All File Changes
v259_preview to v259_preview2 (2011-10-25 to 2011-11-01) v259
- python/lib/setup.py
- lines changed 0, context: html, text, full: html, text
removed execute flag on setup.py. it's now executable
- python/lib/ucscgenomics/mkChangeNotes.py
- lines changed 57, context: html, text, full: html, text
removed executable portion, fixed bug with special mdb
- lines changed 0, context: html, text, full: html, text
unsetting exectuable flag for these
- lines changed 29, context: html, text, full: html, text
moved a function out for cleanliness
- lines changed 386, context: html, text, full: html, text
refactored a bit, removed some random newlines in output
- lines changed 12, context: html, text, full: html, text
fix a reporting error in mkChangeNotes, added in fuctionality to show when newly revoked files go out as a result of a revoke and name change in one release
- lines changed 8, context: html, text, full: html, text
cleaned up output a little
- lines changed 53, context: html, text, full: html, text
pulled out functions that may be useful outside of mkChangeNotes
- lines changed 78, context: html, text, full: html, text
changed output a little, added in some some printing functions, prints out a missing tables list now also
- lines changed 22, context: html, text, full: html, text
declared some attributes earlier to bypass a qa check.
- lines changed 3, context: html, text, full: html, text
put in date notes file was generated
- lines changed 7, context: html, text, full: html, text
using correct path from dropped files
- lines changed 26, context: html, text, full: html, text
added some more human readable stuff, and put in a precheck for a condition that won't exist in release 1 mode.
- python/lib/ucscgenomics/qa.py
- lines changed 111, context: html, text, full: html, text
added some documentation, added in 2 new functions, and corrected some other stuff i noticed
- lines changed 88, context: html, text, full: html, text
reworked qa.py and separated out the executable portion into another app in encode
- lines changed 0, context: html, text, full: html, text
unsetting exectuable flag for these
- lines changed 4, context: html, text, full: html, text
added skipping of comment lines for label check
- lines changed 1, context: html, text, full: html, text
added timeout to error message
- lines changed 1, context: html, text, full: html, text
upped timeout to 20 seconds
- lines changed 22, context: html, text, full: html, text
added smarted filtering error messages
- python/lib/ucscgenomics/track.py
- lines changed 16, context: html, text, full: html, text
added in a property I needed in qaInit
- lines changed 11, context: html, text, full: html, text
added in ability to use a custom mdb
- lines changed 1, context: html, text, full: html, text
minor bug fix for composite track
- lines changed 10, context: html, text, full: html, text
added qa test dir attribute
- lines changed 22, context: html, text, full: html, text
style.txt updated, fixed merge conflict
- python/lib/ucscgenomics/ucscUtils.py
- lines changed 41, context: html, text, full: html, text
pulled out functions that may be useful outside of mkChangeNotes
- python/programs/mkChangeNotes/mkChangeNotes
- lines changed 446, context: html, text, full: html, text
merge conflict resolved
- python/programs/mkGeoPkg/mkGeoPkg
- lines changed 104, context: html, text, full: html, text
minor updates to mkGeoPkg
- lines changed 707, context: html, text, full: html, text
somehow these got removed when I pulled??? I put them back
- python/programs/qaInit/qaInit.py
- lines changed 417, context: html, text, full: html, text
merge conflict resolved
- python/programs/qaUpdateMetadata/qaUpdateMetadata
- python/programs/trackInfo/trackInfo
- lines changed 8, context: html, text, full: html, text
trackInfo now supports the bam/bai comma separated filenames, style guide updated
- lines changed 182, context: html, text, full: html, text
somehow these got removed when I pulled??? I put them back
- python/style.txt
- lines changed 30, context: html, text, full: html, text
trackInfo now supports the bam/bai comma separated filenames, style guide updated
- lines changed 36, context: html, text, full: html, text
style.txt updated, fixed merge conflict
- src/hg/das/das.c
- lines changed 16, context: html, text, full: html, text
skip tables which have "tableBrowser off" in trackDb (e.g. decipher; see redmine #5803)
- src/hg/encode/DAFs/3.0/hg19/wgEncodeBroadHistone.daf
- lines changed 5, context: html, text, full: html, text
Updated DAF to Version 1.8 to add treatment as a variable and removed peaks as required so that lab can submit controls.
- lines changed 2, context: html, text, full: html, text
Updated DAF to be correct composite which is Broad Histone.
- src/hg/encode/DAFs/3.0/hg19/wgEncodeUwRepliSeq.daf
- lines changed 2, context: html, text, full: html, text
Updated DAF say downloadOnly for Alignment files.
- src/hg/encode/encodeMkFilesList/encodeMkFilesList
- src/hg/encode/encodeQaInit/encodeQaInit
- lines changed 550, context: html, text, full: html, text
made directory work with rename
- lines changed 1, context: html, text, full: html, text
changed program name in usage
- src/hg/encode/encodeQaInit/makefile
- lines changed 27, context: html, text, full: html, text
renamed directory qaInit > encodeQaInit
- lines changed 1, context: html, text, full: html, text
made directory work with rename
- src/hg/encode/encodeQaInit/qaInit
- lines changed 550, context: html, text, full: html, text
renamed directory qaInit > encodeQaInit
- lines changed 550, context: html, text, full: html, text
made directory work with rename
- src/hg/encode/encodeQaSqlRelease/encodeQaSqlRelease
- lines changed 96, context: html, text, full: html, text
first draft (still in perl, but it doesn't need library functions, so porting is not a priority) for qa's program to insert a row into the L queue
- src/hg/encode/encodeQaSqlRelease/makefile
- lines changed 27, context: html, text, full: html, text
first draft (still in perl, but it doesn't need library functions, so porting is not a priority) for qa's program to insert a row into the L queue
- src/hg/encode/encodeReport/atticReport.sh
- src/hg/encode/encodeValidate/doEncodeValidate.pl
- lines changed 1, context: html, text, full: html, text
This is not a package that we have installed
- lines changed 1, context: html, text, full: html, text
I do not think this line should have been commented out
- lines changed 2, context: html, text, full: html, text
corrected erroneously commented out line
- src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
- lines changed 2, context: html, text, full: html, text
Swapped tissue and lineage in cell table.
