All File Changes
v252_base to v253_preview (2011-06-07 to 2011-06-14) v253
- python/ucscgenomics/rafile/RaFileTest.py
- lines changed 110, context: html, text, full: html, text
deleted unnecessary files
- python/ucscgenomics/rafile/cv/fakecv.ra
- lines changed 41, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/cv/unittest/input/Antibody/ValidStanza.ra
- lines changed 12, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/cv/unittest/input/Mouse/BlankKey.ra
- lines changed 2, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/cv/unittest/input/Mouse/ExtraKey.ra
- lines changed 2, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/cv/unittest/input/Mouse/MissingKey.ra
- lines changed 2, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/cv/unittest/input/Mouse/NonmatchKey.ra
- lines changed 2, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/cv/unittest/input/Mouse/ValidStanza.ra
- lines changed 2, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/cvClassDiagram
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deleted unnecessary files
- python/ucscgenomics/rafile/cvPseudo
- lines changed 18, context: html, text, full: html, text
deleted unnecessary files
- python/ucscgenomics/rafile/cvValidate.py
- lines changed 62, context: html, text, full: html, text
deleted unnecessary files
- python/ucscgenomics/rafile/filter.ra
- lines changed 30, context: html, text, full: html, text
deleted unnecessary files
- python/ucscgenomics/rafile/filterEntry.py
- lines changed 49, context: html, text, full: html, text
deleted unnecessary files
- python/ucscgenomics/rafile/filterFile.py
- lines changed 107, context: html, text, full: html, text
deleted unnecessary files
- python/ucscgenomics/rafile/raEntry.py
- lines changed 46, context: html, text, full: html, text
deleted unnecessary files
- python/ucscgenomics/rafile/raInspect.py
- lines changed 113, context: html, text, full: html, text
deleted unnecessary files
- python/ucscgenomics/rafile/testinput.ra
- lines changed 8, context: html, text, full: html, text
deleted unnecessary files
- python/ucscgenomics/rafile/testoutput/BasicDiff.out
- lines changed 27, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/testoutput/CommentsDiff.out
- lines changed 31, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/testoutput/DeleteItem.out
- lines changed 39, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/testoutput/ExtraneousWhitespace.out
- lines changed 70, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/testoutput/GetItem.out
- lines changed 13, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/testoutput/InlineCommentsDiff.out
- lines changed 27, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/testoutput/IterEntryItems.out
- lines changed 27, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/testoutput/IterEntryKeys.out
- lines changed 27, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/testoutput/IterEntryValues.out
- lines changed 27, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/testoutput/IterItems.out
- lines changed 19, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/testoutput/IterKeys.out
- lines changed 11, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/testoutput/IterValues.out
- lines changed 41, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/tests/.IterKeysExpected.ra.swp
- lines changed 0, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/tests/BasicDiff.ra
- lines changed 12, context: html, text, full: html, text
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- python/ucscgenomics/rafile/tests/CommentsDiff.ra
- lines changed 14, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/tests/DeleteItem.ra
- lines changed 18, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/tests/DuplicateKeys.ra
- lines changed 8, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/tests/ExtraneousWhitespace.ra
- lines changed 27, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/tests/ExtraneousWhitespaceExpected.ra
- lines changed 14, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/tests/FunctionalityCheck.ra
- lines changed 23, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/tests/GetItem.ra
- lines changed 5, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/tests/InlineCommentsDiff.ra
- lines changed 12, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/tests/InvalidComments.ra
- lines changed 9, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/tests/IterEntryItems.ra
- lines changed 12, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/tests/IterEntryKeys.ra
- lines changed 12, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/tests/IterEntryValues.ra
- lines changed 12, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/tests/IterItems.ra
- lines changed 8, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/tests/IterKeys.ra
- lines changed 4, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/tests/IterValues.ra
- lines changed 19, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/tests/MisplacedKeys.ra
- lines changed 8, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/tests/NonNewlineFile.ra
- lines changed 5, context: html, text, full: html, text
deleted many more unnecessary files
- python/ucscgenomics/rafile/unittest/testRaFile.py
- lines changed 205, context: html, text, full: html, text
re-added unittest for rafile
- python/ucscgenomics/rafile/unittest/testoutput/BasicDiff.out
- lines changed 27, context: html, text, full: html, text
re-added unittest for rafile
- python/ucscgenomics/rafile/unittest/testoutput/CommentsDiff.out
- lines changed 31, context: html, text, full: html, text
re-added unittest for rafile
- python/ucscgenomics/rafile/unittest/testoutput/DeleteItem.out
- lines changed 39, context: html, text, full: html, text
re-added unittest for rafile
- python/ucscgenomics/rafile/unittest/testoutput/ExtraneousWhitespace.out
- lines changed 70, context: html, text, full: html, text
re-added unittest for rafile
- python/ucscgenomics/rafile/unittest/testoutput/GetItem.out
- lines changed 13, context: html, text, full: html, text
re-added unittest for rafile
- python/ucscgenomics/rafile/unittest/testoutput/InlineCommentsDiff.out
- lines changed 27, context: html, text, full: html, text
re-added unittest for rafile
- python/ucscgenomics/rafile/unittest/testoutput/IterEntryItems.out
- lines changed 27, context: html, text, full: html, text
re-added unittest for rafile
- python/ucscgenomics/rafile/unittest/testoutput/IterEntryKeys.out
- lines changed 27, context: html, text, full: html, text
re-added unittest for rafile
- python/ucscgenomics/rafile/unittest/testoutput/IterEntryValues.out
- lines changed 27, context: html, text, full: html, text
re-added unittest for rafile
- python/ucscgenomics/rafile/unittest/testoutput/IterItems.out
- lines changed 19, context: html, text, full: html, text
re-added unittest for rafile
- python/ucscgenomics/rafile/unittest/testoutput/IterKeys.out
- lines changed 11, context: html, text, full: html, text
re-added unittest for rafile
- python/ucscgenomics/rafile/unittest/testoutput/IterValues.out
- lines changed 41, context: html, text, full: html, text
