to goldenPath/help/bam.html.
- lines changed 2, context: html, text, full: html, text
One more place to mention showNames in bam.html.
- src/hg/htdocs/goldenPath/newsarch.html
- lines changed 35, context: html, text, full: html, text
Added UMD cow announcement, archived some news items, fixed some typos etc.
- src/hg/htdocs/goldenPath/pubs.html
- src/hg/htdocs/images/phylo/gorGor3_11way.png
- lines changed 0, context: html, text, full: html, text
phylo tree for Gorilla 11-way primate alignment
- src/hg/htdocs/indexNews.html
- lines changed 112, context: html, text, full: html, text
Added UMD cow announcement, archived some news items, fixed some typos etc.
- src/hg/htdocs/style/HGStyle.css
- lines changed 1, context: html, text, full: html, text
Added '.descTbl th' to declaration so table header rows pick up the style too.
- lines changed 11, context: html, text, full: html, text
add styles for new position input design (#5933)
- src/hg/inc/hgBam.h
- lines changed 4, context: html, text, full: html, text
hgBam.h should include samAlignment.h regardless of USE_BAM, in order toavoid compilation error when USE_BAM is not defined.
- src/hg/js/hgGateway.js
- lines changed 3, context: html, text, full: html, text
work on #3484; corner-case where user hits enter w/o selecting item from list
- src/hg/js/hgTracks.js
- lines changed 33, context: html, text, full: html, text
work on #3484; corner-case where user hits enter w/o selecting item from list. Some experimental code for #5933 (only turned on in larrym's tree)
- lines changed 4, context: html, text, full: html, text
At Angie's request, adding ability to have map items with mouse-over title but no actual link
- lines changed 4, context: html, text, full: html, text
copy coordinates in location input when user clicks on static copy of position
- lines changed 1, context: html, text, full: html, text
use removeAttr to fix a jQuery 1.7 problem
- src/hg/js/utils.js
- lines changed 1, context: html, text, full: html, text
One-line change for an eleventh our bug: trackSearch [+][-] buttons not working. This may be a patch request.
- lines changed 45, context: html, text, full: html, text
Fixed bug occurring on ddcl mdbVals that are beneath an added or removed line.
- src/hg/lib/cosmicRaw.sql
- lines changed 20, context: html, text, full: html, text
Added cosmic_mutation_id as an index key.
- src/hg/lib/hgFind.c
- lines changed 12, context: html, text, full: html, text
allow refLink searches to work when accessions have version numbers (ignore the accession version number) RedMine issue 6040
- src/hg/lib/hui.c
- lines changed 1, context: html, text, full: html, text
Vanessa requested a wording change in redmine 6082.
- src/hg/makeDb/doc/anoCar2.txt
- lines changed 2, context: html, text, full: html, text
add link to WGS Traces information for these assemblies
- src/hg/makeDb/doc/calJac3.txt
- lines changed 4, context: html, text, full: html, text
add link to WGS Traces information for these assemblies
- src/hg/makeDb/doc/danRer7.txt
- lines changed 2, context: html, text, full: html, text
add link to WGS Traces information for these assemblies
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwHistone.release2.notes
- src/hg/makeDb/doc/encodeDccMm9/wgEncodeCaltechTfbs.release1.notes
- lines changed 32, context: html, text, full: html, text
fixed notes after a mkChange bugfix
- src/hg/makeDb/doc/fr3.txt
- lines changed 236, context: html, text, full: html, text
initial genome build with repeat masker, simple repeats, and gaps fixed up
- lines changed 123, context: html, text, full: html, text
windowMasker and blat server now running
- src/hg/makeDb/doc/gorGor3.txt
- lines changed 31, context: html, text, full: html, text
running synNet maf split for 11-way alignment
- src/hg/makeDb/doc/loxAfr3.txt
- lines changed 20, context: html, text, full: html, text
redmine track #5959 pairwise alignment : loxAfr3 <-> monDom5
- lines changed 3, context: html, text, full: html, text
Set chainNet priority and matrix values for loxAfr3 vs. monDom5.
- src/hg/makeDb/doc/melGal1.txt
- lines changed 3, context: html, text, full: html, text
add link to WGS Traces information for these assemblies
- src/hg/makeDb/doc/micMur1.txt
- lines changed 3, context: html, text, full: html, text
add link to WGS Traces information for these assemblies
- src/hg/makeDb/doc/monDom5.txt
- lines changed 67, context: html, text, full: html, text
redmine track #5959 pairwise alignment : loxAfr3 <-> monDom5
- lines changed 7, context: html, text, full: html, text
Set chainNet priority and matrix values for loxAfr3 vs. monDom5.
