All File Changes
v266_preview2 to v266_base (2012-04-17 to 2012-04-24) v266
- python/lib/ucscgenomics/geo.py
- lines changed 17, context: html, text, full: html, text
added track viewing tools for GEO so that venkat can use it
- python/lib/ucscgenomics/mkChangeNotes.py
- lines changed 2, context: html, text, full: html, text
added a check to remove old revoked files from the old fileset
- python/lib/ucscgenomics/track.py
- lines changed 37, context: html, text, full: html, text
added track viewing tools for GEO so that venkat can use it
- python/programs/cvValidate/cvValidate
- python/programs/trackInfo/trackInfo
- lines changed 2, context: html, text, full: html, text
added track viewing tools for GEO so that venkat can use it
- python/programs/viewTrack/viewTrack
- lines changed 225, context: html, text, full: html, text
added track viewing tools for GEO so that venkat can use it
- python/users/kent/django/makefile
- lines changed 2, context: html, text, full: html, text
Adding experiments with Django.
- python/users/kent/django/mysite/__init__.py
- lines changed 0, context: html, text, full: html, text
Adding experiments with Django.
- python/users/kent/django/mysite/cvDb/README
- lines changed 7, context: html, text, full: html, text
Putting in docString style module comments as per style guide.
- python/users/kent/django/mysite/cvDb/__init__.py
- lines changed 0, context: html, text, full: html, text
Adding experiments with Django.
- python/users/kent/django/mysite/cvDb/admin.py
- lines changed 42, context: html, text, full: html, text
Adding experiments with Django.
- lines changed 8, context: html, text, full: html, text
Putting in docString style module comments as per style guide.
- python/users/kent/django/mysite/cvDb/makefile
- lines changed 2, context: html, text, full: html, text
Adding experiments with Django.
- python/users/kent/django/mysite/cvDb/models.py
- lines changed 757, context: html, text, full: html, text
Adding experiments with Django.
- lines changed 2, context: html, text, full: html, text
Putting in docString style module comments as per style guide.
- python/users/kent/django/mysite/cvDb/tests.py
- lines changed 16, context: html, text, full: html, text
Adding experiments with Django.
- python/users/kent/django/mysite/cvDb/urls.py
- lines changed 13, context: html, text, full: html, text
Adding experiments with Django.
- lines changed 5, context: html, text, full: html, text
Putting in docString style module comments as per style guide.
- python/users/kent/django/mysite/cvDb/views.py
- lines changed 1, context: html, text, full: html, text
Adding experiments with Django.
- python/users/kent/django/mysite/jkSp/__init__.py
- lines changed 0, context: html, text, full: html, text
Adding experiments with Django.
- python/users/kent/django/mysite/jkSp/admin.py
- lines changed 53, context: html, text, full: html, text
Adding experiments with Django.
- python/users/kent/django/mysite/jkSp/models.py
- lines changed 326, context: html, text, full: html, text
Adding experiments with Django.
- python/users/kent/django/mysite/jkSp/tests.py
- lines changed 16, context: html, text, full: html, text
Adding experiments with Django.
- python/users/kent/django/mysite/jkSp/views.py
- lines changed 1, context: html, text, full: html, text
Adding experiments with Django.
- python/users/kent/django/mysite/makefile
- lines changed 3, context: html, text, full: html, text
Adding experiments with Django.
- python/users/kent/django/mysite/manage.py
- lines changed 14, context: html, text, full: html, text
Adding experiments with Django.
- lines changed 7, context: html, text, full: html, text
Putting in docString style module comments as per style guide.
- python/users/kent/django/mysite/settings.py
- lines changed 149, context: html, text, full: html, text
Adding experiments with Django.
- lines changed 6, context: html, text, full: html, text
Putting in docString style module comments as per style guide.
- python/users/kent/django/mysite/urls.py
- lines changed 18, context: html, text, full: html, text
Adding experiments with Django.
- lines changed 5, context: html, text, full: html, text
Putting in docString style module comments as per style guide.
- python/users/kent/django/templates/404.html
- lines changed 2, context: html, text, full: html, text
Adding experiments with Django.
- python/users/kent/django/templates/admin/base_site.html
- lines changed 10, context: html, text, full: html, text
Adding experiments with Django.
- python/users/kent/django/templates/cvDb/index.html
- lines changed 9, context: html, text, full: html, text
Adding experiments with Django.
- python/users/kent/django/templates/polls/detail.html
- lines changed 12, context: html, text, full: html, text
Adding experiments with Django.
- python/users/kent/django/templates/polls/index.html
- lines changed 9, context: html, text, full: html, text
Adding experiments with Django.
- python/users/kent/django/templates/polls/results.html
- lines changed 9, context: html, text, full: html, text
Adding experiments with Django.
- src/README
- lines changed 8, context: html, text, full: html, text
Remembered we need real tabs for the makefiles.
- src/cdnaAli/ali2alx/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/cdnaAli/binGood/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/cdnaAli/cdnaOff/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/cdnaAli/cluster/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/cdnaAli/findCdna/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/cdnaAli/g2cCheck/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/cdnaAli/introns/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/cdnaAli/sortFilt/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/cdnaAli/stitchea/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/getgene/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/hg/autoXml/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Another batch of makefile changes to add -lm"
This reverts commit b515245139885e85616db56a4cfd1c6321a84e80.
- src/hg/ctgToChromFa/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Another batch of makefile changes to add -lm"
This reverts commit b515245139885e85616db56a4cfd1c6321a84e80.
- src/hg/encode/DAFs/3.0/hg19/wgEncodeFsuRepliChip.daf
- lines changed 41, context: html, text, full: html, text
Feedback from NHGRI has indicated that tracks should be named Repli-chip rather than Repli-seq. Redmine #6226, #6627.
- src/hg/encode/DAFs/3.0/hg19/wgEncodeFsuRepliSeq.daf
- lines changed 41, context: html, text, full: html, text
Feedback from NHGRI has indicated that tracks should be named Repli-chip rather than Repli-seq. Redmine #6226, #6627.
- src/hg/encode/DAFs/3.0/mm9/wgEncodeFsuRepliChip.daf
- lines changed 44, context: html, text, full: html, text
Feedback from NHGRI has indicated that tracks should be named Repli-chip rather than Repli-seq. Redmine #6226, #6627.
- src/hg/encode/DAFs/3.0/mm9/wgEncodeFsuRepliSeq.daf
- lines changed 44, context: html, text, full: html, text
Feedback from NHGRI has indicated that tracks should be named Repli-chip rather than Repli-seq. Redmine #6226, #6627.
- src/hg/encode/qaAddTrackReferences/qaAddTrackReferences
- lines changed 2, context: html, text, full: html, text
correcting a formatting bug
- src/hg/encode/validateFiles/expected/tagAlign1.out
- lines changed 1, context: html, text, full: html, text
fixing bug in BAM validator, needed if (errs > ), added the old Error Count 0 back to the end of succesful runs, at least for nonBED, fixed make test to actually do something
- src/hg/encode/validateFiles/expected/tagAlign2.out
- lines changed 1, context: html, text, full: html, text
fixing bug in BAM validator, needed if (errs > ), added the old Error Count 0 back to the end of succesful runs, at least for nonBED, fixed make test to actually do something
- src/hg/encode/validateFiles/input/bed12.as
- src/hg/encode/validateFiles/input/bed12.as.note
- src/hg/encode/validateFiles/makefile
- lines changed 12, context: html, text, full: html, text
fixing bug in BAM validator, needed if (errs > ), added the old Error Count 0 back to the end of succesful runs, at least for nonBED, fixed make test to actually do something
- src/hg/encode/validateFiles/tests/goodMaleHg19.bed3
- lines changed 1, context: html, text, full: html, text
removed zero length entries
- src/hg/encode/validateFiles/tests/goodMaleHg19.bed4
- lines changed 1, context: html, text, full: html, text
removed zero length entries
- src/hg/encode/validateFiles/tests/goodMaleHg19.bed5
- src/hg/encode/validateFiles/tests/goodMaleHg19.bed6
- lines changed 1, context: html, text, full: html, text
removed zero length entries
- src/hg/encode/validateFiles/tests/goodMaleHg19.bed7
- lines changed 2, context: html, text, full: html, text
removed zero length entries
- src/hg/encode/validateFiles/tests/goodMaleHg19.bed8
- lines changed 2, context: html, text, full: html, text
removed zero length entries
- src/hg/encode/validateFiles/tests/goodMaleHg19.bed9
- lines changed 2, context: html, text, full: html, text
removed zero length entries
- src/hg/encode/validateFiles/tests/goodMaleHg19.bedRrbs
- lines changed 1, context: html, text, full: html, text
removed zero length entries
- src/hg/encode/validateFiles/tests/goodMaleHg19.short.bedRrbs
- lines changed 2000, context: html, text, full: html, text
added in shortened version of bedRrbs test file
- src/hg/encode/validateFiles/validateFiles.c
- lines changed 2, context: html, text, full: html, text
fixing bug in BAM validator, needed if (errs > ), added the old Error Count 0 back to the end of succesful runs, at least for nonBED, fixed make test to actually do something
- lines changed 8, context: html, text, full: html, text
improving the help msg for vf b2bb hglb
- lines changed 53, context: html, text, full: html, text
fixed long lines per jims review; also removed odd condition on start/end coords
- src/hg/encode/validateFiles/validateFilesUsage
- lines changed 27, context: html, text, full: html, text
Cleaning out duplicate lines
- src/hg/fakeOut/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Another batch of makefile changes to add -lm"
This reverts commit b515245139885e85616db56a4cfd1c6321a84e80.