- src/hg/encode/mkChangeNotes/makefile
- lines changed 27, context: html, text, full: html, text
fix a reporting error in mkChangeNotes, added in fuctionality to show when newly revoked files go out as a result of a revoke and name change in one release
- src/hg/encode/mkChangeNotes/mkChangeNotes
- lines changed 7, context: html, text, full: html, text
added in the ability to custom define a composite mdb
- src/hg/encode/mkChangeNotes/tests/CurrentMkChangeNotes.py
- lines changed 126, context: html, text, full: html, text
new testing structure for mkChangeNotes, still needs full function testing
- lines changed 411, context: html, text, full: html, text
fleshed out function tests in mkChangeTest, added in runner for currentMkchangeNotes
- lines changed 13, context: html, text, full: html, text
fix a reporting error in mkChangeNotes, added in fuctionality to show when newly revoked files go out as a result of a revoke and name change in one release
- lines changed 53, context: html, text, full: html, text
pulled out functions that may be useful outside of mkChangeNotes
- lines changed 123, context: html, text, full: html, text
updated test to reflect newer version of mkChangenotes
- src/hg/encode/mkChangeNotes/tests/mkChangeTest
- lines changed 83, context: html, text, full: html, text
fleshed out function tests in mkChangeTest, added in runner for currentMkchangeNotes
- src/hg/encode/mkChangeNotes/tests/mkChangeTest.py
- lines changed 36, context: html, text, full: html, text
new testing structure for mkChangeNotes, still needs full function testing
- lines changed 72, context: html, text, full: html, text
fleshed out function tests in mkChangeTest, added in runner for currentMkchangeNotes
- src/hg/encode/mkChangeNotes/tests/release1test/wgEncodeTest.ra
- lines changed 73, context: html, text, full: html, text
fleshed out function tests in mkChangeTest, added in runner for currentMkchangeNotes
- src/hg/encode/mkChangeNotes/tests/release2test/wgEncodeTest.ra
- lines changed 143, context: html, text, full: html, text
fleshed out function tests in mkChangeTest, added in runner for currentMkchangeNotes
- src/hg/encode/mkChangeNotes/tests/release3test/wgEncodeTest.ra
- lines changed 145, context: html, text, full: html, text
fleshed out function tests in mkChangeTest, added in runner for currentMkchangeNotes
- src/hg/encode/mkChangeNotes/tests/release4test/wgEncodeTest.ra
- lines changed 173, context: html, text, full: html, text
fleshed out function tests in mkChangeTest, added in runner for currentMkchangeNotes
- src/hg/encode/mkChangeNotes/tests/testRunner
- lines changed 61, context: html, text, full: html, text
fleshed out function tests in mkChangeTest, added in runner for currentMkchangeNotes
- src/hg/encode/mkGeoPkg/mkGeoPkg
- lines changed 707, context: html, text, full: html, text
style.txt updated, fixed merge conflict
- src/hg/encode/qaEncodeTracks2/qaEncodeTracks
- lines changed 67, context: html, text, full: html, text
reworked qa.py and separated out the executable portion into another app in encode
- lines changed 14, context: html, text, full: html, text
added in delimiters for human readibility in script output
- src/hg/encode/qaInit/makefile
- lines changed 27, context: html, text, full: html, text
fix a reporting error in mkChangeNotes, added in fuctionality to show when newly revoked files go out as a result of a revoke and name change in one release
- lines changed 27, context: html, text, full: html, text
renamed directory qaInit > encodeQaInit
- src/hg/encode/qaInit/qaInit
- lines changed 60, context: html, text, full: html, text
added in qa checks from ported qaEncodeTracks
- lines changed 17, context: html, text, full: html, text
bug fixes and added in ability to use custom mdb names
- lines changed 3, context: html, text, full: html, text
added in switch to take errors in local mkChangeNotes data into account
- lines changed 2, context: html, text, full: html, text
Changing the error message and made it not fatal
- lines changed 45, context: html, text, full: html, text
last draft before reviewing for qaInit, added test mode, print out list of subIds
- lines changed 23, context: html, text, full: html, text
changed what initdate means, added function to keep it rolling along everytime init is run
- lines changed 550, context: html, text, full: html, text
renamed directory qaInit > encodeQaInit
- src/hg/encode/qaUpdateMetadata/qaUpdateMetadata
- src/hg/encode/trackInfo/trackInfo
- lines changed 182, context: html, text, full: html, text
style.txt updated, fixed merge conflict
- src/hg/hgApi/hgApi.c
- lines changed 21, context: html, text, full: html, text
Add filtering by assembly
- src/hg/hgFileSearch/hgFileSearch.c
- src/hg/hgHubConnect/hgHubConnect.c
- lines changed 3, context: html, text, full: html, text
note that a routine consumes one of its arguments. om nom nom. #5754
- lines changed 1, context: html, text, full: html, text
added a little snippet of HTML per Greg
- src/hg/hgTrackUi/hgTrackUi.c
- lines changed 44, context: html, text, full: html, text
Long overdue checkboxes added to superTrack config page.
- lines changed 2, context: html, text, full: html, text
Minor fix for turning off SUPERS_WITH_CHECKBOXES
- lines changed 2, context: html, text, full: html, text
Fixed bug where rightClick popup cfg sometimes had wrong visibility
- lines changed 1, context: html, text, full: html, text
Add limited support for bigBeds to have scoreFilter controls.
- src/hg/hgTracks/config.c
- lines changed 6, context: html, text, full: html, text
Long overdue checkboxes added to superTrack config page.
- src/hg/hgTracks/cytoBandTrack.c
- src/hg/hgTracks/hgTracks.c
- src/hg/hgTracks/imageV2.c
- src/hg/hgTracks/rmskTrack.c
- lines changed 9, context: html, text, full: html, text
MLQ #5795 (question mark in repeats table): user asked about the ?'s thatappear at the end of some repClass and repFamily names in rmsk. I asked
Robert Hubley and he said they are just an indication that a new repeat is
suspected to be in some class but hasn't been confirmed yet. He suggested
ignoring the ?. I looked at rmskTrack.c and found that the ? at end was
causing such items to default to the Other category. This change strips
a trailing ? from the class name that we look up in the hash (but leaves
it in the ro.repClass field because that's used for the mouseover title).
Now if repClass is "DNA?" the item will still be drawn in the DNA row.
- src/hg/hgTracks/searchTracks.c
- src/hg/hgTracks/vcfTrack.c
- lines changed 102, context: html, text, full: html, text
merge conflict resolved
- src/hg/hgc/hgc.c
- lines changed 2, context: html, text, full: html, text
Create lincRNAs supertrack
- lines changed 1, context: html, text, full: html, text
Rename track lincRNAsIsoforms to lincRNAsTranscripts
- lines changed 2, context: html, text, full: html, text
Changed punctuation in two places to match commit 39c3f339e5b.