re-added unittest for rafile
- python/ucscgenomics/rafile/unittest/tests/.IterKeysExpected.ra.swp
- lines changed 0, context: html, text, full: html, text
re-added unittest for rafile
- python/ucscgenomics/rafile/unittest/tests/BasicDiff.ra
- lines changed 12, context: html, text, full: html, text
re-added unittest for rafile
- python/ucscgenomics/rafile/unittest/tests/CommentsDiff.ra
- lines changed 14, context: html, text, full: html, text
re-added unittest for rafile
- python/ucscgenomics/rafile/unittest/tests/DeleteItem.ra
- lines changed 18, context: html, text, full: html, text
re-added unittest for rafile
- python/ucscgenomics/rafile/unittest/tests/DuplicateKeys.ra
- lines changed 8, context: html, text, full: html, text
re-added unittest for rafile
- python/ucscgenomics/rafile/unittest/tests/FunctionalityCheck.ra
- lines changed 23, context: html, text, full: html, text
re-added unittest for rafile
- python/ucscgenomics/rafile/unittest/tests/GetItem.ra
- lines changed 5, context: html, text, full: html, text
re-added unittest for rafile
- python/ucscgenomics/rafile/unittest/tests/InlineCommentsDiff.ra
- lines changed 12, context: html, text, full: html, text
re-added unittest for rafile
- python/ucscgenomics/rafile/unittest/tests/IterEntryItems.ra
- lines changed 12, context: html, text, full: html, text
re-added unittest for rafile
- python/ucscgenomics/rafile/unittest/tests/IterEntryKeys.ra
- lines changed 12, context: html, text, full: html, text
re-added unittest for rafile
- python/ucscgenomics/rafile/unittest/tests/IterEntryValues.ra
- lines changed 12, context: html, text, full: html, text
re-added unittest for rafile
- python/ucscgenomics/rafile/unittest/tests/IterItems.ra
- lines changed 8, context: html, text, full: html, text
re-added unittest for rafile
- python/ucscgenomics/rafile/unittest/tests/IterKeys.ra
- lines changed 4, context: html, text, full: html, text
re-added unittest for rafile
- python/ucscgenomics/rafile/unittest/tests/IterValues.ra
- lines changed 19, context: html, text, full: html, text
re-added unittest for rafile
- python/ucscgenomics/rafile/unittest/tests/MisplacedKeys.ra
- lines changed 8, context: html, text, full: html, text
re-added unittest for rafile
- python/ucscgenomics/rafile/unittest/tests/NonNewlineFile.ra
- lines changed 5, context: html, text, full: html, text
re-added unittest for rafile
- python/ucscgenomics/rafile/validatescript.py
- lines changed 4, context: html, text, full: html, text
deleted unnecessary files
- python/ucscgenomics/style.txt
- lines changed 28, context: html, text, full: html, text
deleted many more unnecessary files
- src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
- lines changed 1, context: html, text, full: html, text
Updated encodeDownloadsPage.pl to support .tgz files. Linked to Attic support. Redmine #2462.
- src/hg/encode/encodeExp/encodeExp.c
- lines changed 60, context: html, text, full: html, text
Add 'modify' command to allow (carefully) changing experiments in limited ways
- lines changed 1, context: html, text, full: html, text
Fix typo that disabled 'id' and 'remove' in last checkin
- lines changed 20, context: html, text, full: html, text
Extend modify command to handle expVars
- src/hg/encode/encodeExp/makefile
- lines changed 4, context: html, text, full: html, text
Add 'modify' command to allow (carefully) changing experiments in limited ways
- src/hg/encode/encodeExp/tests/expected/modifyTest.out.ra
- lines changed 7, context: html, text, full: html, text
Add 'modify' command to allow (carefully) changing experiments in limited ways
- lines changed 1, context: html, text, full: html, text
Get tests working (defer a few)
- lines changed 7, context: html, text, full: html, text
Extend modify command to handle expVars
- src/hg/encode/encodeExp/tests/makefile
- lines changed 10, context: html, text, full: html, text
Add 'modify' command to allow (carefully) changing experiments in limited ways
- lines changed 3, context: html, text, full: html, text
Get tests working (defer a few)
- lines changed 2, context: html, text, full: html, text
Fix typo that disabled 'id' and 'remove' in last checkin
- lines changed 2, context: html, text, full: html, text
Extend modify command to handle expVars
- src/hg/encode/encodeValidate/config/expVars.ra
- lines changed 1, context: html, text, full: html, text
Removed replicate from CshlLongRnaSeq
- src/hg/encode/encodeValidate/config/fields.ra
- lines changed 13, context: html, text, full: html, text
Getting the pipeline to accept spikeIns and to accept doc which is Tim's design
- src/hg/encode/encodeValidate/config/labs.ra
- lines changed 3, context: html, text, full: html, text
Changeing wranglers around
- src/hg/encode/encodeValidate/doEncodeValidate.pl
- lines changed 1, context: html, text, full: html, text
Corrected the spelling of auxiliary
- lines changed 2, context: html, text, full: html, text
Getting the pipeline to accept spikeIns and to accept doc which is Tim's design
- src/hg/hgGene/hgGeneData/Human/links.ra
- lines changed 1, context: html, text, full: html, text
changed omim link on KG details page to omim.org
- src/hg/hgGene/makefile
- lines changed 1, context: html, text, full: html, text
fix install target to remove hgGeneData
- lines changed 1, context: html, text, full: html, text
ooops.... didn't use DESTDIR
- src/hg/hgGenome/bedList.c
- lines changed 2, context: html, text, full: html, text
Simple bullet-proofing against tdb->table being empty.
- src/hg/hgGenome/import.c
- lines changed 12, context: html, text, full: html, text
Simple bullet-proofing against tdb->table being empty.
- src/hg/hgSuggest/hgSuggest.c
- lines changed 8, context: html, text, full: html, text
sort by chrom to get normal chroms before _random, _hap etc. (see redmine #4257)
- src/hg/hgTables/hgTables.c
- lines changed 9, context: html, text, full: html, text
Simple bullet-proofing against tdb->table being empty.
- src/hg/hgText/hgText.c
- lines changed 2, context: html, text, full: html, text
Simple bullet-proofing against tdb->table being empty.
- src/hg/hgTracks/.old
- lines changed 0, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/hgTracks/expRatioTracks.c
- lines changed 2, context: html, text, full: html, text
bugfix for microarray tracks with no default grouping e.g. rinnSex (mm7/mm8)
- src/hg/hgTracks/retroGene.c
- lines changed 2, context: html, text, full: html, text
added version1 to retrogene track handler
- src/hg/hgTracks/searchTracks.c
- lines changed 4, context: html, text, full: html, text
Should do tr coloring by bgLevel class to make sure the metadata toggle background coloring works okay.
- lines changed 1, context: html, text, full: html, text
Oops. Let a bit of the new toggling track seep into the last check in.
- lines changed 1, context: html, text, full: html, text
Checking in metadata toggle with up/down arrows. This replaces the '...' link.
- src/hg/hgTracks/simpleTracks.c
- lines changed 168, context: html, text, full: html, text
meger of GENCODE V7 tracks
- lines changed 11, context: html, text, full: html, text
Removed commented out code and minor edit of comment for hasOmimPhenotypeClass().