- src/hg/gbGetEntries/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Another batch of makefile changes to add -lm"
This reverts commit b515245139885e85616db56a4cfd1c6321a84e80.
- src/hg/gbOneAcc/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Another batch of makefile changes to add -lm"
This reverts commit b515245139885e85616db56a4cfd1c6321a84e80.
- src/hg/hgGateway/hgGateway.c
- lines changed 4, context: html, text, full: html, text
tweak/comment geoIpNode query logic
- src/hg/hgTracks/bigBedTrack.c
- lines changed 2, context: html, text, full: html, text
fix bug caused by assumption that limitedVis is always set (#7272)
- src/hg/hgTracks/cutterTrack.c
- lines changed 2, context: html, text, full: html, text
change priorities for oligo and cutter track to ensure they appear after tracks which get the default of 100 (#7309)
- src/hg/hgTracks/hgTracks.c
- lines changed 2, context: html, text, full: html, text
change priorities for oligo and cutter track to ensure they appear after tracks which get the default of 100 (#7309)
- lines changed 2, context: html, text, full: html, text
be more conservative with inPlaceUpdate - turns out tracks can appear/disappear with just center labels turned off (see #6944)
- src/hg/hgTracks/hgTracks.h
- lines changed 6, context: html, text, full: html, text
fix bug caused by assumption that limitedVis is always set (#7272)
- src/hg/hgVarAnnogrator/hgVarAnnogrator.c
- lines changed 1296, context: html, text, full: html, text
Feature #1652 (Variant Annotation Tool): First draft of UI: mostactions trigger an ajax call that sends a JSON description of the
query (and what changed); the response is a JSON description of one
or more page sections, with new HTML content to reflect the change.
There is a lot of code lifted verbatim from hgTables that I intend
to libify when the dust settles a bit (search for "verbatim").
Things that work: group -> track -> table selection; reordering
updates notion of which source is primary (needed for filters);
removed sections are reset, and newly displayed sections always appear
at bottom; all buttons do something, even if it's not yet useful. :)
To do: query execution, position input, output format change handling,
output field selection, and filters.
- src/hg/hgVarAnnogrator/makefile
- lines changed 15, context: html, text, full: html, text
Feature #1652 (Variant Annotation Tool): First draft of UI: mostactions trigger an ajax call that sends a JSON description of the
query (and what changed); the response is a JSON description of one
or more page sections, with new HTML content to reflect the change.
There is a lot of code lifted verbatim from hgTables that I intend
to libify when the dust settles a bit (search for "verbatim").
Things that work: group -> track -> table selection; reordering
updates notion of which source is primary (needed for filters);
removed sections are reset, and newly displayed sections always appear
at bottom; all buttons do something, even if it's not yet useful. :)
To do: query execution, position input, output format change handling,
output field selection, and filters.
- src/hg/htdocs/ENCODE/analysisTools.html
- lines changed 40, context: html, text, full: html, text
Adding new file for ENCODE Software Tools page (redmine #7701)
- lines changed 91, context: html, text, full: html, text
Created new Software Tools pages for ENCODE (redmine #7701)
- lines changed 5, context: html, text, full: html, text
Removed title tags from tool links (redmine #7701)
- lines changed 20, context: html, text, full: html, text
Applied Kate's suggested format changes (redmine #7701)
- src/hg/htdocs/ENCODE/cellTypes.html
- lines changed 2, context: html, text, full: html, text
making the areas for the cell lines bigger because so many have been added
- src/hg/htdocs/ENCODE/dataMatrix/dataMatrix.css
- lines changed 44, context: html, text, full: html, text
1. Add hideable 'Help' panel to Data Matrix page 2. Add 'view matrix' button to ChIP-seq header on Data Matrix page (QA item #8). 3. Change navigation from portal so Data Matrix displayed first.
- lines changed 4, context: html, text, full: html, text
Adjust styling to work with portal panel CSS
- lines changed 2, context: html, text, full: html, text
Color tweaks requested by QA
- src/hg/htdocs/ENCODE/dataMatrix/dataSummary.css
- lines changed 5, context: html, text, full: html, text
Limit hand poiner to clickable items (data items and labels). QA issue 28. Also make row construction clearer
- src/hg/htdocs/ENCODE/dataMatrix/encodeChipMatrixHuman.html
- lines changed 2, context: html, text, full: html, text
More flexible navigation -- expand links on top blue bar to refer to other pages in Data Matrix set and make them customized to each page
- src/hg/htdocs/ENCODE/dataMatrix/encodeChipMatrixInclude.html
- lines changed 1, context: html, text, full: html, text
1. Add cookie to retain user preferences for help screen (also cleanup search cookie handling while the hood is up. 2. Markup help panel to ENCODE portal style (still needs some CSS adjusting)
- src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixHuman.html
- lines changed 3, context: html, text, full: html, text
More flexible navigation -- expand links on top blue bar to refer to other pages in Data Matrix set and make them customized to each page
- src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixInclude.html
- lines changed 15, context: html, text, full: html, text
1. Add hideable 'Help' panel to Data Matrix page 2. Add 'view matrix' button to ChIP-seq header on Data Matrix page (QA item #8). 3. Change navigation from portal so Data Matrix displayed first.
- lines changed 8, context: html, text, full: html, text
1. Add cookie to retain user preferences for help screen (also cleanup search cookie handling while the hood is up. 2. Markup help panel to ENCODE portal style (still needs some CSS adjusting)
- lines changed 1, context: html, text, full: html, text
Move images to ENCODE_specific dir to keep clutter down
- lines changed 25, context: html, text, full: html, text
fixing to adhere to the 100 character line limit and closing <p> tags by adding </p>
- lines changed 7, context: html, text, full: html, text
editing help text: removed a few commas, added commas after e.g., capitalized 'search' for file search for consitency
- src/hg/htdocs/ENCODE/dataMatrix/encodeDataSummaryHuman.html
- lines changed 7, context: html, text, full: html, text
More flexible navigation -- expand links on top blue bar to refer to other pages in Data Matrix set and make them customized to each page
- src/hg/htdocs/ENCODE/dataMatrix/encodeDataSummaryInclude.html
- lines changed 1, context: html, text, full: html, text
1. Add cookie to retain user preferences for help screen (also cleanup search cookie handling while the hood is up. 2. Markup help panel to ENCODE portal style (still needs some CSS adjusting)
- src/hg/htdocs/ENCODE/downloads.html
- lines changed 5, context: html, text, full: html, text
Added entry for FSU Repli-chip (redmine #6626)
- src/hg/htdocs/ENCODE/encodeTools.html
- lines changed 40, context: html, text, full: html, text
Adding new file for ENCODE Software Tools page (redmine #7701)
- lines changed 315, context: html, text, full: html, text
Created new Software Tools pages for ENCODE (redmine #7701)
- lines changed 18, context: html, text, full: html, text
Removed title tags from tool links (redmine #7701)
- lines changed 42, context: html, text, full: html, text
Applied Kate's suggested format changes (redmine #7701)
- src/hg/htdocs/ENCODE/index.html
- lines changed 1, context: html, text, full: html, text
1. Add hideable 'Help' panel to Data Matrix page 2. Add 'view matrix' button to ChIP-seq header on Data Matrix page (QA item #8). 3. Change navigation from portal so Data Matrix displayed first.