- src/hg/htdocs/ENCODE/dataMatrix/chipMatrix.css
- src/hg/htdocs/ENCODE/dataMatrix/dataMatrix.css
- lines changed 39, context: html, text, full: html, text
1. Add panel of radiobuttons to select track or file search 2. Extensive cleanup
- lines changed 2, context: html, text, full: html, text
1. Add spinner while ajax data is loading 2. Clean up ChIP Matrix similarly to others
- src/hg/htdocs/ENCODE/dataMatrix/dataSummary.css
- lines changed 12, context: html, text, full: html, text
1. Add panel of radiobuttons to select track or file search 2. Extensive cleanup
- src/hg/htdocs/ENCODE/dataMatrix/encodeChipMatrixHuman.html
- src/hg/htdocs/ENCODE/dataMatrix/encodeChipMatrixInclude.html
- lines changed 1, context: html, text, full: html, text
Checking in jquery floating table header plugin, and ENCODE data matrix implementations that now use it
- lines changed 25, context: html, text, full: html, text
1. Add spinner while ajax data is loading 2. Clean up ChIP Matrix similarly to others
- lines changed 1, context: html, text, full: html, text
Add filtering by assembly
- src/hg/htdocs/ENCODE/dataMatrix/encodeChipMatrixMouse.html
- src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixHuman.html
- src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixInclude.html
- lines changed 1, context: html, text, full: html, text
Checking in jquery floating table header plugin, and ENCODE data matrix implementations that now use it
- lines changed 20, context: html, text, full: html, text
1. Add panel of radiobuttons to select track or file search 2. Extensive cleanup
- lines changed 2, context: html, text, full: html, text
1. Add spinner while ajax data is loading 2. Clean up ChIP Matrix similarly to others
- lines changed 1, context: html, text, full: html, text
Add filtering by assembly
- src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixMouse.html
- src/hg/htdocs/ENCODE/dataMatrix/encodeDataSummaryHuman.html
- src/hg/htdocs/ENCODE/dataMatrix/encodeDataSummaryInclude.html
- lines changed 11, context: html, text, full: html, text
1. Add panel of radiobuttons to select track or file search 2. Extensive cleanup
- lines changed 2, context: html, text, full: html, text
1. Add spinner while ajax data is loading 2. Clean up ChIP Matrix similarly to others
- lines changed 1, context: html, text, full: html, text
Add filtering by assembly
- src/hg/htdocs/ENCODE/dataMatrix/encodeDataSummaryMouse.html
- src/hg/htdocs/ENCODE/downloads.html
- src/hg/htdocs/ENCODE/experiment_guidelines.html
- src/hg/htdocs/ENCODE/platform_characterization.html
- lines changed 19, context: html, text, full: html, text
related to redmine ticket 5523
- src/hg/htdocs/ENCODE/pubs.html
- lines changed 38, context: html, text, full: html, text
readded seperator lines, moved an entry around
- lines changed 38, context: html, text, full: html, text
This is related to ticket 5526 adding the publications
- lines changed 109, context: html, text, full: html, text
converted to new encode format, updated old html tags, and fixed a character that need to be in ascii format, redmine# 5526
- lines changed 88, context: html, text, full: html, text
The first 2 sections of this are ordered.
- lines changed 754, context: html, text, full: html, text
Large amounts of citations were added and sorted.
- src/hg/htdocs/ENCODE/releaseLog.html
- src/hg/htdocs/FAQ/FAQformat.html
- lines changed 2, context: html, text, full: html, text
Commented out reference to the VCF format page which is not yet active on the RR
- lines changed 7, context: html, text, full: html, text
Changing wording on score handling
- src/hg/htdocs/goldenPath/help/customTrackText.html
- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
- src/hg/htdocs/goldenPath/pubs.html
- src/hg/htdocs/goldenPath/releaseLog.html
- src/hg/htdocs/indexNews.html
- src/hg/htdocs/staff.html
- src/hg/htdocs/style/encodeProject.css
- lines changed 3, context: html, text, full: html, text
Checking in jquery floating table header plugin, and ENCODE data matrix implementations that now use it
- lines changed 26, context: html, text, full: html, text
1. Add panel of radiobuttons to select track or file search 2. Extensive cleanup
- lines changed 9, context: html, text, full: html, text
1. Add spinner while ajax data is loading 2. Clean up ChIP Matrix similarly to others
- lines changed 6, context: html, text, full: html, text
Add filtering by assembly
- src/hg/inc/jsHelper.h
- src/hg/inc/vcfUi.h
- src/hg/js/ajax.js
- src/hg/js/encodeChipMatrix.js
- lines changed 32, context: html, text, full: html, text
Checking in jquery floating table header plugin, and ENCODE data matrix implementations that now use it
- lines changed 4, context: html, text, full: html, text
1. Add panel of radiobuttons to select track or file search 2. Extensive cleanup
- lines changed 93, context: html, text, full: html, text
1. Add spinner while ajax data is loading 2. Clean up ChIP Matrix similarly to others
- lines changed 32, context: html, text, full: html, text
Add filtering by assembly
- src/hg/js/encodeDataMatrix.js
- lines changed 37, context: html, text, full: html, text
Checking in jquery floating table header plugin, and ENCODE data matrix implementations that now use it
- lines changed 111, context: html, text, full: html, text
1. Add panel of radiobuttons to select track or file search 2. Extensive cleanup
- lines changed 11, context: html, text, full: html, text
1. Add spinner while ajax data is loading 2. Clean up ChIP Matrix similarly to others
- lines changed 35, context: html, text, full: html, text
Add filtering by assembly
- src/hg/js/encodeDataSummary.js
- lines changed 43, context: html, text, full: html, text
1. Add panel of radiobuttons to select track or file search 2. Extensive cleanup
- lines changed 9, context: html, text, full: html, text
1. Add spinner while ajax data is loading 2. Clean up ChIP Matrix similarly to others
- lines changed 55, context: html, text, full: html, text
Add filtering by assembly
- src/hg/js/encodeProject.js
- lines changed 27, context: html, text, full: html, text
1. Add panel of radiobuttons to select track or file search 2. Extensive cleanup
- lines changed 23, context: html, text, full: html, text
Add filtering by assembly
- src/hg/js/hgCustom.js
- src/hg/js/hgTracks.js
- lines changed 1956, context: html, text, full: html, text
merge conflict resolved
- lines changed 5, context: html, text, full: html, text
replace some instances of $(#...) with document.getElementById to deal with possible metacharacter in track names
- src/hg/js/hui.js
- lines changed 93, context: html, text, full: html, text
Long overdue checkboxes added to superTrack config page.
- src/hg/js/jquery.floatheader-min.js
- lines changed 143, context: html, text, full: html, text
Checking in jquery floating table header plugin, and ENCODE data matrix implementations that now use it
- src/hg/js/jquery.floatheader.js
- lines changed 282, context: html, text, full: html, text
Checking in jquery floating table header plugin, and ENCODE data matrix implementations that now use it
- src/hg/js/makefile
- lines changed 1, context: html, text, full: html, text
Checking in jquery floating table header plugin, and ENCODE data matrix implementations that now use it
- lines changed 2, context: html, text, full: html, text
Merge branch 'master' into matrix
- src/hg/lib/fileUi.c
- lines changed 37, context: html, text, full: html, text
No functional change. Just better commenting and some name changing as requested by Brian in code review.
- src/hg/lib/hdb.c
- lines changed 1, context: html, text, full: html, text
To resolve Redmine # 1118, repeating domain links. The issue is that when a protein has multiple instances of the same domain, the known gene details page shows multiple (redundant) links to the domain entry. Resolved this by replacing a 'select' statement with a 'select distinct'
- src/hg/lib/hui.c
- lines changed 12, context: html, text, full: html, text
Add limited support for bigBeds to have scoreFilter controls.
- src/hg/lib/jsHelper.c
- src/hg/lib/search.c
- src/hg/lib/trackDbCustom.c
- lines changed 1, context: html, text, full: html, text
Add limited support for bigBeds to have scoreFilter controls.