- lines changed 9, context: html, text, full: html, text
Removed commented out code.
- src/hg/hgc/gencodeClick.c
- lines changed 548, context: html, text, full: html, text
meger of GENCODE V7 tracks
- lines changed 1, context: html, text, full: html, text
fixed gencode comprehensive click through
- src/hg/hgc/gencodeClick.h
- lines changed 12, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/hgc/hgc.c
- lines changed 12, context: html, text, full: html, text
meger of GENCODE V7 tracks
- lines changed 1, context: html, text, full: html, text
Fixed minor sql error on doNumtSHg19Mm9()
- lines changed 16, context: html, text, full: html, text
code review #4180 - Use pointer copy for static character pointers: char *clickMsg = NULL; and clickMsg = openMsg2;
- lines changed 1, context: html, text, full: html, text
Don't show strand when strand is '.'
- lines changed 2, context: html, text, full: html, text
Track #1656 (GWAS Catalog) update: not the usual 5-minute reload,because NHGRI interspersed a bunch of new columns into their download
file, and hg19 is now using snp132.
- lines changed 9, context: html, text, full: html, text
For omimAvSnp, open snp hgc page in the same window instead of opening new one. And go to snp130 for hg18.
- src/hg/hgc/hgc.h
- lines changed 3, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/hgc/makefile
- lines changed 1, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/htdocs/ENCODE/downloads.html
- lines changed 3, context: html, text, full: html, text
adding Open Chrom Synth, redmine 2881
- src/hg/htdocs/goldenPath/credits.html
- src/hg/htdocs/goldenPath/pubs.html
- lines changed 1, context: html, text, full: html, text
Fixed typo found by Luvina.
- src/hg/htdocs/images/downBlue.png
- lines changed 0, context: html, text, full: html, text
Adding images for the '...' replacement of metadata toggle.
- src/hg/htdocs/images/phylo/ce10.9way.png
- src/hg/htdocs/images/phylo/ce10_9way.png
- src/hg/htdocs/images/upBlue.png
- lines changed 0, context: html, text, full: html, text
Adding images for the '...' replacement of metadata toggle.
- src/hg/htdocs/indexNews.html
- lines changed 34, context: html, text, full: html, text
Added lizard announcement.
- lines changed 18, context: html, text, full: html, text
announcing preview browser
- src/hg/htdocs/style/HGStyle.css
- lines changed 15, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/inc/encode/encodeExp.h
- lines changed 9, context: html, text, full: html, text
Extend modify command to handle expVars
- src/hg/inc/encode/wgEncodeGencodeAttrs.h
- lines changed 73, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/inc/encode/wgEncodeGencodeExonSupport.h
- lines changed 67, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/inc/encode/wgEncodeGencodeGeneSource.h
- lines changed 62, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/inc/encode/wgEncodeGencodePdb.h
- lines changed 62, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/inc/encode/wgEncodeGencodePubMed.h
- lines changed 62, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/inc/encode/wgEncodeGencodeRefSeq.h
- lines changed 63, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/inc/encode/wgEncodeGencodeTag.h
- lines changed 62, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/inc/encode/wgEncodeGencodeTranscriptSource.h
- lines changed 62, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/inc/encode/wgEncodeGencodeTranscriptSupport.h
- lines changed 63, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/inc/encode/wgEncodeGencodeUniProt.h
- lines changed 69, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/inc/fileUi.h
- lines changed 7, context: html, text, full: html, text
tdbIsDownloadsOnly moved to trackDb.h to be more widely available
- src/hg/inc/genePred.h
- lines changed 4, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/inc/hui.h
- lines changed 11, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/inc/trackDb.h
- lines changed 8, context: html, text, full: html, text
tdbIsDownloadsOnly moved to trackDb.h to be more widely available
- src/hg/inc/wgEncodeGencodeExonSupport.h
- lines changed 62, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/inc/wgEncodeGencodeGeneSymbol.h
- lines changed 62, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/inc/wgEncodeGencodePdb.h
- lines changed 62, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/inc/wgEncodeGencodePubmed.h
- lines changed 62, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/inc/wgEncodeGencodeRefSeq.h
- lines changed 63, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/inc/wgEncodeGencodeSource.h
- lines changed 68, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/inc/wgEncodeGencodeTranscriptSupport.h
- lines changed 62, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/inc/wgEncodeGencodeUniProt.h
- lines changed 62, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/js/hgTracks.js
- lines changed 2, context: html, text, full: html, text
fix for redmine 4216. JS bug was tolerated by some browser? Not sure why this one wasn't seen before.
- lines changed 116, context: html, text, full: html, text
code to update just the imgTbl in response to navigation buttons; currently live only in larrym's tree
- src/hg/js/hui.js
- lines changed 2, context: html, text, full: html, text
Checking in metadata toggle with up/down arrows. This replaces the '...' link.
- src/hg/js/utils.js
- lines changed 10, context: html, text, full: html, text
Fix for redmine 4206, toggle metadata background color gets lost.
- lines changed 8, context: html, text, full: html, text
Checking in metadata toggle with up/down arrows. This replaces the '...' link.
- src/hg/lib/encode/encodeExp.c
- lines changed 1, context: html, text, full: html, text
Add 'modify' command to allow (carefully) changing experiments in limited ways
- lines changed 73, context: html, text, full: html, text
Extend modify command to handle expVars
- src/hg/lib/encode/openChromCombinedPeaks.as
- lines changed 12, context: html, text, full: html, text
After some tests, I think buildTableDescriptions will finally understand what to do with OpenChromSynth tables
- lines changed 1, context: html, text, full: html, text
When am I going to learn how to spell?