- lines changed 1, context: html, text, full: html, text
Created new Software Tools pages for ENCODE (redmine #7701)
- lines changed 3, context: html, text, full: html, text
Moved Software Tools menu item and changed red color code so the text would display as red in both IE and Firefox (redmine #7701)
- lines changed 163, context: html, text, full: html, text
Major news additions. Culling old ones is TBD
- lines changed 67, context: html, text, full: html, text
Update News section for last quarter's releases
- lines changed 17, context: html, text, full: html, text
Made corrections to Kate's news updates. Made some styling corrections.
- lines changed 4, context: html, text, full: html, text
Uncommented Experiment Matrix and Software Tools menu items for dev
- src/hg/htdocs/ENCODE/newsarch.html
- lines changed 69, context: html, text, full: html, text
Update News section for last quarter's releases
- src/hg/htdocs/ENCODE/softwareTools.html
- lines changed 50, context: html, text, full: html, text
Adding new file for ENCODE Software Tools page (redmine #7701)
- lines changed 1, context: html, text, full: html, text
Created new Software Tools pages for ENCODE (redmine #7701)
- src/hg/htdocs/goldenPath/newsarch.html
- lines changed 40, context: html, text, full: html, text
Added news item about GRCh38.
- lines changed 2, context: html, text, full: html, text
Oops, need new window for remote links.
- src/hg/htdocs/images/Heterocephalus_glaber.jpg
- lines changed 0, context: html, text, full: html, text
Scaled down to 300x210 hetGla1 picture.
- src/hg/htdocs/images/Sarcophilus_harrisii.jpg
- lines changed 0, context: html, text, full: html, text
an image of Tasmanian devil from WIkipedia with GNU license
- src/hg/htdocs/images/encode/dataMatrixSearchPanel.png
- lines changed 0, context: html, text, full: html, text
Images for help screen of Data Matrix app
- src/hg/htdocs/images/encode/greenBox.png
- lines changed 0, context: html, text, full: html, text
Images for help screen of Data Matrix app
- src/hg/htdocs/images/phylo/mm10_60way.png
- lines changed 0, context: html, text, full: html, text
first pass an a 60-way tree diagram
- src/hg/htdocs/inc/encodeProject.topbar.html
- lines changed 10, context: html, text, full: html, text
More flexible navigation -- expand links on top blue bar to refer to other pages in Data Matrix set and make them customized to each page
- src/hg/htdocs/indexNews.html
- lines changed 65, context: html, text, full: html, text
Added news item about GRCh38.
- lines changed 2, context: html, text, full: html, text
Oops, need new window for remote links.
- src/hg/htdocs/style/HGStyle.css
- lines changed 23, context: html, text, full: html, text
Added a few styles needed for max's new publications track. Moved a comment to the correct location.
- lines changed 1, context: html, text, full: html, text
Added needed bottom margin to .section style
- lines changed 38, context: html, text, full: html, text
Added new styles used for Chin's new login system
- src/hg/htdocs/style/encodeProject.css
- lines changed 2, context: html, text, full: html, text
1. Add hideable 'Help' panel to Data Matrix page 2. Add 'view matrix' button to ChIP-seq header on Data Matrix page (QA item #8). 3. Change navigation from portal so Data Matrix displayed first.
- src/hg/inc/genePred.h
- lines changed 2, context: html, text, full: html, text
more work to advance #6152. Now with documentation of synonymous changes, the actual changes in (non)synonumous changes, and a fix to gnawing problem of the exonstarts in the genePred disappearing
- src/hg/inc/gpFx.h
- lines changed 1, context: html, text, full: html, text
ongoing work on #6152. Now with non-synonymous changes! (well, at least with respect to the genomic DNA)
- src/hg/inc/jsHelper.h
- lines changed 26, context: html, text, full: html, text
add jsonParse; refactor some existing code to accomodate parsed data
- src/hg/inc/soterm.h
- lines changed 12, context: html, text, full: html, text
ongoing work on #6152. Now with non-synonymous changes! (well, at least with respect to the genomic DNA)
- src/hg/inc/variant.h
- lines changed 1, context: html, text, full: html, text
ongoing work on #6152. Now with non-synonymous changes! (well, at least with respect to the genomic DNA)
- src/hg/inc/versionInfo.h
- src/hg/js/encodeChipMatrix.js
- lines changed 14, context: html, text, full: html, text
Search needs to clear first three fields in Advanced Tab. Taking this opportunity to generalize generation of search url and move to encodeMatrix lib
- src/hg/js/encodeDataMatrix.js
- lines changed 11, context: html, text, full: html, text
Search needs to clear first three fields in Advanced Tab. Taking this opportunity to generalize generation of search url and move to encodeMatrix lib
- lines changed 9, context: html, text, full: html, text
1. Add hideable 'Help' panel to Data Matrix page 2. Add 'view matrix' button to ChIP-seq header on Data Matrix page (QA item #8). 3. Change navigation from portal so Data Matrix displayed first.
- lines changed 3, context: html, text, full: html, text
Suppress special ChIP-seq launcher button on IE as it dont work
- src/hg/js/encodeDataSummary.js
- lines changed 10, context: html, text, full: html, text
Limit hand poiner to clickable items (data items and labels). QA issue 28. Also make row construction clearer
- lines changed 18, context: html, text, full: html, text
Search needs to clear first three fields in Advanced Tab. Taking this opportunity to generalize generation of search url and move to encodeMatrix lib
- src/hg/js/encodeMatrix.js
- lines changed 31, context: html, text, full: html, text
Search needs to clear first three fields in Advanced Tab. Taking this opportunity to generalize generation of search url and move to encodeMatrix lib
- lines changed 15, context: html, text, full: html, text
1. Add hideable 'Help' panel to Data Matrix page 2. Add 'view matrix' button to ChIP-seq header on Data Matrix page (QA item #8). 3. Change navigation from portal so Data Matrix displayed first.
- lines changed 4, context: html, text, full: html, text
Cleanup handling of spinner
- lines changed 4, context: html, text, full: html, text
Repairing overly zealous cleanup of spinner handling
- lines changed 42, context: html, text, full: html, text
1. Add cookie to retain user preferences for help screen (also cleanup search cookie handling while the hood is up. 2. Markup help panel to ENCODE portal style (still needs some CSS adjusting)
- lines changed 7, context: html, text, full: html, text
Fix bug that crept in adopting jQuery cookie plugin for search cookie]
- src/hg/js/encodeProject.js
- lines changed 4, context: html, text, full: html, text
Search needs to clear first three fields in Advanced Tab. Taking this opportunity to generalize generation of search url and move to encodeMatrix lib
- src/hg/js/hgVarAnnogrator.js
- lines changed 111, context: html, text, full: html, text
Feature #1652 (Variant Annotation Tool): First draft of UI: mostactions trigger an ajax call that sends a JSON description of the
query (and what changed); the response is a JSON description of one
or more page sections, with new HTML content to reflect the change.
There is a lot of code lifted verbatim from hgTables that I intend
to libify when the dust settles a bit (search for "verbatim").
Things that work: group -> track -> table selection; reordering
updates notion of which source is primary (needed for filters);
removed sections are reset, and newly displayed sections always appear
at bottom; all buttons do something, even if it's not yet useful. :)
To do: query execution, position input, output format change handling,
output field selection, and filters.
- src/hg/js/jquery.contextmenu.js
- lines changed 5, context: html, text, full: html, text
fix problem where context menu disappeared off the top of the screen (#7687)
- src/hg/js/makefile
- lines changed 1, context: html, text, full: html, text
remove obsolete and unusued jquery-1.2.6.pack.js
- lines changed 1, context: html, text, full: html, text
Feature #1652 (Variant Annotation Tool): First draft of UI: mostactions trigger an ajax call that sends a JSON description of the
query (and what changed); the response is a JSON description of one
or more page sections, with new HTML content to reflect the change.