- src/hg/lib/vcfUi.c
- src/hg/lib/web.c
- lines changed 280, context: html, text, full: html, text
remove obsolete TOO_TIMID_FOR_CURRENT_HTML_STANDARDS code (code cleanup to get ready for jabico related menu redesign)
- lines changed 3, context: html, text, full: html, text
This should be a safe change to js and css links in the CGI ouutput. It will eliminate problems with htmlCheck linkChecker.
- lines changed 44, context: html, text, full: html, text
add NEW_MENUS code to experiment with using jabico derived menus (see redmine #5245)
- src/hg/makeDb/doc/bosTau4.txt
- src/hg/makeDb/doc/bosTau6.txt
- src/hg/makeDb/doc/calJac3.txt
- lines changed 15, context: html, text, full: html, text
finishing up the lastz runs to gorGor3
- src/hg/makeDb/doc/encodeDccEncodetest/wgEncodeTest.release1.notes
- lines changed 60, context: html, text, full: html, text
notes location for encodeTest
- src/hg/makeDb/doc/encodeDccEncodetest/wgEncodeTest.release2.notes
- lines changed 117, context: html, text, full: html, text
notes location for encodeTest
- src/hg/makeDb/doc/encodeDccEncodetest/wgEncodeTest.release3.notes
- lines changed 119, context: html, text, full: html, text
notes location for encodeTest
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeCaltechRnaSeq.release2.notes
- lines changed 1503, context: html, text, full: html, text
added some more human readable stuff, and put in a precheck for a condition that won't exist in release 1 mode.
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeMapability.release3.notes
- lines changed 120, context: html, text, full: html, text
Newer version of mkChangeNotes generated this one. However, it is hand edited to compensate for minor discrepency
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeRikenCage.release2.notes
- lines changed 1418, context: html, text, full: html, text
Fixing the long labels and removing the preamble from the notes file
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhTfbs.release1.notes
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwAffyExonArray.release2.notes
- lines changed 395, context: html, text, full: html, text
added some more human readable stuff, and put in a precheck for a condition that won't exist in release 1 mode.
- src/hg/makeDb/doc/encodeDccMm9/wgEncodeCaltechHist.release1.notes
- lines changed 178, context: html, text, full: html, text
merge conflict resolved
- lines changed 35, context: html, text, full: html, text
added some more human readable stuff, and put in a precheck for a condition that won't exist in release 1 mode.
- src/hg/makeDb/doc/encodeDccMm9/wgEncodeCaltechTfbs.release1.notes
- lines changed 284, context: html, text, full: html, text
merge conflict resolved
- lines changed 49, context: html, text, full: html, text
added some more human readable stuff, and put in a precheck for a condition that won't exist in release 1 mode.
- src/hg/makeDb/doc/gorGor3.txt
- lines changed 40, context: html, text, full: html, text
done with Chimp and Orangutan lastz
- lines changed 97, context: html, text, full: html, text
finishing up the lastz runs to gorGor3
- src/hg/makeDb/doc/hg18.txt
- src/hg/makeDb/doc/hg19.txt
- lines changed 150, context: html, text, full: html, text
merge conflict resolved
- src/hg/makeDb/doc/melGal1.txt
- src/hg/makeDb/doc/nomLeu1.txt
- lines changed 24, context: html, text, full: html, text
finishing up the lastz runs to gorGor3
- src/hg/makeDb/doc/panTro3.txt
- lines changed 30, context: html, text, full: html, text
finishing up the lastz runs to gorGor3
- src/hg/makeDb/doc/ponAbe2.txt
- lines changed 7, context: html, text, full: html, text
finished with lastz gorGor3 to rheMac2 and ponAbe2
- src/hg/makeDb/doc/rheMac2.txt
- lines changed 7, context: html, text, full: html, text
finished with lastz gorGor3 to rheMac2 and ponAbe2
- src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
- src/hg/makeDb/genbank/etc/align.dbs
- src/hg/makeDb/genbank/etc/genbank.conf
- src/hg/makeDb/genbank/etc/hgwbeta.dbs
- lines changed 3, context: html, text, full: html, text
Added melGal1, myoLuc2 and xenTro3
- src/hg/makeDb/genbank/etc/hgwdev.dbs
- src/hg/makeDb/genbank/etc/rr.dbs
- lines changed 4, context: html, text, full: html, text
Added bosTau6, melGal1, myoLuc2 and xenTro3
- src/hg/makeDb/hgCgiData/Human/microarrayGroups.ra
- lines changed 13, context: html, text, full: html, text
Initial set up for expression data of lincRNAs
- lines changed 10, context: html, text, full: html, text
Group lincRNAs microarray data
- src/hg/makeDb/hgKgGetText/hgKgGetText.c
- src/hg/makeDb/schema/all.joiner
- lines changed 1, context: html, text, full: html, text
Track #34 (dbVar/ISCA): added isca% to tablesIgnored $hg.
- src/hg/makeDb/trackDb/cat/felCat3/trackDb.ra
- lines changed 4, context: html, text, full: html, text
fixup sgpGene searchTable rule to match these scaffold names
- src/hg/makeDb/trackDb/chicken/trackDb.chainNet.ra
- src/hg/makeDb/trackDb/cow/bosTau4/trackDb.ra
- lines changed 13, context: html, text, full: html, text
fixup checkHgFindSpec errors
- src/hg/makeDb/trackDb/cow/bosTau6/description.html
- lines changed 2, context: html, text, full: html, text
Temporarily commented out 'pseudogene mRNA' sample query from gateway page
- src/hg/makeDb/trackDb/cow/trackDb.chainNet.ra
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 140, context: html, text, full: html, text
merge conflict resolved
- lines changed 17, context: html, text, full: html, text
Adding TCF4 details to clear up ambiguity with TCF7L2
- lines changed 1, context: html, text, full: html, text
Adding more TCF-4 detail to description
- lines changed 1, context: html, text, full: html, text
Adding more TCF7L2 detail to description
- lines changed 20, context: html, text, full: html, text
Adding CD14 stanza for tier 2 cells from second draw
- lines changed 434, context: html, text, full: html, text
A was trying to change the antibodies to have the target description, see ticket #1017, I ended up having a very difficult merge conflict surrounding the doner IDs. I think Jeff needs to look at this
- lines changed 442, context: html, text, full: html, text
Adding CD14, Removing redundant redundancies, CaPiToLiZaTiOn stuff
- lines changed 129, context: html, text, full: html, text
CaPiToLiZaTiOn and more redundant redundanciesremoved
- src/hg/makeDb/trackDb/cv/beta/cv.ra
- src/hg/makeDb/trackDb/cv/public/cv.ra
- lines changed 22, context: html, text, full: html, text
pushing reviewed cv.ra changes to public
- lines changed 2, context: html, text, full: html, text
copying over fixes from code review Jeff made in beta/cv.ra
- src/hg/makeDb/trackDb/dog/trackDb.chainNet.ra
- src/hg/makeDb/trackDb/drosophila/dm2/trackDb.ra
- lines changed 4, context: html, text, full: html, text
fixup nscanGene checkHgFindSpec
- src/hg/makeDb/trackDb/drosophila/dm3/trackDb.ra
- lines changed 31, context: html, text, full: html, text
fixup ensGene and flyBase gene search rules to match the new patterns
- src/hg/makeDb/trackDb/drosophila/trackDb.ra
- lines changed 2, context: html, text, full: html, text
fixup ensGene and flyBase gene search rules to match the new patterns