- src/hg/makeDb/doc/nomLeu1.txt
- lines changed 18, context: html, text, full: html, text
Sort rmsk tables by chromStart (redmine Bug #5557)
- lines changed 14, context: html, text, full: html, text
Document blat server assignment for gibbon nonLeu1
- lines changed 18, context: html, text, full: html, text
Document how to set gibbon/trackDb.chainNet.ra
- src/hg/makeDb/doc/otoGar1.txt
- lines changed 3, context: html, text, full: html, text
add link to WGS Traces information for these assemblies
- src/hg/makeDb/doc/panTro3.txt
- lines changed 2, context: html, text, full: html, text
add link to WGS Traces information for these assemblies
- src/hg/makeDb/doc/papHam1.txt
- lines changed 193, context: html, text, full: html, text
catch up some ancient instructions for Baboon
- lines changed 2, context: html, text, full: html, text
add link to WGS Traces information for these assemblies
- src/hg/makeDb/doc/ponAbe2.txt
- lines changed 2, context: html, text, full: html, text
add link to WGS Traces information for these assemblies
- src/hg/makeDb/doc/rheMac2.txt
- lines changed 3, context: html, text, full: html, text
add link to WGS Traces information for these assemblies
- src/hg/makeDb/doc/tarSyr1.txt
- lines changed 3, context: html, text, full: html, text
add link to WGS Traces information for these assemblies
- src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
- lines changed 2, context: html, text, full: html, text
Removing the commands to build the knownToCdsSnp and knownToGnf1h tables. knownToGnf1h is obsolete, superceded by knownToGnfAtlas2. knownToCdsSnp never really worked out, and decisions were made to drop it (see git #20, comment #49)
- src/hg/makeDb/genbank/etc/genbank.conf
- lines changed 1, context: html, text, full: html, text
no refseq natives for gorGor3
- lines changed 16, context: html, text, full: html, text
adding definitions for fr3 Fugu
- src/hg/makeDb/genbank/etc/hgwbeta.dbs
- lines changed 2, context: html, text, full: html, text
Added gorGor3 and nomLeu1
- src/hg/makeDb/schema/all.joiner
- lines changed 3, context: html, text, full: html, text
Removing some dependencies to tables pepMwAa and pepPi, which are/were specific to the Proteome Browser
- lines changed 5, context: html, text, full: html, text
eliminate felCat3 from identifier ensemblTranscriptId checks
- src/hg/makeDb/trackDb/README
- lines changed 4, context: html, text, full: html, text
Doc #5964 (document some trackDb variables): added BAM-specificsettings showNames and noColorTag to trackDb/README. noColorTag
is internal-use-only, and I'm considering dropping it and just
not offering the bamColorTag UI option if the bamColorTag setting
is not present. So I added only showNames to goldenPath/help/bam.html.
- src/hg/makeDb/trackDb/chimp/trackDb.chainNet.ra
- lines changed 4, context: html, text, full: html, text
Added override section for gorGor3. Added shortLabel tag to gorGor1 override section.
- lines changed 1, context: html, text, full: html, text
Added matrix line to gorGor3 override section so chain/net description page matches results of getMatrixLines.csh
- src/hg/makeDb/trackDb/cow/bosTau6/description.html
- lines changed 57, context: html, text, full: html, text
Edited this file for readability and added some info.
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 1, context: html, text, full: html, text
Fixing cell line protocol
- lines changed 241, context: html, text, full: html, text
Added Mouse and Human tags for Antibody validation documents to clearly indicate when an antibody has been validated for Mouse or Human. Redmine #1012.
- lines changed 0, context: html, text, full: html, text
Fixed spacing issues in validation files list.
- lines changed 36, context: html, text, full: html, text
added cell line stanzas to cv
- lines changed 47, context: html, text, full: html, text
Adding Differentiation Protocol Treatments, Removing Myocyte Diff Protocols
- src/hg/makeDb/trackDb/cv/beta/cv.ra
- lines changed 311, context: html, text, full: html, text
Copying alpha cv to beta
- src/hg/makeDb/trackDb/cv/public/cv.ra
- lines changed 237, context: html, text, full: html, text
Moved over Labels from beta/cv.ra only.