There is a lot of code lifted verbatim from hgTables that I intend
to libify when the dust settles a bit (search for "verbatim").
Things that work: group -> track -> table selection; reordering
updates notion of which source is primary (needed for filters);
removed sections are reset, and newly displayed sections always appear
at bottom; all buttons do something, even if it's not yet useful. :)
To do: query execution, position input, output format change handling,
output field selection, and filters.
- src/hg/lib/annoGrateWig.c
- lines changed 2, context: html, text, full: html, text
Removing silly debug printf caught by Brian in code review (thanks!).
- src/hg/lib/annoGratorGpVar.c
- lines changed 61, context: html, text, full: html, text
ongoing work on #6152. Now with non-synonymous changes! (well, at least with respect to the genomic DNA)
- lines changed 10, context: html, text, full: html, text
more work to advance #6152. Now with documentation of synonymous changes, the actual changes in (non)synonumous changes, and a fix to gnawing problem of the exonstarts in the genePred disappearing
- src/hg/lib/annoStreamDb.c
- lines changed 4, context: html, text, full: html, text
annoStreamDb: use superclass's numCols instead of own now (#6152).
- src/hg/lib/customFactory.c
- lines changed 2, context: html, text, full: html, text
simple optimization suggested by jim
- src/hg/lib/encode/bedLogR.as
- lines changed 1, context: html, text, full: html, text
Trying to bring the as files and sql files in line wiht each other, specifically score is uint and reserved is uint and strand is char[1]
- src/hg/lib/encode/bedLogR.sql
- lines changed 5, context: html, text, full: html, text
Trying to bring the as files and sql files in line wiht each other, specifically score is uint and reserved is uint and strand is char[1]
- src/hg/lib/encode/bedRnaJunctions.as
- lines changed 2, context: html, text, full: html, text
Trying to bring the as files and sql files in line wiht each other, specifically score is uint and reserved is uint and strand is char[1]
- src/hg/lib/encode/bedRrbs.as
- lines changed 1, context: html, text, full: html, text
Trying to bring the as files and sql files in line wiht each other, specifically score is uint and reserved is uint and strand is char[1]
- src/hg/lib/encode/bedRrbs.sql
- lines changed 8, context: html, text, full: html, text
Trying to bring the as files and sql files in line wiht each other, specifically score is uint and reserved is uint and strand is char[1]
- src/hg/lib/encode/broadPeak.sql
- lines changed 5, context: html, text, full: html, text
Trying to bring the as files and sql files in line wiht each other, specifically score is uint and reserved is uint and strand is char[1]
- src/hg/lib/encode/encodeBuPromCerebrum.sql
- lines changed 24, context: html, text, full: html, text
Moving more things into unsed because they were in obsolete or because they are a .sql file with no .as and no .c
- src/hg/lib/encode/encodeBuPromColon.sql
- lines changed 24, context: html, text, full: html, text
Moving more things into unsed because they were in obsolete or because they are a .sql file with no .as and no .c
- src/hg/lib/encode/encodeBuPromHeart.sql
- lines changed 24, context: html, text, full: html, text
Moving more things into unsed because they were in obsolete or because they are a .sql file with no .as and no .c
- src/hg/lib/encode/encodeBuPromKidney.sql
- lines changed 24, context: html, text, full: html, text
Moving more things into unsed because they were in obsolete or because they are a .sql file with no .as and no .c
- src/hg/lib/encode/encodeBuPromLiver.sql
- lines changed 24, context: html, text, full: html, text
Moving more things into unsed because they were in obsolete or because they are a .sql file with no .as and no .c
- src/hg/lib/encode/encodeBuPromLung.sql
- lines changed 24, context: html, text, full: html, text
Moving more things into unsed because they were in obsolete or because they are a .sql file with no .as and no .c
- src/hg/lib/encode/encodeBuPromSkMuscle.sql
- lines changed 24, context: html, text, full: html, text
Moving more things into unsed because they were in obsolete or because they are a .sql file with no .as and no .c
- src/hg/lib/encode/encodeBuPromSpleen.sql
- lines changed 24, context: html, text, full: html, text
Moving more things into unsed because they were in obsolete or because they are a .sql file with no .as and no .c
- src/hg/lib/encode/encodeBuPromStomach.sql
- lines changed 24, context: html, text, full: html, text
Moving more things into unsed because they were in obsolete or because they are a .sql file with no .as and no .c
- src/hg/lib/encode/encodeBuPromTestis.sql
- lines changed 24, context: html, text, full: html, text
Moving more things into unsed because they were in obsolete or because they are a .sql file with no .as and no .c
- src/hg/lib/encode/encodeErge5race.c
- lines changed 204, context: html, text, full: html, text
Non of these .c files are made. We suspect they were generated by autosql and commited without thought
- src/hg/lib/encode/encodeErgeBinding.c
- lines changed 204, context: html, text, full: html, text
Non of these .c files are made. We suspect they were generated by autosql and commited without thought
- src/hg/lib/encode/encodeErgeDNAseI.c
- lines changed 204, context: html, text, full: html, text
Non of these .c files are made. We suspect they were generated by autosql and commited without thought
- src/hg/lib/encode/encodeErgeExpProm.c
- lines changed 204, context: html, text, full: html, text
Non of these .c files are made. We suspect they were generated by autosql and commited without thought
- src/hg/lib/encode/encodeErgeInVitroFoot.c
- lines changed 204, context: html, text, full: html, text
Non of these .c files are made. We suspect they were generated by autosql and commited without thought
- src/hg/lib/encode/encodeErgeMethProm.c
- lines changed 204, context: html, text, full: html, text
Non of these .c files are made. We suspect they were generated by autosql and commited without thought
- src/hg/lib/encode/encodeErgeStableTransf.c
- lines changed 204, context: html, text, full: html, text
Non of these .c files are made. We suspect they were generated by autosql and commited without thought
- src/hg/lib/encode/encodeErgeSummary.c
- lines changed 204, context: html, text, full: html, text
Non of these .c files are made. We suspect they were generated by autosql and commited without thought
- src/hg/lib/encode/encodeErgeTransTransf.c
- lines changed 204, context: html, text, full: html, text
Non of these .c files are made. We suspect they were generated by autosql and commited without thought
- src/hg/lib/encode/encodePrimateAlleles.c
- lines changed 303, context: html, text, full: html, text
Non of these .c files are made. We suspect they were generated by autosql and commited without thought
- src/hg/lib/encode/gappedPeak.as
- lines changed 1, context: html, text, full: html, text
Trying to bring the as files and sql files in line wiht each other, specifically score is uint and reserved is uint and strand is char[1]
- src/hg/lib/encode/gappedPeak.sql
- lines changed 6, context: html, text, full: html, text
Trying to bring the as files and sql files in line wiht each other, specifically score is uint and reserved is uint and strand is char[1]
- src/hg/lib/encode/narrowPeak.sql
- lines changed 1, context: html, text, full: html, text
Trying to bring the as files and sql files in line wiht each other, specifically score is uint and reserved is uint and strand is char[1]
- src/hg/lib/encode/obsolete/shortFrags.as
- lines changed 31, context: html, text, full: html, text
Moving more things into unsed because they were in obsolete or because they are a .sql file with no .as and no .c
- src/hg/lib/encode/obsolete/shortFrags.sql
- lines changed 37, context: html, text, full: html, text
Moving more things into unsed because they were in obsolete or because they are a .sql file with no .as and no .c
- src/hg/lib/encode/tagAlign.as
- lines changed 1, context: html, text, full: html, text
Trying to bring the as files and sql files in line wiht each other, specifically score is uint and reserved is uint and strand is char[1]
- src/hg/lib/encode/tagAlign.sql
- lines changed 2, context: html, text, full: html, text
Trying to bring the as files and sql files in line wiht each other, specifically score is uint and reserved is uint and strand is char[1]
- src/hg/lib/encode/unused/encodeBuPromCerebrum.sql
- lines changed 24, context: html, text, full: html, text
Moving more things into unsed because they were in obsolete or because they are a .sql file with no .as and no .c
- src/hg/lib/encode/unused/encodeBuPromColon.sql
- lines changed 24, context: html, text, full: html, text