- src/hg/makeDb/trackDb/fugu/fr1/trackDb.ra
- lines changed 32, context: html, text, full: html, text
update ensGene search rules to work with the Ensembl naming pattern here
- src/hg/makeDb/trackDb/human/encodeTest/metaDb/alpha/makefile
- lines changed 7, context: html, text, full: html, text
putting in structure for the new encodeTest database
- src/hg/makeDb/trackDb/human/encodeTest/metaDb/alpha/wgEncodeTest1.ra
- lines changed 72, context: html, text, full: html, text
putting in structure for the new encodeTest database
- src/hg/makeDb/trackDb/human/encodeTest/metaDb/alpha/wgEncodeTest2.ra
- lines changed 143, context: html, text, full: html, text
putting in structure for the new encodeTest database
- src/hg/makeDb/trackDb/human/encodeTest/metaDb/alpha/wgEncodeTest3.ra
- lines changed 145, context: html, text, full: html, text
putting in structure for the new encodeTest database
- src/hg/makeDb/trackDb/human/encodeTest/metaDb/alpha/wgEncodeTest4.ra
- lines changed 173, context: html, text, full: html, text
putting in structure for the new encodeTest database
- src/hg/makeDb/trackDb/human/encodeTest/metaDb/beta/makefile
- lines changed 7, context: html, text, full: html, text
putting in structure for the new encodeTest database
- src/hg/makeDb/trackDb/human/encodeTest/metaDb/beta/wgEncodeTest1.ra
- lines changed 0, context: html, text, full: html, text
putting in structure for the new encodeTest database
- src/hg/makeDb/trackDb/human/encodeTest/metaDb/beta/wgEncodeTest2.ra
- lines changed 73, context: html, text, full: html, text
putting in structure for the new encodeTest database
- src/hg/makeDb/trackDb/human/encodeTest/metaDb/beta/wgEncodeTest3.ra
- lines changed 143, context: html, text, full: html, text
putting in structure for the new encodeTest database
- src/hg/makeDb/trackDb/human/encodeTest/metaDb/beta/wgEncodeTest4.ra
- lines changed 145, context: html, text, full: html, text
putting in structure for the new encodeTest database
- src/hg/makeDb/trackDb/human/encodeTest/metaDb/public/makefile
- lines changed 7, context: html, text, full: html, text
putting in structure for the new encodeTest database
- src/hg/makeDb/trackDb/human/encodeTest/metaDb/public/wgEncodeTest.ra
- lines changed 145, context: html, text, full: html, text
putting in structure for the new encodeTest database
- src/hg/makeDb/trackDb/human/encodeTest/metaDb/public/wgEncodeTest1.ra
- lines changed 0, context: html, text, full: html, text
putting in structure for the new encodeTest database
- src/hg/makeDb/trackDb/human/encodeTest/metaDb/public/wgEncodeTest2.ra
- lines changed 73, context: html, text, full: html, text
putting in structure for the new encodeTest database
- src/hg/makeDb/trackDb/human/encodeTest/metaDb/public/wgEncodeTest3.ra
- lines changed 143, context: html, text, full: html, text
putting in structure for the new encodeTest database
- src/hg/makeDb/trackDb/human/encodeTest/metaDb/public/wgEncodeTest4.ra
- lines changed 145, context: html, text, full: html, text
putting in structure for the new encodeTest database
- src/hg/makeDb/trackDb/human/encodeTest/metaDb/testRelease1/wgEncodeTest.ra
- lines changed 73, context: html, text, full: html, text
putting in structure for the new encodeTest database
- src/hg/makeDb/trackDb/human/encodeTest/metaDb/testRelease2/wgEncodeTest.ra
- lines changed 143, context: html, text, full: html, text
putting in structure for the new encodeTest database
- src/hg/makeDb/trackDb/human/encodeTest/metaDb/testRelease3/wgEncodeTest.ra
- lines changed 145, context: html, text, full: html, text
putting in structure for the new encodeTest database
- src/hg/makeDb/trackDb/human/encodeTest/metaDb/testRelease4/wgEncodeTest.ra
- lines changed 173, context: html, text, full: html, text
putting in structure for the new encodeTest database
- src/hg/makeDb/trackDb/human/encodeTest/trackDb.wgEncode.ra
- lines changed 1, context: html, text, full: html, text
putting in structure for the new encodeTest database
- src/hg/makeDb/trackDb/human/encodeTest/wgEncodeTest.html
- lines changed 0, context: html, text, full: html, text
putting in structure for the new encodeTest database
- src/hg/makeDb/trackDb/human/encodeTest/wgEncodeTest.ra
- lines changed 0, context: html, text, full: html, text
putting in structure for the new encodeTest database
- src/hg/makeDb/trackDb/human/encodeTest/wgEncodeTest1.html
- lines changed 0, context: html, text, full: html, text
putting in structure for the new encodeTest database
- src/hg/makeDb/trackDb/human/encodeTest/wgEncodeTest1.ra
- lines changed 0, context: html, text, full: html, text
putting in structure for the new encodeTest database
- src/hg/makeDb/trackDb/human/encodeTest/wgEncodeTest2.html
- lines changed 0, context: html, text, full: html, text
putting in structure for the new encodeTest database
- src/hg/makeDb/trackDb/human/encodeTest/wgEncodeTest2.ra
- lines changed 0, context: html, text, full: html, text
putting in structure for the new encodeTest database
- src/hg/makeDb/trackDb/human/encodeTest/wgEncodeTest3.html
- lines changed 0, context: html, text, full: html, text
putting in structure for the new encodeTest database
- src/hg/makeDb/trackDb/human/encodeTest/wgEncodeTest3.ra
- lines changed 0, context: html, text, full: html, text
putting in structure for the new encodeTest database
- src/hg/makeDb/trackDb/human/geneReviews.html
- lines changed 23, context: html, text, full: html, text
Edit html based on feedback from Lauren
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
- lines changed 268, context: html, text, full: html, text
merge conflict resolved
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeChromatinMap.ra
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaChipSeq.ra
- lines changed 24, context: html, text, full: html, text
Meta-data for depercated file was left in by accident. Redmine 4558.
- src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeCaltechRnaSeq.ra
- lines changed 856, context: html, text, full: html, text
merge conflict resolved
- src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeChromatinMap.ra
- lines changed 541, context: html, text, full: html, text
merge conflict resolved
- src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeCaltechRnaSeq.ra
- lines changed 856, context: html, text, full: html, text
merge conflict resolved
- src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeChromatinMap.ra
- lines changed 541, context: html, text, full: html, text
merge conflict resolved
- src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.new.ra
- lines changed 1256, context: html, text, full: html, text
merge conflict resolved
- src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.ra
- src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.new.html
- src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.new.ra
- src/hg/makeDb/trackDb/human/hg19/cosmic.html
- lines changed 10, context: html, text, full: html, text
Made all the listed URLs into actual links from the text. Corrected a couple target+ attributes. Added some css obfuscation to the listed email address.