Two labels that were modified to not include semicolon are:
1. ELAVL1 (SC-5261) which is ELAVL1 (SC-5261; 07-1735 is recommended replacement for AB5831) beta/cv.ra
2. T7Tag (AB3790) which is T7Tag (AB3790; Nov_69522) in beta/cv.ra
Need to discuss with Jeff about those labels, but these should suffice for now.
- src/hg/makeDb/trackDb/elephant/trackDb.chainNet.ra
- lines changed 2, context: html, text, full: html, text
Set chainNet priority and matrix values for loxAfr3 vs. monDom5.
- src/hg/makeDb/trackDb/fugu/fr3/description.html
- lines changed 129, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/fugu/fr3/gap.html
- lines changed 64, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/fugu/fr3/gold.html
- lines changed 23, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/fugu/fr3/trackDb.ra
- lines changed 8, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- lines changed 6, context: html, text, full: html, text
proper searching for gold table
- src/hg/makeDb/trackDb/gibbon/nomLeu1/description.html
- lines changed 3, context: html, text, full: html, text
Changed the URL to NCBI to a simpler, yet still-correct one. Fixed an html formatting error.
- src/hg/makeDb/trackDb/gibbon/nomLeu1/gap.html
- lines changed 16, context: html, text, full: html, text
Rearranged first sentence. Added links to NCBI, WashU and Baylor.
- src/hg/makeDb/trackDb/gibbon/nomLeu1/gold.html
- lines changed 20, context: html, text, full: html, text
Rearranged first sentence. Added links to NCBI, WashU and Baylor. Made other minor formatting changes.
- src/hg/makeDb/trackDb/gibbon/nomLeu1/trackDb.ra
- lines changed 32, context: html, text, full: html, text
remove all_mrna and all_est and fixup gold search
- src/hg/makeDb/trackDb/gibbon/trackDb.chainNet.ra
- lines changed 8, context: html, text, full: html, text
overrides for hg19 and gorGor3
- lines changed 8, context: html, text, full: html, text
Set the priority and matrix value based on chainNet.pl and findScore.pl results.
- lines changed 1, context: html, text, full: html, text
Removed blank line from the top of the file
- src/hg/makeDb/trackDb/gibbon/trackDb.ra
- lines changed 3, context: html, text, full: html, text
overrides for hg19 and gorGor3
- src/hg/makeDb/trackDb/gorilla/gorGor3/description.html
- lines changed 4, context: html, text, full: html, text
add a two item name between region display example
- lines changed 4, context: html, text, full: html, text
indicate NM version number searches ignore the version extension
- lines changed 1, context: html, text, full: html, text
Changed the URL to NCBI to a simpler, yet still-correct one
- src/hg/makeDb/trackDb/gorilla/gorGor3/gap.html
- lines changed 10, context: html, text, full: html, text
Changed the structure of the first sentence and included links to the Wellcome Trust Sanger Institute. Made various formatting corrections.
- src/hg/makeDb/trackDb/gorilla/gorGor3/gold.html
- lines changed 3, context: html, text, full: html, text
Moved a period from inside to outside a hyperlink. Removed an unnecessary period. Italicized the species name.
- lines changed 1, context: html, text, full: html, text
Removed an unnecessary period
- lines changed 1, context: html, text, full: html, text
Changed the URL to NCBI to a simpler, yet still-correct one
- src/hg/makeDb/trackDb/gorilla/gorGor3/trackDb.chainNet.ra
- lines changed 40, context: html, text, full: html, text
adding chainNet overrides and proper search for gold track
- lines changed 2, context: html, text, full: html, text
Added matrix line to calJac3 override section so chain/net description page matches results of getMatrixLines.csh
- src/hg/makeDb/trackDb/gorilla/gorGor3/trackDb.ra
- lines changed 7, context: html, text, full: html, text
adding proper search rule for gold table
- lines changed 7, context: html, text, full: html, text
adding chainNet overrides and proper search for gold track
- src/hg/makeDb/trackDb/human/hg19/agilentCgh.html
- lines changed 117, context: html, text, full: html, text
Did some major cleanup to html table: simplified code greatly, got rid of depricated attributes and used css, lowercased tags, and fixed issue with alternating colored rows where two of the same color were together. Colors are still really ugly, but we can fix that later. ;-)
- lines changed 5, context: html, text, full: html, text
Correct two links that were out of date and hit redirects on Agilent's website.