Moving more things into unsed because they were in obsolete or because they are a .sql file with no .as and no .c
- src/hg/lib/encode/unused/encodeBuPromHeart.sql
- lines changed 24, context: html, text, full: html, text
Moving more things into unsed because they were in obsolete or because they are a .sql file with no .as and no .c
- src/hg/lib/encode/unused/encodeBuPromKidney.sql
- lines changed 24, context: html, text, full: html, text
Moving more things into unsed because they were in obsolete or because they are a .sql file with no .as and no .c
- src/hg/lib/encode/unused/encodeBuPromLiver.sql
- lines changed 24, context: html, text, full: html, text
Moving more things into unsed because they were in obsolete or because they are a .sql file with no .as and no .c
- src/hg/lib/encode/unused/encodeBuPromLung.sql
- lines changed 24, context: html, text, full: html, text
Moving more things into unsed because they were in obsolete or because they are a .sql file with no .as and no .c
- src/hg/lib/encode/unused/encodeBuPromSkMuscle.sql
- lines changed 24, context: html, text, full: html, text
Moving more things into unsed because they were in obsolete or because they are a .sql file with no .as and no .c
- src/hg/lib/encode/unused/encodeBuPromSpleen.sql
- lines changed 24, context: html, text, full: html, text
Moving more things into unsed because they were in obsolete or because they are a .sql file with no .as and no .c
- src/hg/lib/encode/unused/encodeBuPromStomach.sql
- lines changed 24, context: html, text, full: html, text
Moving more things into unsed because they were in obsolete or because they are a .sql file with no .as and no .c
- src/hg/lib/encode/unused/encodeBuPromTestis.sql
- lines changed 24, context: html, text, full: html, text
Moving more things into unsed because they were in obsolete or because they are a .sql file with no .as and no .c
- src/hg/lib/encode/unused/encodeErge5race.c
- lines changed 204, context: html, text, full: html, text
Non of these .c files are made. We suspect they were generated by autosql and commited without thought
- src/hg/lib/encode/unused/encodeErgeBinding.c
- lines changed 204, context: html, text, full: html, text
Non of these .c files are made. We suspect they were generated by autosql and commited without thought
- src/hg/lib/encode/unused/encodeErgeDNAseI.c
- lines changed 204, context: html, text, full: html, text
Non of these .c files are made. We suspect they were generated by autosql and commited without thought
- src/hg/lib/encode/unused/encodeErgeExpProm.c
- lines changed 204, context: html, text, full: html, text
Non of these .c files are made. We suspect they were generated by autosql and commited without thought
- src/hg/lib/encode/unused/encodeErgeInVitroFoot.c
- lines changed 204, context: html, text, full: html, text
Non of these .c files are made. We suspect they were generated by autosql and commited without thought
- src/hg/lib/encode/unused/encodeErgeMethProm.c
- lines changed 204, context: html, text, full: html, text
Non of these .c files are made. We suspect they were generated by autosql and commited without thought
- src/hg/lib/encode/unused/encodeErgeStableTransf.c
- lines changed 204, context: html, text, full: html, text
Non of these .c files are made. We suspect they were generated by autosql and commited without thought
- src/hg/lib/encode/unused/encodeErgeSummary.c
- lines changed 204, context: html, text, full: html, text
Non of these .c files are made. We suspect they were generated by autosql and commited without thought
- src/hg/lib/encode/unused/encodeErgeTransTransf.c
- lines changed 204, context: html, text, full: html, text
Non of these .c files are made. We suspect they were generated by autosql and commited without thought
- src/hg/lib/encode/unused/encodePrimateAlleles.c
- lines changed 303, context: html, text, full: html, text
Non of these .c files are made. We suspect they were generated by autosql and commited without thought
- src/hg/lib/encode/unused/shortFrags.as
- lines changed 31, context: html, text, full: html, text
Moving more things into unsed because they were in obsolete or because they are a .sql file with no .as and no .c
- src/hg/lib/encode/unused/shortFrags.sql
- lines changed 37, context: html, text, full: html, text
Moving more things into unsed because they were in obsolete or because they are a .sql file with no .as and no .c
- src/hg/lib/fullBed.as
- lines changed 1, context: html, text, full: html, text
keeping .as score as uint for many reasons. stuck with int for bed struct still in support of old CTs
- src/hg/lib/fullBed.sql
- lines changed 1, context: html, text, full: html, text
keeping .as score as uint for many reasons. stuck with int for bed struct still in support of old CTs
- src/hg/lib/genePred.c
- lines changed 2, context: html, text, full: html, text
more work to advance #6152. Now with documentation of synonymous changes, the actual changes in (non)synonumous changes, and a fix to gnawing problem of the exonstarts in the genePred disappearing
- src/hg/lib/gpFx.c
- lines changed 165, context: html, text, full: html, text
ongoing work on #6152. Now with non-synonymous changes! (well, at least with respect to the genomic DNA)
- lines changed 19, context: html, text, full: html, text
ongoing work #6152. non-synonymous change in gene on the negative strand
- lines changed 51, context: html, text, full: html, text
more work to advance #6152. Now with documentation of synonymous changes, the actual changes in (non)synonumous changes, and a fix to gnawing problem of the exonstarts in the genePred disappearing
- lines changed 158, context: html, text, full: html, text
some clean up for #6152
- src/hg/lib/hui.c
- lines changed 2, context: html, text, full: html, text
Dealing with a name conflict I just introduced between lib and hg/lib.
- src/hg/lib/jsHelper.c
- lines changed 221, context: html, text, full: html, text
add jsonParse; refactor some existing code to accomodate parsed data
- lines changed 60, context: html, text, full: html, text
support escaped chars in json strings
- lines changed 7, context: html, text, full: html, text
cleanup string escape code
- lines changed 14, context: html, text, full: html, text
yet more tweaking to JSON string escape code
- lines changed 14, context: html, text, full: html, text
support scientific notation in jsonParseNumber
- src/hg/lib/tests/annoGratorTester.c
- lines changed 10, context: html, text, full: html, text
ongoing work on #6152. Now with non-synonymous changes! (well, at least with respect to the genomic DNA)
- lines changed 9, context: html, text, full: html, text
ongoing work #6152. non-synonymous change in gene on the negative strand
- lines changed 1, context: html, text, full: html, text
more work to advance #6152. Now with documentation of synonymous changes, the actual changes in (non)synonumous changes, and a fix to gnawing problem of the exonstarts in the genePred disappearing
- src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToGpFx.txt
- lines changed 15, context: html, text, full: html, text
ongoing work on #6152. Now with non-synonymous changes! (well, at least with respect to the genomic DNA)
- lines changed 7, context: html, text, full: html, text
ongoing work #6152. non-synonymous change in gene on the negative strand
- lines changed 17, context: html, text, full: html, text
more work to advance #6152. Now with documentation of synonymous changes, the actual changes in (non)synonumous changes, and a fix to gnawing problem of the exonstarts in the genePred disappearing
- src/hg/lib/variant.c
- lines changed 1, context: html, text, full: html, text
ongoing work on #6152. Now with non-synonymous changes! (well, at least with respect to the genomic DNA)
- src/hg/lib/web.c
- lines changed 1, context: html, text, full: html, text
fix something per tim's code review
- lines changed 3, context: html, text, full: html, text
Feature #1652 (Variant Annotation Tool): First draft of UI: mostactions trigger an ajax call that sends a JSON description of the
query (and what changed); the response is a JSON description of one
or more page sections, with new HTML content to reflect the change.
There is a lot of code lifted verbatim from hgTables that I intend
to libify when the dust settles a bit (search for "verbatim").
Things that work: group -> track -> table selection; reordering
updates notion of which source is primary (needed for filters);
removed sections are reset, and newly displayed sections always appear
at bottom; all buttons do something, even if it's not yet useful. :)
To do: query execution, position input, output format change handling,
output field selection, and filters.
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeFsuRepliChip.release1.notes
- lines changed 92, context: html, text, full: html, text
Added release 1 notes. Redmine #6626.