- lines changed 58, context: html, text, full: html, text
Created a hard wrap to 100 characters. Added missing <p> and </p> tags. Set html tags to lower case.
- lines changed 19, context: html, text, full: html, text
Added missing </li> tags. Cleaned up citations.
- lines changed 1, context: html, text, full: html, text
Cleaned up one non-standard character.
- src/hg/makeDb/trackDb/human/hg19/lincRNAs.ra
- lines changed 64, context: html, text, full: html, text
Create lincRNAs supertrack
- lines changed 175, context: html, text, full: html, text
finished lincRNAs with shadesOfSea color
- lines changed 6, context: html, text, full: html, text
Rename track lincRNAsIsoforms to lincRNAsTranscripts
- lines changed 8, context: html, text, full: html, text
Changed many lables names for lincRNAs
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
- lines changed 1, context: html, text, full: html, text
Added metadata file for Uw Repli-seq track to makefile.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
- lines changed 5980, context: html, text, full: html, text
Add 46 submission for track's second release. Redmine #4145.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
- lines changed 59, context: html, text, full: html, text
Removing duplicate objects
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV4.ra
- lines changed 1, context: html, text, full: html, text
Related to ticket 5577, removing some obsolete objects and changing a table name
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisChiaPet.ra
- lines changed 43, context: html, text, full: html, text
Related to ticket 5577, removing some obsolete objects and changing a table name
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethyl450.ra
- lines changed 103, context: html, text, full: html, text
merge conflict resolved
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylSeq.ra
- lines changed 253, context: html, text, full: html, text
removed 12 objects - Willy via Cricket
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
- lines changed 301, context: html, text, full: html, text
added in geo accessions - Willy
- lines changed 3, context: html, text, full: html, text
Removing to incoorect geoNumbers
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
- lines changed 348, context: html, text, full: html, text
merge conflict resolved
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeReg.ra
- lines changed 4, context: html, text, full: html, text
There was a duplicate object in here
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
- lines changed 133, context: html, text, full: html, text
merge conflict resolved
- lines changed 867, context: html, text, full: html, text
Fixes Redmine #69
1. Fixed ordering of antibodies to be alphabetical AP-2α, AP-2γ then ATF3
2. Updated origAssembly. Inaddition added expVar for K562/JunD experiment that was missing it.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwAffyExonArray.ra
- lines changed 51, context: html, text, full: html, text
Removing geoAccessions from the trackDB display and adding expIds
- lines changed 26, context: html, text, full: html, text
Adding md5sums and changing hgFileUi columns
- lines changed 34, context: html, text, full: html, text
Removing treatment=None to be consistent with previous entires
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwRepliSeq.ra
- lines changed 5587, context: html, text, full: html, text
Added meta-data and initial display of peaks and Valley's as bed 9 files. Redmine 4577.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
- lines changed 83, context: html, text, full: html, text
fixed control metadata terms
- lines changed 742, context: html, text, full: html, text
added treatment = None for items that needed it
- lines changed 741, context: html, text, full: html, text
added in None for treatment field in controlId
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeCshlLongRnaSeq.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeGencode.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeMapability.ra
- lines changed 104, context: html, text, full: html, text
merge conflict resolved
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSydhTfbs.ra
- lines changed 357, context: html, text, full: html, text
merge conflict resolved
- lines changed 867, context: html, text, full: html, text
moving metadata changes to beta: added missing origAssembly, dccAccessions, expId
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwDnase.ra
- lines changed 654, context: html, text, full: html, text
merge conflict resolved
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
- lines changed 1, context: html, text, full: html, text
moving metatdata to public in preparation for release, redmine #69
- lines changed 1, context: html, text, full: html, text
adding '\' separator because make public wasn't working
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeCshlLongRnaSeq.ra
- lines changed 35579, context: html, text, full: html, text
merge conflict resolved
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeGencode.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeGisRnaPet.ra
- lines changed 3550, context: html, text, full: html, text
merge conflict resolved
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeMapability.ra
- lines changed 104, context: html, text, full: html, text
releasing mapability track, redmine #3138
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeSydhTfbs.ra
- lines changed 50560, context: html, text, full: html, text
moving metatdata to public in preparation for release, redmine #69
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwDnase.ra
- lines changed 4672, context: html, text, full: html, text
merge conflict resolved
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 16, context: html, text, full: html, text
Initial set up for expression data of lincRNAs
- lines changed 1, context: html, text, full: html, text
Add lincRNAs.html for track description
- lines changed 12, context: html, text, full: html, text
Covert the lincRNAs custom track to native UCSC GB track
- lines changed 1, context: html, text, full: html, text
anoCar2 to dino alignment
- lines changed 1, context: html, text, full: html, text
initital work to use composite tracks for lincRNAs.
- lines changed 24, context: html, text, full: html, text
finished lincRNAs with shadesOfSea color
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- lines changed 3, context: html, text, full: html, text
Preliminary comitting the Replication Seq Timing data. Redmine #4577.
- lines changed 2, context: html, text, full: html, text
releasing mapability track, redmine #3138
- lines changed 3, context: html, text, full: html, text
Staging a new release 3 for this composite.
- lines changed 4, context: html, text, full: html, text
added new release for HaibGenotype composite
- lines changed 2, context: html, text, full: html, text
adding new release for CshlLong
- lines changed 5, context: html, text, full: html, text
Merge branch 'master' into UwReliSeq
- src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.new.ra
- lines changed 1088, context: html, text, full: html, text
Add 46 submission for track's second release. Redmine #4145.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.html
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.new.html
- lines changed 174, context: html, text, full: html, text
adding new release for CshlLong
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.new.ra
- lines changed 4635, context: html, text, full: html, text
adding new release for CshlLong
- src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.new.html
- lines changed 1, context: html, text, full: html, text
Staging a new release 3 for this composite.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.ra
- lines changed 8, context: html, text, full: html, text
removed duplicate lines, I am not sure how this worked with this trackless stanza before, but those lines were redundant
- lines changed 1, context: html, text, full: html, text
Added back track line for track wgEncodeGisRnaPetNhekNucleusPapAlnRep.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.new.html
- lines changed 82, context: html, text, full: html, text
added new release for HaibGenotype composite
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.new.ra
- lines changed 735, context: html, text, full: html, text
added new release for HaibGenotype composite
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.html
- lines changed 6, context: html, text, full: html, text
Cleaning up labels and such
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl450.ra
- lines changed 196, context: html, text, full: html, text
Cleaning up labels and such
- src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.html
- lines changed 107, context: html, text, full: html, text
releasing mapability track, redmine #3138
- src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.new.html
- lines changed 1, context: html, text, full: html, text
changed released date for mapability track, redmine# 3138
- src/hg/makeDb/trackDb/human/hg19/wgEncodeMapability.ra
- lines changed 100, context: html, text, full: html, text
releasing mapability track, redmine #3138
- src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
- lines changed 6, context: html, text, full: html, text
removing visibility lines from multiWig container stanzas because they don't control the visibility and just add confusion. The visibility of the container tracks is controlled by the the superTrack line which has the visibility of the container at the end of the line, e.g. the multiWig stanza would have a line like: superTrack wgEncodeReg hide, redmine 5713, note 4