- src/hg/makeDb/trackDb/human/hg19/altSeqComposite5.ra
- lines changed 2, context: html, text, full: html, text
fixup URL for alternate sequence
- src/hg/makeDb/trackDb/human/hg19/lincRNAs.html
- lines changed 2, context: html, text, full: html, text
Remove the last sentnece 'From which all the raw data can be downloaded'
- lines changed 32, context: html, text, full: html, text
Hard wrapped text to 100 chars. Reformatted and lower-cased tags.
- lines changed 16, context: html, text, full: html, text
Corrected grammar for redundant wording, redundant workding. Split main paragraph into two for better readability. Corrected citation format and links.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
- lines changed 19, context: html, text, full: html, text
added md5sums to V2 entries
- lines changed 63, context: html, text, full: html, text
Added GEO Accession numbers for track. Redmine #2783.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethyl450.ra
- lines changed 3, context: html, text, full: html, text
fixing rename problem when encodeRenameObj accepted an incorrect target name without the full composite prefix
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
- lines changed 185, context: html, text, full: html, text
Adding the Caltech submitted files for the HAIB track.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
- lines changed 20, context: html, text, full: html, text
just finishing up an encode rename for Matt
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
- lines changed 7, context: html, text, full: html, text
revoking monocytes cd13 from uw dnase hs and uw dgf for alpha
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
- lines changed 6, context: html, text, full: html, text
revoking monocytes cd13 from uw dnase hs and uw dgf for alpha
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeCaltechRnaSeq.ra
- lines changed 98, context: html, text, full: html, text
Adding dccAccession only
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwDnase.ra
- lines changed 5, context: html, text, full: html, text
revoked monocytes cd14 on uw dnase for beta
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwHistone.ra
- lines changed 1, context: html, text, full: html, text
restaging UW Histone metaDb with Matts changes, redmine # 4459
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwHistone.ra
- lines changed 11267, context: html, text, full: html, text
Releasing UW Histone, redmine# 4459
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 1, context: html, text, full: html, text
changed to match the config page
- lines changed 28, context: html, text, full: html, text
Changed 'bosTau4' to 'bosTau6' in placental mammal section. Added oviAri1 to placental mammal section.
- lines changed 43, context: html, text, full: html, text
Changed 'xenTro2' to 'xenTro3' in vertebrate section. Added melGal1 to vertebrate section.
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- lines changed 2, context: html, text, full: html, text
Adding the Chromatin supertrack and moving three tracks into it
- lines changed 2, context: html, text, full: html, text
Releasing UW Histone, redmine# 4459
- src/hg/makeDb/trackDb/human/hg19/wgEncodeChromSuper.html
- lines changed 132, context: html, text, full: html, text
New Super track description for chromatin interaction
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV7.html
- lines changed 5, context: html, text, full: html, text
Changing the track description according to ticket #5901, letting this small fix leak to public.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV9.html
- lines changed 2, context: html, text, full: html, text
changed according to ticket 5901 (removed 'but not annotated...')
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.ra
- lines changed 1, context: html, text, full: html, text
Adding the Chromatin supertrack and moving three tracks into it
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.ra
- lines changed 1, context: html, text, full: html, text
fixing rename problem when encodeRenameObj accepted an incorrect target name without the full composite prefix
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSuper.ra
- lines changed 7, context: html, text, full: html, text
Adding the Chromatin supertrack and moving three tracks into it
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.new.ra
- lines changed 3, context: html, text, full: html, text
Fixed mistake in label for MCF7 and SH-SY5Y GATA3 experiments. The Label for the matrix and subGroup didn't match meta-data.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
- lines changed 3, context: html, text, full: html, text
Fixed mistake in label for MCF7 and SH-SY5Y GATA3 experiments. The Label for the matrix and subGroup didn't match meta-data.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeTfBindingSuper.html
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUmassDekker5C.ra
- lines changed 2, context: html, text, full: html, text
Adding the Chromatin supertrack and moving three tracks into it
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.new.ra
- lines changed 12, context: html, text, full: html, text
Adding the Chromatin supertrack and moving three tracks into it
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.new.ra
- lines changed 36, context: html, text, full: html, text
revoking monocytes cd13 from uw dnase hs and uw dgf for alpha
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.ra
- lines changed 21, context: html, text, full: html, text
revoking monocytes cd13 from uw dnase hs and uw dgf for alpha
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra
- lines changed 21, context: html, text, full: html, text
revoked monocytes cd14 on uw dnase for beta
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.html
- lines changed 18, context: html, text, full: html, text
Releasing UW Histone, redmine# 4459
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.ra
- lines changed 2491, context: html, text, full: html, text
Releasing UW Histone, redmine# 4459
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.html
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.ra
- src/hg/makeDb/trackDb/human/trackDb.chainNet.ra
- lines changed 4, context: html, text, full: html, text
Added override section for gorGor3. Added shortLabel tag to gorGor1 override section.