- src/hg/lib/encode/wgEncodeGencodeAttrs.as
- lines changed 17, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodeAttrs.c
- lines changed 209, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodeAttrs.sql
- lines changed 28, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodeClasses.as
- lines changed 14, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodeClasses.sql
- lines changed 23, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodeExonSupport.as
- lines changed 8, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodeExonSupport.c
- lines changed 42, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodeExonSupport.sql
- lines changed 9, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodeGeneSource.as
- lines changed 6, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodeGeneSource.c
- lines changed 124, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodeGeneSource.sql
- lines changed 12, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodeGeneSymbol.as
- lines changed 6, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodeGeneSymbol.c
- lines changed 124, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodeGeneSymbol.sql
- lines changed 12, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodePdb.as
- lines changed 3, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodePdb.c
- lines changed 6, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodePdb.sql
- lines changed 4, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodePubMed.as
- lines changed 6, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodePubMed.c
- lines changed 121, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodePubMed.sql
- lines changed 12, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodePubmed.as
- lines changed 6, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodePubmed.c
- lines changed 124, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodePubmed.sql
- lines changed 12, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodeRefSeq.as
- lines changed 4, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodeRefSeq.c
- lines changed 11, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodeRefSeq.sql
- lines changed 5, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodeSource.as
- lines changed 6, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodeSource.c
- lines changed 127, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodeSource.sql
- lines changed 12, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodeTag.as
- lines changed 6, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodeTag.c
- lines changed 124, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodeTag.sql
- lines changed 12, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodeTranscriptSource.as
- lines changed 6, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodeTranscriptSource.c
- lines changed 124, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodeTranscriptSource.sql
- lines changed 12, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodeTranscriptSupport.as
- lines changed 4, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodeTranscriptSupport.c
- lines changed 16, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodeTranscriptSupport.sql
- lines changed 5, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodeUniProt.as
- lines changed 5, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodeUniProt.c
- lines changed 27, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/encode/wgEncodeGencodeUniProt.sql
- lines changed 6, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/lib/hdb.c
- lines changed 25, context: html, text, full: html, text
downloadsOnly tracks will continue to have a 'table' value, even though that is meaningless. This is because CGIs need bullet-proofing. I have done hgTracks, hgTrackUi, hgTables and hgGenome.
- src/hg/lib/hgFind.c
- lines changed 1, context: html, text, full: html, text
Bug #3301 aligned mRNAs are showing up in 'Unaligned mRNAs' search results
- src/hg/lib/hui.c
- lines changed 22, context: html, text, full: html, text
meger of GENCODE V7 tracks
- lines changed 3, context: html, text, full: html, text
Checking in metadata toggle with up/down arrows. This replaces the '...' link.
- lines changed 3, context: html, text, full: html, text
Simple bullet-proofing against tdb->table being empty.
- src/hg/lib/makefile
- lines changed 4, context: html, text, full: html, text
meger of GENCODE V7 tracks
- lines changed 2, context: html, text, full: html, text
Extend modify command to handle expVars
- src/hg/lib/mdb.c
- lines changed 1, context: html, text, full: html, text
Simple bullet-proofing against tdb->table being empty.
- src/hg/lib/microarray.c
- lines changed 2, context: html, text, full: html, text
bugfix for microarray tracks with no default grouping e.g. rinnSex (mm7/mm8)
- src/hg/lib/omimPhenotype.as
- src/hg/makeDb/doc/caeAng1.txt
- lines changed 315, context: html, text, full: html, text
finished with all lastz operations to ce10
- lines changed 16, context: html, text, full: html, text
makeDownloads.pl has been run and all README files in download directories have been edited
- src/hg/makeDb/doc/caeJap4.txt
- lines changed 29, context: html, text, full: html, text
lastz runs done for almost all to ce10
- lines changed 12, context: html, text, full: html, text
makeDownloads.pl has been run and all README files in download directories have been edited
- src/hg/makeDb/doc/caePb3.txt
- lines changed 142, context: html, text, full: html, text
finished with all lastz operations to ce10
- lines changed 12, context: html, text, full: html, text
makeDownloads.pl has been run and all README files in download directories have been edited
- src/hg/makeDb/doc/caeRem4.txt
- lines changed 18, context: html, text, full: html, text
lastz runs done for almost all to ce10
- lines changed 12, context: html, text, full: html, text
makeDownloads.pl has been run and all README files in download directories have been edited
- src/hg/makeDb/doc/caeSp111.txt
- lines changed 18, context: html, text, full: html, text
lastz runs done for almost all to ce10
- lines changed 12, context: html, text, full: html, text
makeDownloads.pl has been run and all README files in download directories have been edited
- src/hg/makeDb/doc/caeSp71.txt
- lines changed 18, context: html, text, full: html, text
lastz runs done for almost all to ce10
- lines changed 12, context: html, text, full: html, text
makeDownloads.pl has been run and all README files in download directories have been edited
- src/hg/makeDb/doc/caeSp91.txt
- lines changed 17, context: html, text, full: html, text
lastz runs done for almost all to ce10
- lines changed 13, context: html, text, full: html, text
makeDownloads.pl has been run and all README files in download directories have been edited
- src/hg/makeDb/doc/cb4.txt
- lines changed 18, context: html, text, full: html, text
lastz runs done for almost all to ce10
- lines changed 13, context: html, text, full: html, text
makeDownloads.pl has been run and all README files in download directories have been edited
- src/hg/makeDb/doc/ce10.txt
- lines changed 301, context: html, text, full: html, text
lastz runs done for almost all to ce10
- lines changed 124, context: html, text, full: html, text
finished with all lastz operations to ce10
- lines changed 195, context: html, text, full: html, text
9-way multiz initial done and ensGene v62 loaded
- lines changed 563, context: html, text, full: html, text
maf gaps annotated and phastCons and phyloP runs done
- lines changed 81, context: html, text, full: html, text
downloads have been constructed
- src/hg/makeDb/doc/encodeDccHg19/gencodeV7.txt
- lines changed 136, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeCaltechRnaSeq.release2.notes
- src/hg/makeDb/doc/encodeDccMm9/wgEncodeUwDnase.release1.notes
- lines changed 89, context: html, text, full: html, text
Updated relase 1 notes that excludes attic gbdb files and tables.
- lines changed 2, context: html, text, full: html, text
Miss counted gbdb files should be 38 and not 31.
- src/hg/makeDb/doc/hg18.txt
- lines changed 46, context: html, text, full: html, text
Track #1656 (GWAS Catalog) update: not the usual 5-minute reload,because NHGRI interspersed a bunch of new columns into their download
file, and hg19 is now using snp132.
- lines changed 30, context: html, text, full: html, text
Added steps for omimPhenotype table build and removal of gray entries in omimLocation table.
- src/hg/makeDb/doc/hg19.txt
- lines changed 6, context: html, text, full: html, text
Track #1656 (GWAS Catalog) update: not the usual 5-minute reload,because NHGRI interspersed a bunch of new columns into their download
file, and hg19 is now using snp132.
- lines changed 31, context: html, text, full: html, text
Added steps for omimPhenotype table build and removal of gray entries in omimLocation table.