- src/hg/makeDb/doc/encodeDccMm9/wgEncodePsuHistone.release1.notes
- lines changed 26, context: html, text, full: html, text
Removed G1E H3k4me1 experiment due to peaks being suspect. Moved experiment to release 2. Redmine #111.
- src/hg/makeDb/doc/fr3.txt
- lines changed 157, context: html, text, full: html, text
adding cpgIsland and genscan tracks
- src/hg/makeDb/doc/hetGla1.txt
- lines changed 13, context: html, text, full: html, text
Add N50 and coverage information to hetGla1's descrition page.
- src/hg/makeDb/doc/hg19.txt
- lines changed 65, context: html, text, full: html, text
added windowMasker track
- src/hg/makeDb/doc/mm10.txt
- lines changed 173, context: html, text, full: html, text
loading up the first 60-way result
- lines changed 65, context: html, text, full: html, text
the multiz60waySummary table is loaded and fix a bunch of broken path names
- lines changed 7, context: html, text, full: html, text
Finished tRNAs track for mm10.
- lines changed 1, context: html, text, full: html, text
Modifier the DONE date for the tRNAs track of mm10.
- src/hg/makeDb/hgLoadBed/hgLoadBed.c
- lines changed 7, context: html, text, full: html, text
improving the help msg for vf b2bb hglb
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 7, context: html, text, full: html, text
Feedback from NHGRI has indicated that tracks should be named Repli-chip rather than Repli-seq. Redmine #6226, #6627.
- lines changed 2, context: html, text, full: html, text
Removing the _ in a label where it is supposed to be a space
- lines changed 13, context: html, text, full: html, text
removed mouseCellType from cv (it was just there for temporary validation solution)
- lines changed 2, context: html, text, full: html, text
Fixing a couple of errors in the CV
- lines changed 123, context: html, text, full: html, text
Fixed spelling of Provisional. Also fixed biochain links.
- lines changed 1, context: html, text, full: html, text
reversing a temporary tag chagne
- lines changed 1, context: html, text, full: html, text
changing insertLength to allow None as a field
- lines changed 10, context: html, text, full: html, text
Adding lineage and karyotype to CD20 cells in CV
- lines changed 5, context: html, text, full: html, text
Added readTypes for LICR RNA-seq data set.
- lines changed 54, context: html, text, full: html, text
Adding new cell lines to CV
- lines changed 26, context: html, text, full: html, text
Fixed B cells and T cells in CV
- src/hg/makeDb/trackDb/cv/beta/cv.ra
- lines changed 471, context: html, text, full: html, text
Moving alpha CV to beta
- src/hg/makeDb/trackDb/cv/public/cv.ra
- lines changed 355, context: html, text, full: html, text
Moved approved changes from beta to public. Redmine #7641.
- src/hg/makeDb/trackDb/grcIncidentDb.html
- src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeq.html
- lines changed 27, context: html, text, full: html, text
Removed rel='nofollow' tag from hg18 files (redmine #7533)
- lines changed 6, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg18)
- src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeqRelease2.html
- lines changed 26, context: html, text, full: html, text
Removed rel='nofollow' tag from hg18 files (redmine #7533)
- lines changed 7, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg18)
- src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeqRelease3original.html
- lines changed 26, context: html, text, full: html, text
Removed rel='nofollow' tag from hg18 files (redmine #7533)
- lines changed 7, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg18)
- src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadHmm.html
- lines changed 20, context: html, text, full: html, text
Removed rel='nofollow' tag from hg18 files (redmine #7533)
- lines changed 4, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg18)
- src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.html
- lines changed 35, context: html, text, full: html, text
Removed rel='nofollow' tag from hg18 files (redmine #7533)
- lines changed 9, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg18)
- src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.new.html
- lines changed 35, context: html, text, full: html, text
Removed rel='nofollow' tag from hg18 files (redmine #7533)
- lines changed 8, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg18)
- src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeqProv.html
- lines changed 30, context: html, text, full: html, text
Removed rel='nofollow' tag from hg18 files (redmine #7533)
- lines changed 6, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg18)
- src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeqRelease1.html
- lines changed 30, context: html, text, full: html, text
Removed rel='nofollow' tag from hg18 files (redmine #7533)
- lines changed 6, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg18)
- src/hg/makeDb/trackDb/human/hg18/wgEncodeNhgriNre.html
- lines changed 10, context: html, text, full: html, text
Removed rel='nofollow' tag from hg18 files (redmine #7533)
- lines changed 2, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg18)
- src/hg/makeDb/trackDb/human/hg18/wgEncodeRegTfbsClustered.html
- lines changed 14, context: html, text, full: html, text
Removed rel='nofollow' tag from hg18 files (redmine #7533)
- src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseq.html
- lines changed 64, context: html, text, full: html, text
Removed rel='nofollow' tag from hg18 files (redmine #7533)
- lines changed 10, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg18)
- src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseqRelease2.html
- lines changed 66, context: html, text, full: html, text
Removed rel='nofollow' tag from hg18 files (redmine #7533)
- lines changed 10, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg18)
- src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleRNAseq.html
- lines changed 46, context: html, text, full: html, text
Removed rel='nofollow' tag from hg18 files (redmine #7533)
- lines changed 6, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg18)
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
- lines changed 1, context: html, text, full: html, text
Changed RepliSeq to Repli-chip. Redmine #6626.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
- lines changed 53, context: html, text, full: html, text
restored geo sample accessions from beta for ones that were missing
- lines changed 5, context: html, text, full: html, text
filled in missing labExpIds
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeFsuRepliChip.ra
- lines changed 406, context: html, text, full: html, text
Changed RepliSeq to Repli-chip. Redmine #6626.
- lines changed 41, context: html, text, full: html, text
Added UCSC accessions to the track and ready for approval. Redmine #6626.
- lines changed 13, context: html, text, full: html, text
30. Removed dateUnrestricted for: H9ES, H7-ESC, GM06990, BG02ES. Redmine #6626.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeFsuRepliSeq.ra
- lines changed 406, context: html, text, full: html, text
Changed RepliSeq to Repli-chip. Redmine #6626.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisChiaPet.ra
- lines changed 5, context: html, text, full: html, text
Adding missing accession numbers
- lines changed 60, context: html, text, full: html, text
Fixing date submitted for 4 samples
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
- lines changed 504, context: html, text, full: html, text
added in new track's metadat
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
- lines changed 370, context: html, text, full: html, text
Trying to get the metaCheck to resolve and deal with old revoke policy weirdness
- lines changed 1247, context: html, text, full: html, text
Trying to clean up this track for release, see notes in ticket 6579, working on short labels, long labels, dealing with the DCC Rep issue, removing origAssembly and labProtocolId as redundant information, removing the duplicate trackDb entries
- lines changed 731, context: html, text, full: html, text
Riken changes to merge with Matts
- lines changed 1173, context: html, text, full: html, text
added in dcc accessions and expIdes
- lines changed 19, context: html, text, full: html, text
added in biorep for the tracks that were missing it and we were confident in the source
- lines changed 139, context: html, text, full: html, text
added in new generation 0 data for huvec and helaS3
- lines changed 573, context: html, text, full: html, text
moving platform to seqPlatform
- lines changed 199, context: html, text, full: html, text
removed old rep 162/3 stuff
- lines changed 7, context: html, text, full: html, text
adding in known expIds and accessions
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
- lines changed 261, context: html, text, full: html, text
Fixed pairing of controls. Redmine #4486.
- lines changed 65, context: html, text, full: html, text
Added missign control for GM08174. Redmine #4486.
- lines changed 27, context: html, text, full: html, text
Fixed naming of control for experiment from UCD to STD. Redmine #4486.