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.ra
- lines changed 138, context: html, text, full: html, text
Fixing the long labels and removing the preamble from the notes file
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.html
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.new.ra
- lines changed 593, context: html, text, full: html, text
Fixed errors found in Redmine #69
1. Updated the longLabels to be consnsitent with the terminology ChIP-seq instead of ChIP-Seq.
2. Removed nextItem button
3. Fixed so that all MCF10A-Er-Src stated control Standard as does its meta-data
4. Updated the track wgEncodeSydhTfbsGm12878Znf274StdSig to use the standard color for GM12878 cell line "153,38,0"
- lines changed 1, context: html, text, full: html, text
Fixes Redmine #69
1. Fixed ordering of antibodies to be alphabetical AP-2α, AP-2γ then ATF3
2. Updated origAssembly. Inaddition added expVar for K562/JunD experiment that was missing it.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
- lines changed 595, context: html, text, full: html, text
Fixed errors found in Redmine #69
1. Updated the longLabels to be consnsitent with the terminology ChIP-seq instead of ChIP-Seq.
2. Removed nextItem button
3. Fixed so that all MCF10A-Er-Src stated control Standard as does its meta-data
4. Updated the track wgEncodeSydhTfbsGm12878Znf274StdSig to use the standard color for GM12878 cell line "153,38,0"
- lines changed 1, context: html, text, full: html, text
Fixes Redmine #69
1. Fixed ordering of antibodies to be alphabetical AP-2α, AP-2γ then ATF3
2. Updated origAssembly. Inaddition added expVar for K562/JunD experiment that was missing it.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProtFasp.html
- lines changed 147, context: html, text, full: html, text
Making the super track correct and adding the base of a track description
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProtFasp.ra
- lines changed 2, context: html, text, full: html, text
Making the super track correct and adding the base of a track description
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.new.html
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.new.ra
- lines changed 135, context: html, text, full: html, text
Removing geoAccessions from the trackDB display and adding expIds
- lines changed 1, context: html, text, full: html, text
Adding md5sums and changing hgFileUi columns
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.html
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.html
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.ra
- lines changed 493, context: html, text, full: html, text
merge conflict resolved
- lines changed 4, context: html, text, full: html, text
Updated tags for CD20 cell line to not include +, as configuration can only handle alphanumeric tags.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.ra
- lines changed 916, context: html, text, full: html, text
merge conflict resolved
- lines changed 8, context: html, text, full: html, text
Fixing the no speacial characters in the tags rule
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwRepliSeq.ra
- lines changed 1198, context: html, text, full: html, text
Preliminary comitting the Replication Seq Timing data. Redmine #4577.
- lines changed 219, context: html, text, full: html, text
Added meta-data and initial display of peaks and Valley's as bed 9 files. Redmine 4577.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.ra
- src/hg/makeDb/trackDb/human/iscaComposite.html
- lines changed 135, context: html, text, full: html, text
merge conflict resolved
- lines changed 5, context: html, text, full: html, text
Fixed a reference, fixed some grammar/punctuation. Redmine #5752.
- src/hg/makeDb/trackDb/human/iscaRetrospectiveComposite.html
- lines changed 123, context: html, text, full: html, text
merge conflict resolved
- src/hg/makeDb/trackDb/human/trackDb.chainNet.ra
- src/hg/makeDb/trackDb/human/trackDb.ra
- src/hg/makeDb/trackDb/lizard/trackDb.chainNet.ra
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechHist.ra
- lines changed 127, context: html, text, full: html, text
Updated expId's and dccAccession for 2 tracks. Redmine #4155 and #4154.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechTfbs.ra
- lines changed 122, context: html, text, full: html, text
merge conflict resolved
- lines changed 247, context: html, text, full: html, text
Updated expId's and dccAccession for 2 tracks. Redmine #4155 and #4154.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuHistone.ra
- lines changed 2431, context: html, text, full: html, text
Added 10 submission, three of which were previously submitted 3041,3042,3043. Redmine #111.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
- lines changed 817, context: html, text, full: html, text
Added 3 submissions for track. Redmine #110.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/makefile
- src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechHist.html
- lines changed 6, context: html, text, full: html, text
Fixes issues in Redmine #4155
1. Set diplay for Peaks to dense
2. Fixed the matrix hyperlinks for treatment and factor so they link to correct cv item.
3. Decreassed header size for "Rationale for the Mouse ENCODE project"
4. Updated the the following
"An" -> "A"
"consiting" -> "consisting"
deleted duplicate the
"contructed " -> "constructed"
"avaialble " -> "available"
"paramteres " -> "parameters"
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechHist.ra
- lines changed 4, context: html, text, full: html, text
Fixes issues in Redmine #4155
1. Set diplay for Peaks to dense
2. Fixed the matrix hyperlinks for treatment and factor so they link to correct cv item.
3. Decreassed header size for "Rationale for the Mouse ENCODE project"
4. Updated the the following
"An" -> "A"
"consiting" -> "consisting"
deleted duplicate the
"contructed " -> "constructed"
"avaialble " -> "available"
"paramteres " -> "parameters"
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechTfbs.html
- lines changed 6, context: html, text, full: html, text
Forgot thes files in commit:652519aed933b3d975c3feaa034873160f55cbf3
Fixes issues in Redmine #4154
1. Set diplay for Peaks to dense
2. Fixed the matrix hyperlinks for treatment and factor so they link to correct cv item.
3. Decreassed header size for "Rationale for the Mouse ENCODE project"
4. Updated the the following
"An" -> "A"
"consiting" -> "consisting"
deleted duplicate the
"contructed " -> "constructed"
"avaialble " -> "available"
"paramteres " -> "parameters"
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechTfbs.new.ra
- lines changed 668, context: html, text, full: html, text
merge conflict resolved
- lines changed 4, context: html, text, full: html, text
Forgot thes files in commit:652519aed933b3d975c3feaa034873160f55cbf3
Fixes issues in Redmine #4154
1. Set diplay for Peaks to dense
2. Fixed the matrix hyperlinks for treatment and factor so they link to correct cv item.
3. Decreassed header size for "Rationale for the Mouse ENCODE project"
4. Updated the the following
"An" -> "A"
"consiting" -> "consisting"
deleted duplicate the
"contructed " -> "constructed"
"avaialble " -> "available"
"paramteres " -> "parameters"
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechTfbs.ra
- lines changed 183, context: html, text, full: html, text
merge conflict resolved
- lines changed 4, context: html, text, full: html, text
Fixes issues in Redmine #4154
1. Set diplay for Peaks to dense
2. Fixed the matrix hyperlinks for treatment and factor so they link to correct cv item.
3. Decreassed header size for "Rationale for the Mouse ENCODE project"
4. Updated the the following
"An" -> "A"
"consiting" -> "consisting"
deleted duplicate the
"contructed " -> "constructed"
"avaialble " -> "available"
"paramteres " -> "parameters"
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.ra
- lines changed 243, context: html, text, full: html, text
Added 10 submission, three of which were previously submitted 3041,3042,3043. Redmine #111.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.ra
- lines changed 55, context: html, text, full: html, text
Added 3 submissions for track. Redmine #110.