- src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
- lines changed 14, context: html, text, full: html, text
Fixing Redmine bug 411: the refseq column in the kgXref table (which was built from genomic evidence) didn't always match knownToRefseq (which was built post-hoc according to transcript similarity heuristics). After looking into this for a while, I decided that no transcript heuristic would ever be perfect, and it was best to just grab the assignment from design-time evidence. hgMapToGene had a hook for this that almost worked: the -lookup switch. It almost worked because at the crucial lookup step, there was a bug in the code in which there was a hash lookup, a key-value pair, and value was being used as the key in place of key (i.e. 'val=lookup(hash,val)'). Now that that's fixed, the UCSC Genes script uses this -lookup switch to specify expected ucscGenes-refseq mappings from kgXref, to populate knownGeneMrna
- src/hg/makeDb/genbank/etc/align.dbs
- lines changed 1, context: html, text, full: html, text
adding caeJap4 to the build
- src/hg/makeDb/genbank/etc/hgwdev.dbs
- lines changed 1, context: html, text, full: html, text
adding caeJap4 to the build
- src/hg/makeDb/genbank/etc/rr.dbs
- src/hg/makeDb/hgCgiData/Mouse/microarrayGroups.ra
- lines changed 1, context: html, text, full: html, text
Added default combine line to rinnSexGroups stanza to keep track working in v252 CGIs (redmine 4027, note-22).
- lines changed 1, context: html, text, full: html, text
Removing combine line from rinnSexGroups stanza. This was just a temporary fix for v252 CGIs, and it has already been cherry-picked into that release. (Redmine #4027, note-45.)
- src/hg/makeDb/schema/all.joiner
- lines changed 6, context: html, text, full: html, text
Track #1656 (GWAS Catalog): need to update all.joiner too, since hg19is now using snp132.
- src/hg/makeDb/trackDb/README
- lines changed 13, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 6, context: html, text, full: html, text
Added back correct definitions for attic that I had accidently trounced commit 48c40b956b858138186093eec647d73a8a6563ac.
- lines changed 6, context: html, text, full: html, text
adding new view ExonGencV3c
- lines changed 22, context: html, text, full: html, text
Removed freezeDate from cv and meta-data for Gencode Genes. Updated Data Version to map with version of files in hgdownload-test. Added labExpId to map to GENCODE Version number and to facilitate as a experiment variable, such that each file for GENCODE version will get a different dccAccession number. Update fileSortOrder (downloads page) for GENCODE V4 to show potential for new downloads page with dccAccession numbers. Solves Redmine issue #2390.
- lines changed 11, context: html, text, full: html, text
Added spikeInLib and corrected run validation
- lines changed 4, context: html, text, full: html, text
changed Estradiol tags to be more descriptive
- lines changed 4, context: html, text, full: html, text
Trying to get spikeInPool to work
- lines changed 6, context: html, text, full: html, text
added in proposal for changing dmso's term and tag
- lines changed 383, context: html, text, full: html, text
Merging some changes, mostly relating to alphabetizing and spacing
- lines changed 13, context: html, text, full: html, text
added in mock proposals for new DMSO entries
- lines changed 4, context: html, text, full: html, text
Addressing the stanzas where the orderUrl is N/A, which is apparently something that breaks the CGI
- lines changed 2, context: html, text, full: html, text
Cleaning up some missing vendor information that came up during this week's code review
- lines changed 1, context: html, text, full: html, text
Fixed enderName to venderName
- lines changed 20, context: html, text, full: html, text
added some views and changed nhek to be unknown tissue
- lines changed 2, context: html, text, full: html, text
added tissue category to NHEK
- lines changed 25, context: html, text, full: html, text
Trying out new tags for DMSO, they are commented out
- lines changed 8, context: html, text, full: html, text
actually changed the dmso tags this time
- lines changed 6, context: html, text, full: html, text
Removing the duplicate of ExonGencV3c
- lines changed 8, context: html, text, full: html, text
Addressing the last of the feedback from this week's code review
- src/hg/makeDb/trackDb/cv/beta/cv.ra
- lines changed 1917, context: html, text, full: html, text
Copying changes from alpha to beta
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeDukeAffyExonArray.ra
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaChipSeq.ra
- lines changed 89, context: html, text, full: html, text
changed experiment names on 2 experiments who used input instead of control
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeSangerGencode.ra
- lines changed 14, context: html, text, full: html, text
Removed freezeDate from cv and meta-data for Gencode Genes. Updated Data Version to map with version of files in hgdownload-test. Added labExpId to map to GENCODE Version number and to facilitate as a experiment variable, such that each file for GENCODE version will get a different dccAccession number. Update fileSortOrder (downloads page) for GENCODE V4 to show potential for new downloads page with dccAccession numbers. Solves Redmine issue #2390.
- lines changed 4, context: html, text, full: html, text
Removed submittedDataVersion because these data are not resubmitted versions of these files but a new version of gencode that can be identified in the labExpId field.
- lines changed 15, context: html, text, full: html, text
Added the wgEncodeGencodeClassesV3 obj meta-data into the metaData fileName, which previously was not.
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleChIPseq.ra
- lines changed 1076, context: html, text, full: html, text
added expId's to yale chipseq hg18
- src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeDukeAffyExonArray.ra
- lines changed 132, context: html, text, full: html, text
releasing Release 2 of hg18 Duke Affy Exon track; dropped 4 subtracks (lhsr) and added experiment ids, redmine #2199
- src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeHudsonalphaCnv.ra
- lines changed 18, context: html, text, full: html, text
releasing metadata update (CNV->Genotype & adding expIds), pqId 85
- src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeHudsonalphaMethyl27.ra
- lines changed 24, context: html, text, full: html, text
releasing metadata update (including adding expIds), pqId 86
- src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeNhgriBip.ra
- lines changed 4, context: html, text, full: html, text
releasing metadata update (including adding expIds), pqId 87
- src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeNhgriNRE.ra
- lines changed 14, context: html, text, full: html, text
releasing metadata update (including adding expIds), pqId 87
- src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeDukeAffyExonArray.ra
- lines changed 132, context: html, text, full: html, text
releasing Release 2 of hg18 Duke Affy Exon track; dropped 4 subtracks (lhsr) and added experiment ids, redmine #2199
- src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeHudsonalphaCnv.ra
- lines changed 18, context: html, text, full: html, text
releasing metadata update (CNV->Genotype & adding expIds), pqId 85
- src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeHudsonalphaMethyl27.ra
- lines changed 24, context: html, text, full: html, text
releasing metadata update (including adding expIds), pqId 86
- src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeNhgriBip.ra
- lines changed 4, context: html, text, full: html, text
releasing metadata update (including adding expIds), pqId 87
- src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeNhgriNRE.ra
- lines changed 14, context: html, text, full: html, text
releasing metadata update (including adding expIds), pqId 87
- src/hg/makeDb/trackDb/human/hg18/omimAvSnp.html
- lines changed 1, context: html, text, full: html, text
Removed the hg18 copy of omimDescriptionText.html and changed hg18 omimAvSnp.html so that it uses the one at the human level. No reason to have multiple copies of the same included text.