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
- lines changed 1, context: html, text, full: html, text
Staging FSU Replication Timing (Release 1) on beta (redmine #6626)
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeCaltechRnaSeq.ra
- lines changed 122, context: html, text, full: html, text
Matt fixed the metadata (redmine #7425)
- lines changed 118, context: html, text, full: html, text
Matt changed insertLength from 'ilNA' to 'None' (redmine #7425)
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeFsuRepliChip.ra
- lines changed 446, context: html, text, full: html, text
Staging FSU Replication Timing (Release 1) on beta (redmine #6626)
- lines changed 13, context: html, text, full: html, text
Venkat removed dateUnrestricted info (redmine #6626)
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
- lines changed 1, context: html, text, full: html, text
Releasing FSU Replication Timing (Release 1) to the RR (redmine #6626)
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeCaltechRnaSeq.ra
- lines changed 2692, context: html, text, full: html, text
Releasing Caltech RNA-Seq (Release 3) Fix release to the RR (redmine #7425)
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeFsuRepliChip.ra
- lines changed 434, context: html, text, full: html, text
Releasing FSU Replication Timing (Release 1) to the RR (redmine #6626)
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- lines changed 2, context: html, text, full: html, text
Changed RepliSeq to Repli-chip. Redmine #6626.
- lines changed 2, context: html, text, full: html, text
movign release2.ra to release3.ra
- lines changed 1, context: html, text, full: html, text
Staging FSU Replication Timing (Release 1) on beta (redmine #6626)
- lines changed 1, context: html, text, full: html, text
Releasing FSU Replication Timing (Release 1) to the RR (redmine #6626)
- lines changed 2, context: html, text, full: html, text
Releasing Caltech RNA-Seq (Release 3) Fix release to the RR (redmine #7425)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.html
- lines changed 52, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- lines changed 10, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release2.html
- lines changed 21, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- lines changed 10, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release3.html
- lines changed 2, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHmm.html
- lines changed 17, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- lines changed 4, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.release3.html
- lines changed 8, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.release3.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeChromSuper.html
- lines changed 36, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- lines changed 8, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra
- lines changed 6, context: html, text, full: html, text
Getting rid of extraFields
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release2.html
- lines changed 9, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- lines changed 4, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.release3.html
- lines changed 16, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- lines changed 8, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliChip.html
- lines changed 150, context: html, text, full: html, text
Changed RepliSeq to Repli-chip. Redmine #6626.
- lines changed 14, context: html, text, full: html, text
Fixes for Redmine #6626
1. Description section: In the first sentence, changed "is" to "was".
2. Description section: In the third sentence, "loess-smoothed" added hyphen
3. Description section: In the third sentence, "individual" fixed spelling
4. Methods section, first paragraph: In the Hiratani reference, removed "i"
5. Methods section, first paragraph: Added month to reference to specify with Ryba paper
6. Methods section, Extraction protocol subsection: Lower cased the protocol
7. Methods section, Extraction protocol subsection: In the second sentence, removed "briefly"
8. Methods section, Extraction protocol subsection: changed "are" to "were".
11. Methods section, Hybridization protocol subsection: fixed link
12. Methods section, Hybridization protocol subsection: Change "The hybridization step used the standard NimbleGen protocol."
13. Methods section, Hybridization protocol subsection: In the second sentence, removed "briefly"
14. Methods section, Hybridization protocol subsection: In the second sentence, added hyphen after "Cy3" and a hyphen between "Cy5" and "labeled".
15. Methods section, Hybridization protocol subsection: In the second sentence,replaced "u" with "μ" for micrograms.
16. Methods section, Hybridization protocol subsection: In the second sentence, added hyphen "evenly-spaced"
18. Methods section, Scan protocol subsection: Removed special chacter
19. Methods section, Scan protocol subsection: made "pe" to "per".
20. Methods section, Scan protocol subsection: Fixed link.
21. Methods section, Data processing subsection: In the second sentence, added hyphen after "early" and "late-replicating"
22. Methods section, Data processing subsection: At the end of the second sentence, add "then" before "averaged"
23. Methods section, Data processing subsection: In the last sentence, removed - after 300
24. Credits section: Fixed email link
- lines changed 1, context: html, text, full: html, text
Fixes for Redmine #6626
9. Methods section, Extraction protocol subsection: Merged second and third sentence.
- lines changed 3, context: html, text, full: html, text
Fixes for redmine #6626
11b. Fixed link to not be relative link
20b. Fixed link to not be relative link
24b. Removed < in email link
28. Track Height set to 32
- src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliChip.ra
- lines changed 103, context: html, text, full: html, text
Changed RepliSeq to Repli-chip. Redmine #6626.
- lines changed 1, context: html, text, full: html, text
Fixes for redmine #6626
11b. Fixed link to not be relative link
20b. Fixed link to not be relative link
24b. Removed < in email link
28. Track Height set to 32
- src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliSeq.html
- lines changed 150, context: html, text, full: html, text
Changed RepliSeq to Repli-chip. Redmine #6626.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliSeq.ra
- lines changed 103, context: html, text, full: html, text
Changed RepliSeq to Repli-chip. Redmine #6626.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV11.html
- lines changed 7, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- lines changed 4, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.html
- lines changed 6, context: html, text, full: html, text
Fixing up ChIA-PET html issues
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.ra
- lines changed 7, context: html, text, full: html, text
Changing the - to underbar or space
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.html
- lines changed 14, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- lines changed 2, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.ra
- lines changed 1, context: html, text, full: html, text
removed extraFields from haib genotype old trackDb.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.release2.html
- lines changed 14, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- lines changed 2, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.html
- lines changed 8, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- lines changed 2, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.release3.html
- lines changed 8, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- lines changed 2, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylWgbs.html
- lines changed 4, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- lines changed 2, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.html
- lines changed 16, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- lines changed 10, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release2.html
- lines changed 15, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- lines changed 10, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.release3.ra
- lines changed 9424, context: html, text, full: html, text
movign release2.ra to release3.ra
- lines changed 163, context: html, text, full: html, text
adding in tracks i forogt to add
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.html
- lines changed 43, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- lines changed 22, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.ra
- lines changed 12, context: html, text, full: html, text
removed extra fields from old synth trackDb.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.release2.html
- lines changed 33, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- lines changed 22, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRbpSuper.html
- lines changed 39, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTfbsClustered.html
- lines changed 11, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release3.html
- lines changed 11, context: html, text, full: html, text
Starting the release notes and the changes to the displayed views
- lines changed 1, context: html, text, full: html, text
Adding the cell lines to the release notes
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.release3.ra
- lines changed 1, context: html, text, full: html, text
Taking Riken out of the RNA-seq super track per Kate request
- lines changed 2581, context: html, text, full: html, text
Trying to clean up this track for release, see notes in ticket 6579, working on short labels, long labels, dealing with the DCC Rep issue, removing origAssembly and labProtocolId as redundant information, removing the duplicate trackDb entries
- lines changed 424, context: html, text, full: html, text
Riken changes to merge with Matts
- lines changed 264, context: html, text, full: html, text
fixed a lot of trackDb problems
- lines changed 8, context: html, text, full: html, text
Changing rank and label for a few to line them up with the meta data
- lines changed 248, context: html, text, full: html, text
trying to show the Generation 0 information in the label, also ditched the errang hg19 line and changed bedRnaElements to bed 6 which I Thought was already done
- lines changed 54, context: html, text, full: html, text
added in new generation 0 data for huvec and helaS3
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.html
- lines changed 45, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- lines changed 6, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhNsome.html
- lines changed 28, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- lines changed 11, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhRnaSeq.html
- lines changed 42, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- lines changed 6, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.html
- lines changed 75, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- lines changed 14, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release2.html
- lines changed 71, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- lines changed 14, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release2.ra
- lines changed 60, context: html, text, full: html, text
Fixed pairing of controls. Redmine #4486.
- lines changed 8, context: html, text, full: html, text
Added missign control for GM08174. Redmine #4486.
- lines changed 6, context: html, text, full: html, text
Fixed naming of control for experiment from UCD to STD. Redmine #4486.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeTfBindingSuper.html
- lines changed 15, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- lines changed 4, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUmassDekker5C.html
- lines changed 23, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- lines changed 18, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.html
- lines changed 34, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- lines changed 14, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.release2.html
- lines changed 34, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- lines changed 14, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.html
- lines changed 10, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- lines changed 14, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.release2.html
- lines changed 8, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- lines changed 16, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.html
- lines changed 12, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- lines changed 7, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.release3.html
- lines changed 7, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- lines changed 11, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.release4.html
- lines changed 8, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- lines changed 10, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release4.html
- lines changed 7, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- lines changed 9, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release5.html
- lines changed 8, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- lines changed 9, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release3.html
- lines changed 4, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- lines changed 3, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.release4.html
- lines changed 5, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwRepliSeq.html
- lines changed 12, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- lines changed 6, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.release3.html
- lines changed 5, context: html, text, full: html, text
Removed rel='nofollow' tag from hg19 files (redmine #7533)
- lines changed 4, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period (hg19)
- src/hg/makeDb/trackDb/moleRat/hetGla1/description.html
- lines changed 17, context: html, text, full: html, text
Add N50 and coverage information to hetGla1's descrition page.