- src/hg/makeDb/trackDb/mouse/trackDb.chainNet.ra
- src/hg/makeDb/trackDb/opossum/monDom5/trackDb.chainNet.ra
- src/hg/makeDb/trackDb/opossum/trackDb.chainNet.ra
- src/hg/makeDb/trackDb/pig/trackDb.chainNet.ra
- src/hg/makeDb/trackDb/platypus/trackDb.chainNet.ra
- src/hg/makeDb/trackDb/rat/rn4/trackDb.chainNet.ra
- src/hg/makeDb/trackDb/rat/rn4/trackDb.ra
- lines changed 7, context: html, text, full: html, text
extend ctgPos search rule to function OK here
- src/hg/makeDb/trackDb/rat/trackDb.chainNet.ra
- src/hg/makeDb/trackDb/rhesus/rheMac2/trackDb.ra
- lines changed 8, context: html, text, full: html, text
search rules to eliminate any errors from checkHgFindSpec -checkTermRegex
- src/hg/makeDb/trackDb/sacCer/sacCer3/trackDb.ra
- lines changed 33, context: html, text, full: html, text
update ensGene search rules to match the names in this genome
- lines changed 33, context: html, text, full: html, text
same ensGene search rules for all sacCer assemblies
- src/hg/makeDb/trackDb/sacCer/trackDb.ra
- lines changed 33, context: html, text, full: html, text
same ensGene search rules for all sacCer assemblies
- src/hg/makeDb/trackDb/squirt/cioSav2/trackDb.ra
- lines changed 34, context: html, text, full: html, text
fixup ensGene name searches for the extra letters in the ENS gene names
- src/hg/makeDb/trackDb/stickleback/gasAcu1/trackDb.ra
- lines changed 1, context: html, text, full: html, text
search rules to eliminate any errors from checkHgFindSpec -checkTermRegex
- src/hg/makeDb/trackDb/stickleback/trackDb.chainNet.ra
- src/hg/makeDb/trackDb/tetraodon/tetNig1/trackDb.ra
- lines changed 23, context: html, text, full: html, text
fixup some of the checkHgFindSpec errors
- src/hg/makeDb/trackDb/turkey/trackDb.chainNet.ra
- src/hg/makeDb/trackDb/worm/ce10/trackDb.ra
- lines changed 16, context: html, text, full: html, text
search rules to eliminate any errors from checkHgFindSpec -checkTermRegex
- lines changed 1, context: html, text, full: html, text
fixup checkHgFindSpec errors
- src/hg/makeDb/trackDb/worm/ce6/trackDb.ra
- lines changed 33, context: html, text, full: html, text
fixup checkHgFindSpec errors
- src/hg/makeDb/trackDb/xenTro/trackDb.chainNet.ra
- src/hg/makeDb/trackDb/xenTro/xenTro2/trackDb.chainNet.ra
- src/hg/makeDb/trackDb/zebrafish/UMassChIP-Seq.html
- lines changed 76, context: html, text, full: html, text
UMassChIP-Seq.html in danRer5 and 7 were identical. I moved danRer7's copy one dir up and removed the copy from danRer5.
- src/hg/makeDb/trackDb/zebrafish/danRer3/trackDb.ra
- lines changed 1, context: html, text, full: html, text
fixup ctgPos2 search rule
- src/hg/makeDb/trackDb/zebrafish/danRer4/trackDb.ra
- lines changed 6, context: html, text, full: html, text
fixup search for gold and ctgPos2
- src/hg/makeDb/trackDb/zebrafish/danRer5/UMassChIP-Seq.html
- lines changed 31, context: html, text, full: html, text
UMassChIP-Seq.html in danRer5 and 7 were identical. I moved danRer7's copy one dir up and removed the copy from danRer5.
- src/hg/makeDb/trackDb/zebrafish/danRer5/trackDb.ra
- lines changed 9, context: html, text, full: html, text
fixup checkHgFindSpec errors
- src/hg/makeDb/trackDb/zebrafish/danRer6/trackDb.ra
- lines changed 8, context: html, text, full: html, text
fixup checkHgFindSpec errors
- src/hg/makeDb/trackDb/zebrafish/danRer7/UMassChIP-Seq.html
- lines changed 34, context: html, text, full: html, text
Cleaned up grammar, html, and citations.....a lot.
- lines changed 49, context: html, text, full: html, text
Set hard line wrap to 100 chars. Obfuscated email address.
- lines changed 76, context: html, text, full: html, text
UMassChIP-Seq.html in danRer5 and 7 were identical. I moved danRer7's copy one dir up and removed the copy from danRer5.
- src/hg/makeDb/trackDb/zebrafish/danRer7/trackDb.ra
- lines changed 5, context: html, text, full: html, text
fixup gold search rule to allow all fragment names to match
- src/hg/makeDb/trackDb/zebrafish/trackDb.chainNet.ra
- src/hg/protein/lib/spKgMap.c
- src/hg/snp/snpLoad/snpNcbiToUcsc.c
- lines changed 38, context: html, text, full: html, text
Adding new UCSC exception flag for dbSNP: InconsistentAlleles (the setof alleles for which frequencies are given does not match the set of
observed alleles). This is in response to Ben and Ngan's finding some
inconsistencies, and MLQ #5794 in which a user reported some strange
non-base characters used as alleles for allele frequencies. Sent a
couple test cases of inconsistent bases to dbSNP, and when build 135
FTP files are available, I can send them a more comprehensive list.
- src/hg/txCds/txInfoAssemble/txInfoAssemble.c
- lines changed 1, context: html, text, full: html, text
Addressing code review #5758 feedback: I'd written a nice new function but then had forgotten to call it
- src/hg/utils/refSeqGet/tests/expected/basicListTest.meta
- lines changed 1, context: html, text, full: html, text
update expected results to match database
- src/hg/utils/tdbQuery/tdbQuery.c
- lines changed 33, context: html, text, full: html, text
add the ability to check for shortLabel and longLabel max lengths #5799
- src/lib/chainBlock.c
- src/lib/cheapcgi.c
- lines changed 2, context: html, text, full: html, text
removing an unused variable as gcc 4.6 complained
- lines changed 1, context: html, text, full: html, text
This variable is used and does need to be initialized.
- lines changed 2, context: html, text, full: html, text
oops that must have been the wrong unused instance of ct being reported by gcc 4.6 warning
- src/lib/udc.c
- lines changed 1, context: html, text, full: html, text
fix problem with udcCleanup on tiny corrupt bitmap files
- src/lib/vcf.c
- src/utils/qa/alertBqueue.csh
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed: 158491
- files changed: 481