- lines changed 38, context: html, text, full: html, text
Changed to match human-level omimAvSnp.html. Moved warning up.
- src/hg/makeDb/trackDb/human/hg18/omimDescriptionText.html
- lines changed 21, context: html, text, full: html, text
Removed the hg18 copy of omimDescriptionText.html and changed hg18 omimAvSnp.html so that it uses the one at the human level. No reason to have multiple copies of the same included text.
- src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
- lines changed 2, context: html, text, full: html, text
releasing Release 2 of hg18 Duke Affy Exon track; dropped 4 subtracks (lhsr) and added experiment ids, redmine #2199
- src/hg/makeDb/trackDb/human/hg18/wgEncodeDukeAffyExon.new.ra
- src/hg/makeDb/trackDb/human/hg18/wgEncodeDukeAffyExon.ra
- lines changed 29, context: html, text, full: html, text
releasing Release 2 of hg18 Duke Affy Exon track; dropped 4 subtracks (lhsr) and added experiment ids, redmine #2199
- src/hg/makeDb/trackDb/human/hg18/wgEncodeDukeAffyExonArray.html
- lines changed 13, context: html, text, full: html, text
releasing Release 2 of hg18 Duke Affy Exon track; dropped 4 subtracks (lhsr) and added experiment ids, redmine #2199
- src/hg/makeDb/trackDb/human/hg18/wgEncodeDukeAffyExonArray.new.html
- lines changed 1, context: html, text, full: html, text
Small description clarification for release notes
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
- lines changed 1, context: html, text, full: html, text
Added trackDb for UMass Decker and metaDb for UW 5C. Both of these for Kate.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
- lines changed 3, context: html, text, full: html, text
cleaned up some metadata that wasn't passing cv validation
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
- lines changed 735, context: html, text, full: html, text
cleaned out suspect data references and the metaData (pooled, 1,2) that was failing validate, added a link to the supplimental directory
- lines changed 24, context: html, text, full: html, text
bringing in lost metaData
- lines changed 2623, context: html, text, full: html, text
added a whole bunch of Spikein submissions
- lines changed 2638, context: html, text, full: html, text
added a whole bunch of spikein submissions a second time after merge conflict
- lines changed 473, context: html, text, full: html, text
Added tier 2 labels and filtering, added origAssembly and dccRep where missing, fixed retinoic acid label
- lines changed 13, context: html, text, full: html, text
added subId 4053 and 4055 to cshllongRnaSeq
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
- lines changed 22, context: html, text, full: html, text
bringing in lost metaData
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencode.ra
- lines changed 18, context: html, text, full: html, text
Removed freezeDate from cv and meta-data for Gencode Genes. Updated Data Version to map with version of files in hgdownload-test. Added labExpId to map to GENCODE Version number and to facilitate as a experiment variable, such that each file for GENCODE version will get a different dccAccession number. Update fileSortOrder (downloads page) for GENCODE V4 to show potential for new downloads page with dccAccession numbers. Solves Redmine issue #2390.
- lines changed 7, context: html, text, full: html, text
Removed submittedDataVersion because these data are not resubmitted versions of these files but a new version of gencode that can be identified in the labExpId field.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
- lines changed 113, context: html, text, full: html, text
Cleaning up metaData to match validate. Solexa is dropped and TranscriptGencV3c is fixed where required
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
- lines changed 11, context: html, text, full: html, text
changed dmso tags in hg19 and mm9 to the new ones
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibRnaSeq.ra
- lines changed 13, context: html, text, full: html, text
Cleaning up metaData to match validate. Solexa is dropped and TranscriptGencV3c is fixed where required
- lines changed 41, context: html, text, full: html, text
changed dmso tags in hg19 and mm9 to the new ones
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
- lines changed 680, context: html, text, full: html, text
revoked an experiment from 4160, chagned controlId for an experiment, and changed treatments names for DEX and Estradiol
- lines changed 49, context: html, text, full: html, text
Completley removed the meta-data for experiment with submission 4160.
- lines changed 167, context: html, text, full: html, text
changed dmso tags in hg19 and mm9 to the new ones
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
- lines changed 7, context: html, text, full: html, text
some labs weren't validating in the cv because they had the pi's name in the term. removed the name
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
- lines changed 7, context: html, text, full: html, text
some labs weren't validating in the cv because they had the pi's name in the term. removed the name
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
- lines changed 752, context: html, text, full: html, text
Final details from the inventory, removed 1 duplicate experiment, changed the metadata for labExpId J84
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
- lines changed 18, context: html, text, full: html, text
cleaned up some metadata that wasn't passing cv validation
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
- lines changed 6, context: html, text, full: html, text
cleaned up some metadata that wasn't passing cv validation
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUw5C.ra
- lines changed 613, context: html, text, full: html, text
Added trackDb for UMass Decker and metaDb for UW 5C. Both of these for Kate.
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeAffyRnaChip.ra
- lines changed 1091, context: html, text, full: html, text
releasing updated metadata (extraneous entries removed, addition of ucscId) and addition of filesortorder
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeGisDnaPet.ra
- lines changed 588, context: html, text, full: html, text
releasing geo accessions, ucsc accessions, fileSortOrder, and metadata for fasta, fastq and csqual download files
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeGisRnaSeq.ra
- lines changed 92, context: html, text, full: html, text
releasing metadata updates for GIS RNA-seq (hg19), pushQ id 92
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeOpenChromSynth.ra
- lines changed 16, context: html, text, full: html, text
staging update to metadat on beta, redmine #2881
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSunyAlbanyTiling.ra
- lines changed 14, context: html, text, full: html, text
updating metadata: RipChip changed to RipTiliing
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
- lines changed 1, context: html, text, full: html, text
preparing metadata for Open Chrom Synth track release, redmine 2881
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeAffyRnaChip.ra
- lines changed 1091, context: html, text, full: html, text
releasing updated metadata (extraneous entries removed, addition of ucscId) and addition of filesortorder
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeGisDnaPet.ra
- lines changed 588, context: html, text, full: html, text
releasing geo accessions, ucsc accessions, fileSortOrder, and metadata for fasta, fastq and csqual download files
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeGisRnaSeq.ra
- lines changed 92, context: html, text, full: html, text
releasing metadata updates for GIS RNA-seq (hg19), pushQ id 92
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeOpenChromSynth.ra
- lines changed 146, context: html, text, full: html, text
preparing metadata for Open Chrom Synth track release, redmine 2881
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeSunyAlbanyTiling.ra
- lines changed 14, context: html, text, full: html, text
updating metadata: RipChip changed to RipTiliing
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 6, context: html, text, full: html, text
Track #1656 (GWAS Catalog) update: not the usual 5-minute reload,because NHGRI interspersed a bunch of new columns into their download
file, and hg19 is now using snp132.