- lines changed 1, context: html, text, full: html, text
Added matrix line to gorGor3 override section so chain/net description page matches results of getMatrixLines.csh
- lines changed 6, context: html, text, full: html, text
Set correct priority and matrix of gibbon nomLeu1 in hg19.
- src/hg/makeDb/trackDb/makefile
- lines changed 1, context: html, text, full: html, text
adding fr3 fugu to the build
- src/hg/makeDb/trackDb/marmoset/trackDb.chainNet.ra
- lines changed 4, context: html, text, full: html, text
Added override section for gorGor3. Added shortLabel tag to gorGor2 override section.
- lines changed 1, context: html, text, full: html, text
Added matrix line to gorGor3 override section so chain/net description page matches results of getMatrixLines.csh
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuHistone.ra
- lines changed 1441, context: html, text, full: html, text
Added 6 submissions to track. Redmine # 111.
- lines changed 961, context: html, text, full: html, text
Added 4 submissions to track. Redmine #111.
- lines changed 241, context: html, text, full: html, text
Added new submission for track. Redmine #111.
- lines changed 241, context: html, text, full: html, text
Added another submissions to track. Redmine #111.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
- lines changed 817, context: html, text, full: html, text
Added 3 new submissions for track. Redmine #110.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/makefile
- lines changed 1, context: html, text, full: html, text
staging caltech tfbs mm9, redmine# 4154
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeCaltechTfbs.ra
- lines changed 3758, context: html, text, full: html, text
staging caltech tfbs mm9, redmine# 4154
- src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
- lines changed 1, context: html, text, full: html, text
staging caltech tfbs mm9, redmine# 4154
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechHist.html
- lines changed 6, context: html, text, full: html, text
Fixed errors found in Redmine #4154, that were the same inRedmine #4155
1. Changed header size from h2 -> h3 for "Maps of Occupancy by Transcription Factors"
2. Update "Information on antibodies used is available via the hyperlinks in the "Select subtracks" menu." ->
"Information on antibodies used is available via the metadata for each sub-track."
3. Added spaces between units and scalars and added period for: "Reads of 32bp, 36bp or 50bp length were generated"
4. Added comma after Thus in "Thus we will be...."
5. Fixed sentence "was used to map reads to the male of female version of the mouse genome" to read "... male or female ... "
- lines changed 2, context: html, text, full: html, text
Fixed the issues found in Redmine #4154 which are relevant to Redmine #4155
1. Added period after Signal View description
2. Updated Sentences about information on Antibodies to read:
"Information on the antibodies used is available via the metadata (click the down arrow in the subtrack list) for each subtrack"
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechTfbs.html
- lines changed 6, context: html, text, full: html, text
Fixed errors found in Redmine #4154, that were the same inRedmine #4155
1. Changed header size from h2 -> h3 for "Maps of Occupancy by Transcription Factors"
2. Update "Information on antibodies used is available via the hyperlinks in the "Select subtracks" menu." ->
"Information on antibodies used is available via the metadata for each sub-track."
3. Added spaces between units and scalars and added period for: "Reads of 32bp, 36bp or 50bp length were generated"
4. Added comma after Thus in "Thus we will be...."
5. Fixed sentence "was used to map reads to the male of female version of the mouse genome" to read "... male or female ... "
- lines changed 2, context: html, text, full: html, text
Fixed the issues found in Redmine #4154 which are relevant to Redmine #4155
1. Added period after Signal View description
2. Updated Sentences about information on Antibodies to read:
"Information on the antibodies used is available via the metadata (click the down arrow in the subtrack list) for each subtrack"
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.ra
- lines changed 110, context: html, text, full: html, text
Added 6 submissions to track. Redmine # 111.
- lines changed 72, context: html, text, full: html, text
Added 4 submissions to track. Redmine #111.
- lines changed 18, context: html, text, full: html, text
Added new submission for track. Redmine #111.