- lines changed 23, context: html, text, full: html, text
turtle/alligator multiz for washU
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- lines changed 141, context: html, text, full: html, text
meger of GENCODE V7 tracks
- lines changed 2, context: html, text, full: html, text
Removed freezeDate from cv and meta-data for Gencode Genes. Updated Data Version to map with version of files in hgdownload-test. Added labExpId to map to GENCODE Version number and to facilitate as a experiment variable, such that each file for GENCODE version will get a different dccAccession number. Update fileSortOrder (downloads page) for GENCODE V4 to show potential for new downloads page with dccAccession numbers. Solves Redmine issue #2390.
- lines changed 2, context: html, text, full: html, text
Removed use of fileSortOrder and fileUi for track, as this will be repalced by GENCODE V7 on the public browswer.
- lines changed 1, context: html, text, full: html, text
Added trackDb for UMass Decker and metaDb for UW 5C. Both of these for Kate.
- lines changed 1, context: html, text, full: html, text
take out 5c since it's killing the table browser
- lines changed 2, context: html, text, full: html, text
releasing geo accessions, ucsc accessions, fileSortOrder, and metadata for fasta, fastq and csqual download files
- lines changed 2, context: html, text, full: html, text
releasing updated metadata (extraneous entries removed, addition of ucscId) and addition of filesortorder
- lines changed 1, context: html, text, full: html, text
Adding Kate's UmassDekker%C again because tdb->table being empty is now guarded against.
- lines changed 2, context: html, text, full: html, text
releasing metadata updates for GIS RNA-seq (hg19), pushQ id 92
- src/hg/makeDb/trackDb/human/hg19/wgEncodeAffyRnaChip.ra
- lines changed 1, context: html, text, full: html, text
releasing updated metadata (extraneous entries removed, addition of ucscId) and addition of filesortorder
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.html
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.html
- lines changed 2, context: html, text, full: html, text
cleaned out suspect data references and the metaData (pooled, 1,2) that was failing validate, added a link to the supplimental directory
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra
- lines changed 90, context: html, text, full: html, text
cleaned out suspect data references and the metaData (pooled, 1,2) that was failing validate, added a link to the supplimental directory
- lines changed 38, context: html, text, full: html, text
added some spikein submissions
- lines changed 8, context: html, text, full: html, text
added back missing Contig
- lines changed 297, context: html, text, full: html, text
Added tier 2 labels and filtering, added origAssembly and dccRep where missing, fixed retinoic acid label
- lines changed 29, context: html, text, full: html, text
added subId 4053 and 4055 to cshllongRnaSeq
- src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.html
- lines changed 20, context: html, text, full: html, text
started QA of this description page for Duke Affy, reorganized content and fixed a space, redmine# 60
- lines changed 2, context: html, text, full: html, text
removed references to replicates since they are all being displayed and restructured a sentence, redmine# 60
- lines changed 5, context: html, text, full: html, text
actually saved the file so this commit actually has the sentence that I said I fixed in that last commit, fixed sentence that references another track, redmine #60
- lines changed 1, context: html, text, full: html, text
fixed typo and added space between units, redmine #60
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencode.ra
- lines changed 150, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV3.ra
- lines changed 114, context: html, text, full: html, text
meger of GENCODE V7 tracks
- lines changed 3, context: html, text, full: html, text
Removed dateUnrestricted, submittedDataVersion, freezeDate. Also added labExpId with the correct GENCODE Version number. This matches the meta-data of the track that is live on hg18. Redmine #2390.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV4.new.ra
- lines changed 129, context: html, text, full: html, text
Removed freezeDate from cv and meta-data for Gencode Genes. Updated Data Version to map with version of files in hgdownload-test. Added labExpId to map to GENCODE Version number and to facilitate as a experiment variable, such that each file for GENCODE version will get a different dccAccession number. Update fileSortOrder (downloads page) for GENCODE V4 to show potential for new downloads page with dccAccession numbers. Solves Redmine issue #2390.
- lines changed 129, context: html, text, full: html, text
Removed use of fileSortOrder and fileUi for track, as this will be repalced by GENCODE V7 on the public browswer.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV4.ra
- lines changed 129, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV6.ra
- lines changed 128, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV7.html
- lines changed 226, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV7.ra
- lines changed 179, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisDnaPet.ra
- lines changed 1, context: html, text, full: html, text
releasing file sort order
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.ra
- lines changed 1, context: html, text, full: html, text
releasing metadata updates for GIS RNA-seq (hg19), pushQ id 92
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.html
- lines changed 21, context: html, text, full: html, text
Changed release notes according to #2254
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.ra
- lines changed 7, context: html, text, full: html, text
changed dmso tags in hg19 and mm9 to the new ones
- lines changed 4, context: html, text, full: html, text
changed OHTAM1 back to TAM in track db for haib rrbs and sydh tfbsd
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.ra
- lines changed 29, context: html, text, full: html, text
changed dmso tags in hg19 and mm9 to the new ones
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
- lines changed 105, context: html, text, full: html, text
revoked an experiment from 4160, chagned controlId for an experiment, and changed treatments names for DEX and Estradiol
- lines changed 91, context: html, text, full: html, text
changed dmso tags in hg19 and mm9 to the new ones
- lines changed 30, context: html, text, full: html, text
left out = when i regex last time
- lines changed 0, context: html, text, full: html, text
fixed error in short label
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.html
- lines changed 10, context: html, text, full: html, text
adding log -10 equivalents to p-values that were missing it, redmine #2881
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.ra
- lines changed 1, context: html, text, full: html, text
Katrina wants this dense.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRbpSuper.html
- lines changed 28, context: html, text, full: html, text
releasing the revised RbpSupertrack html, redmine 460
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.ra
- lines changed 9, context: html, text, full: html, text
Final details from the inventory, removed 1 duplicate experiment, changed the metadata for labExpId J84
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSunySwitchgear.html
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
- lines changed 5, context: html, text, full: html, text
changed OHTAM1 back to TAM in track db for haib rrbs and sydh tfbsd
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUmassDekker5C.ra
- lines changed 11, context: html, text, full: html, text
Added trackDb for UMass Decker and metaDb for UW 5C. Both of these for Kate.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.new.ra
- lines changed 1, context: html, text, full: html, text
Updated the submission IDs for the subtracks recently revoked and replaced with newer subtracks
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.ra
- lines changed 2, context: html, text, full: html, text
Updated the submission IDs for the subtracks recently revoked and replaced with newer subtracks
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.ra
- lines changed 1, context: html, text, full: html, text
added geo to filesort order for uw dnase
- src/hg/makeDb/trackDb/human/omimAvSnp.html
- lines changed 25, context: html, text, full: html, text
Bolded track name, reordered references, reworded methods and display sections.
- lines changed 4, context: html, text, full: html, text
Made full/pack mode description consistent with other omim tracks.
- lines changed 9, context: html, text, full: html, text
Made the main description of the track more precise, moved the link to dbSNP up, pointed out that our dbSNP link is to the details page of the All SNPs (132) track.
- src/hg/makeDb/trackDb/human/omimGene2.html
- src/hg/makeDb/trackDb/human/omimLocation.html
- lines changed 31, context: html, text, full: html, text
Bolded track name, reordered references, small grammar/punctuation fixes, made wording consistent with other omim tracks, reworded methods, removed reference to ftp file that is no longer available (Redmine #2153, note-132).
- lines changed 5, context: html, text, full: html, text
Clarified the first description sentence and removed the line in the methods section about mim2gene, as per redmine #2153, note-156.
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 3, context: html, text, full: html, text
changed some OMIM labels per Ada and Joanna
- lines changed 2, context: html, text, full: html, text
miRNA Registry -> miRBase text change
- src/hg/makeDb/trackDb/human/wgRna.html
- lines changed 1, context: html, text, full: html, text
miRNA Registry -> miRBase text change
- src/hg/makeDb/trackDb/lizard/anoCar2/description.html
- lines changed 33, context: html, text, full: html, text
Edited text in this file.
- src/hg/makeDb/trackDb/makefile
- lines changed 1, context: html, text, full: html, text
adding caePb3 to the build
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
- lines changed 341, context: html, text, full: html, text
Added expId's and dccAccession for 4 mouse tracks.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrRnaSeq.ra
- lines changed 121, context: html, text, full: html, text
Added expId's and dccAccession for 4 mouse tracks.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
- lines changed 373, context: html, text, full: html, text
Added expId's and dccAccession for 4 mouse tracks.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhRnaSeq.ra
- lines changed 9, context: html, text, full: html, text
changed dmso tags in hg19 and mm9 to the new ones
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
- lines changed 36, context: html, text, full: html, text
changed dmso tags in hg19 and mm9 to the new ones
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
- lines changed 19, context: html, text, full: html, text
renamed Raw to Sig for .bigwig files that were missed previously
- lines changed 571, context: html, text, full: html, text
Added expId's and dccAccession for 4 mouse tracks.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.html
- lines changed 6, context: html, text, full: html, text
Fixed use of first person in track descriptions. Also fixed use of usually to describe pooling effect.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.ra
- lines changed 1, context: html, text, full: html, text
Added support for dccAccession=UCSC_Accession in fileSortOrder and fileUi.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.ra
- lines changed 1, context: html, text, full: html, text
Added support for dccAccession=UCSC_Accession in fileSortOrder and fileUi.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.html
- lines changed 6, context: html, text, full: html, text
Fixed use of first person in track descriptions. Also fixed use of usually to describe pooling effect.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.ra
- lines changed 1, context: html, text, full: html, text
Added support for dccAccession=UCSC_Accession in fileSortOrder and fileUi.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhRnaSeq.ra
- lines changed 7, context: html, text, full: html, text
changed dmso tags in hg19 and mm9 to the new ones
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.newR2.ra
- lines changed 18, context: html, text, full: html, text
changed dmso tags in hg19 and mm9 to the new ones
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.ra
- lines changed 12, context: html, text, full: html, text
renamed Raw to Sig for .bigwig files that were missed previously
- lines changed 29, context: html, text, full: html, text
To have shorter long labels shortented Embryonic -> Embryo. Also to be consistent with age in short labels substituted A8wks -> 8wks.
- lines changed 1, context: html, text, full: html, text
Added support for dccAccession=UCSC_Accession in fileSortOrder and fileUi.
- src/hg/makeDb/trackDb/sacCer/sacCer2/description.html
- lines changed 2, context: html, text, full: html, text
fixed extra space found by Mary in code review
- src/hg/makeDb/trackDb/tagTypes.tab
- lines changed 22, context: html, text, full: html, text
meger of GENCODE V7 tracks
- src/hg/makeDb/trackDb/worm/ce10/cons9way.html
- lines changed 403, context: html, text, full: html, text
text from ce9 cons10way and edited for this 9-way alignment
- lines changed 5, context: html, text, full: html, text
reference to hgdownload-test instead of hgdownload
- src/hg/makeDb/trackDb/worm/ce10/trackDb.ra
- lines changed 110, context: html, text, full: html, text
adding 9-way multiple alignment definition
- lines changed 1, context: html, text, full: html, text
perhaps better order of organisms in phylo distance maybe
- src/hg/near/hgMapToGene/hgMapToGene.c
- lines changed 1, context: html, text, full: html, text
Fixing Redmine bug 411: the refseq column in the kgXref table (which was built from genomic evidence) didn't always match knownToRefseq (which was built post-hoc according to transcript similarity heuristics). After looking into this for a while, I decided that no transcript heuristic would ever be perfect, and it was best to just grab the assignment from design-time evidence. hgMapToGene had a hook for this that almost worked: the -lookup switch. It almost worked because at the crucial lookup step, there was a bug in the code in which there was a hash lookup, a key-value pair, and value was being used as the key in place of key (i.e. 'val=lookup(hash,val)'). Now that that's fixed, the UCSC Genes script uses this -lookup switch to specify expected ucscGenes-refseq mappings from kgXref, to populate knownGeneMrna
- src/hg/near/hgNear/makefile
- lines changed 1, context: html, text, full: html, text
remove hgNearData in install target
- src/hg/snp/snpLoad/snpNcbiToUcsc.c
- lines changed 1, context: html, text, full: html, text
Added new function code from dbSNP.
- src/hg/utils/automation/doDbSnp.pl
- lines changed 11, context: html, text, full: html, text
Added -snpBase option to doDbSnp.pl for test runs; added new SQL-twiddle to make mysql happier with dbSNP dump files.
- src/hg/utils/makeTableList/makeTableList.c
- lines changed 9, context: html, text, full: html, text
use showTableCache config option
- src/hg/utils/phyloTrees/nematode.14way.nh
- lines changed 1, context: html, text, full: html, text
adjust some branch lengths given lastz chain net coverage
- src/test/buildTableDescriptions.pl
- lines changed 2, context: html, text, full: html, text
Special case added for openChromSynth, because without it only the first 8 fields are described in hgTable schema.
- lines changed 2, context: html, text, full: html, text
After some tests, I think buildTableDescriptions will finally understand what to do with OpenChromSynth tables
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed: 32963
- files changed: 440