- lines changed 18, context: html, text, full: html, text
Added another submissions to track. Redmine #111.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.ra
- lines changed 55, context: html, text, full: html, text
Added 3 new submissions for track. Redmine #110.
- src/hg/makeDb/trackDb/mrna.html
- lines changed 2, context: html, text, full: html, text
Changed capitalization of journal article title to match actual journal article. Journal article URL was being redirected. Replaced the URL with the new target.
- src/hg/makeDb/trackDb/nestedRepeats.html
- lines changed 5, context: html, text, full: html, text
Corrected 'RepBase' to 'Repbase Update'. Link to Repbase Update was being redirected, so replaced the URL with the new target. Corrected capitalization of journal article title.
- src/hg/makeDb/trackDb/opossum/trackDb.chainNet.ra
- lines changed 6, context: html, text, full: html, text
Set chainNet priority and matrix values for loxAfr3 vs. monDom5.
- src/hg/makeDb/trackDb/orangutan/trackDb.chainNet.ra
- lines changed 4, context: html, text, full: html, text
set priorities for gorGor3 chain net tracks
- src/hg/makeDb/trackDb/rhesus/trackDb.chainNet.ra
- lines changed 4, context: html, text, full: html, text
set priorities for gorGor3 chain net tracks
- src/hg/makeDb/trackDb/rmsk.html
- lines changed 5, context: html, text, full: html, text
Corrected 'RepBase' to 'Repbase Update'. Link to Repbase Update was being redirected, so replaced the URL with the new target. Corrected capitalization of journal article title.
- src/hg/makeDb/trackDb/t2g.html
- lines changed 9, context: html, text, full: html, text
t2g track desc corrections
- lines changed 7, context: html, text, full: html, text
t2g track desc corrections
- src/hg/makeDb/trackDb/trackDb.ra
- lines changed 12, context: html, text, full: html, text
removed t2g track from trackDb (name clash with sandbox)
- lines changed 32, context: html, text, full: html, text
setting t2g to hide in trackDb
- lines changed 2, context: html, text, full: html, text
second try to commit trackDb
- lines changed 2, context: html, text, full: html, text
fixed missing release tags in trackDb
- src/hg/makeDb/trackDb/xenTro/xenTro3/cons9way.html
- lines changed 8, context: html, text, full: html, text
clarify language issues and formatting
- src/hg/makeDb/trackDb/xenTro/xenTro3/description.html
- lines changed 2, context: html, text, full: html, text
Removed '.7' from gateway page sample query
- src/hg/makeDb/trackDb/xenoMrna.html
- lines changed 2, context: html, text, full: html, text
Changed capitalization of journal article title to match actual journal article. Journal article URL was being redirected. Replaced the URL with the new target.
- src/hg/makeDb/trackDb/xenoRefGene.html
- lines changed 1, context: html, text, full: html, text
Adjusted capitalization of journal article title to match actual journal article
- lines changed 1, context: html, text, full: html, text
Journal article URL was being redirected. Replaced URL with the new target.
- src/hg/utils/automation/Encode.pm
- lines changed 13, context: html, text, full: html, text
added switch for beta and prod assembly choices
- lines changed 13, context: html, text, full: html, text
Revert "added switch for beta and prod assembly choices"
This reverts commit fd53bd21cb46b029ddffa44ee38a9c47be116d98.
- lines changed 6, context: html, text, full: html, text
updated usage statement, and renamed variables
- src/hg/utils/automation/doRepeatMasker.pl
- lines changed 16, context: html, text, full: html, text
load a sorted fa.out file to satisify the QA ordered table check
- lines changed 1, context: html, text, full: html, text
one line too much in the head to sorted operation
- src/hg/utils/automation/makeGenomeDb.pl
- lines changed 37, context: html, text, full: html, text
eliminate teh obsolete all_mrna and all_est entries in the initial trackDb.ra file
- src/hg/utils/automation/makefile
- lines changed 22, context: html, text, full: html, text
reworked the makefiles to allow for a split pipeline
- src/inc/common.mk
- lines changed 10, context: html, text, full: html, text
reworked the makefiles to allow for a split pipeline
- src/inc/htmshell.h
- lines changed 3, context: html, text, full: html, text
add htmlTextReplaceTagsWithChar
- src/lib/htmshell.c
- lines changed 27, context: html, text, full: html, text
add htmlTextReplaceTagsWithChar
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed: 29850
- files changed: 267