- src/hg/makeDb/trackDb/moleRat/hetGla1/gap.html
- src/hg/makeDb/trackDb/mouse/mm10/chainNet.html
- lines changed 154, context: html, text, full: html, text
updated with reference to one single html page
- lines changed 14, context: html, text, full: html, text
renamed the Metatheria clade to Mammalia because of platypus. added text to chainNet.html to explain why the groupings on hgTrackUi are at a lot of different levels of taxonomic heirarchy
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.60way.ra
- lines changed 195, context: html, text, full: html, text
initial look at the 60way alignment
- lines changed 5, context: html, text, full: html, text
fixup Glire group display and treeImage
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.gliersChainNet.ra
- lines changed 6, context: html, text, full: html, text
updated to new assemblies
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.gliresChainNet.ra
- lines changed 162, context: html, text, full: html, text
moved squirrel in Conservation ordering and changes gliers to glires everywhere
- lines changed 7, context: html, text, full: html, text
updated with reference to one single html page
- lines changed 7, context: html, text, full: html, text
made new clade for rabbit and pike, Lagomorpha, to get them out of Rodentia
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.placentalsChainNet.ra
- lines changed 24, context: html, text, full: html, text
updated to new assemblies
- lines changed 1, context: html, text, full: html, text
updated with reference to one single html page
- lines changed 7, context: html, text, full: html, text
moved hyrax next to elephant
- lines changed 24, context: html, text, full: html, text
moved clades and orgs around so checkboxes are in order
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.previousVersionsChainNet.ra
- lines changed 116, context: html, text, full: html, text
updated to new assemblies
- lines changed 1, context: html, text, full: html, text
updated with reference to one single html page
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.primatesChainNet.ra
- lines changed 6, context: html, text, full: html, text
updated to new assemblies
- lines changed 1, context: html, text, full: html, text
updated with reference to one single html page
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
- lines changed 1, context: html, text, full: html, text
moved squirrel in Conservation ordering and changes gliers to glires everywhere
- lines changed 2, context: html, text, full: html, text
initial look at the 60way alignment
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.vertebrateChainNet.ra
- lines changed 6, context: html, text, full: html, text
updated to new assemblies
- lines changed 1, context: html, text, full: html, text
update reference to html file
- lines changed 5, context: html, text, full: html, text
moved chicken next to turkey
- lines changed 18, context: html, text, full: html, text
added new clade, Teleostei, to get cod and zfish together and away from frogs, etc.
- lines changed 9, context: html, text, full: html, text
renamed the Metatheria clade to Mammalia because of platypus. added text to chainNet.html to explain why the groupings on hgTrackUi are at a lot of different levels of taxonomic heirarchy
- src/hg/makeDb/trackDb/mouse/mm9/description.html
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/makefile
- lines changed 1, context: html, text, full: html, text
Changed RepliSeq to Repli-chip. Redmine #6627.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
- lines changed 169, context: html, text, full: html, text
update with new/resubmissions, change view of unique.bigwig, which contains only unique reads from RawSignal to Signal, use Signal for bigwig, which contains both unique and multi-reads
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeFsuRepliChip.ra
- lines changed 1158, context: html, text, full: html, text
Changed RepliSeq to Repli-chip. Redmine #6627.
- lines changed 219, context: html, text, full: html, text
Fixed meta-data that was missed in the renaming . Redmine #6627.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeFsuRepliSeq.ra
- lines changed 1158, context: html, text, full: html, text
Changed RepliSeq to Repli-chip. Redmine #6627.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrRnaSeq.ra
- lines changed 134, context: html, text, full: html, text
Added readTypes for LICR RNA-seq data set.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwRnaSeq.ra
- lines changed 217, context: html, text, full: html, text
Added readtype. Redmine #4469.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodePsuHistone.ra
- lines changed 151, context: html, text, full: html, text
Staging PSU Histone (Release 1) on beta (redmine #111)
- src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
- lines changed 2, context: html, text, full: html, text
Changed RepliSeq to Repli-chip. Redmine #6627.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechHist.html
- lines changed 21, context: html, text, full: html, text
Removed rel='nofollow' tag from mm9 files (redmine #7533)
- lines changed 6, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period
- lines changed 2, context: html, text, full: html, text
Edited links that were causing 'More ..'s than directories in cgi-bin' messages in broken links report
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechRnaSeq.html
- lines changed 4, context: html, text, full: html, text
Edited links that were causing 'More ..'s than directories in cgi-bin' messages in broken links report
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechRnaSeq.release1.html
- lines changed 8, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period
- lines changed 4, context: html, text, full: html, text
Edited links that were causing 'More ..'s than directories in cgi-bin' messages in broken links report
- lines changed 3, context: html, text, full: html, text
modify display convention
- lines changed 7, context: html, text, full: html, text
typo, display convention after approval call
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechRnaSeq.release1.ra
- lines changed 11, context: html, text, full: html, text
add view Signal for displaying xxx.unique.bigwig, which only contains unique reads, the RawSignal view was used for xxx.unique.bigwig and now it's being used for bigwig, the unfiltered mapping results containing both uniq- and multi-reads
- lines changed 148, context: html, text, full: html, text
update with new/resubmissions, change view of unique.bigwig, which contains only unique reads from RawSignal to Signal, use Signal for bigwig, which contains both unique and multi-reads
- lines changed 29, context: html, text, full: html, text
modify labels, setting default display setting
- lines changed 1, context: html, text, full: html, text
typo, display convention after approval call
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechTfbs.html
- lines changed 19, context: html, text, full: html, text
Removed rel='nofollow' tag from mm9 files (redmine #7533)
- lines changed 6, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period
- lines changed 2, context: html, text, full: html, text
Edited links that were causing 'More ..'s than directories in cgi-bin' messages in broken links report
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCaltechTfbs.release2.html
- lines changed 19, context: html, text, full: html, text
Removed rel='nofollow' tag from mm9 files (redmine #7533)
- lines changed 6, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period
- lines changed 2, context: html, text, full: html, text
Edited links that were causing 'More ..'s than directories in cgi-bin' messages in broken links report
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.html
- lines changed 7, context: html, text, full: html, text
Removed rel='nofollow' tag from mm9 files (redmine #7533)
- lines changed 4, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period
- lines changed 4, context: html, text, full: html, text
Edited links that were causing 'More ..'s than directories in cgi-bin' messages in broken links report
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeCshlLongRnaSeq.release2.html
- lines changed 4, context: html, text, full: html, text
Edited links that were causing 'More ..'s than directories in cgi-bin' messages in broken links report
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeFsuRepliChip.html
- lines changed 149, context: html, text, full: html, text
Changed RepliSeq to Repli-chip. Redmine #6627.
- lines changed 1, context: html, text, full: html, text
Edited links that were causing 'More ..'s than directories in cgi-bin' messages in broken links report
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeFsuRepliChip.ra
- lines changed 238, context: html, text, full: html, text
Changed RepliSeq to Repli-chip. Redmine #6627.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeFsuRepliSeq.html
- lines changed 149, context: html, text, full: html, text
Changed RepliSeq to Repli-chip. Redmine #6627.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeFsuRepliSeq.ra
- lines changed 238, context: html, text, full: html, text
Changed RepliSeq to Repli-chip. Redmine #6627.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.html
- lines changed 147, context: html, text, full: html, text
Removed rel='nofollow' tag from mm9 files (redmine #7533)
- lines changed 16, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period
- lines changed 2, context: html, text, full: html, text
Edited links that were causing 'More ..'s than directories in cgi-bin' messages in broken links report
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release2.html
- lines changed 77, context: html, text, full: html, text
Removed rel='nofollow' tag from mm9 files (redmine #7533)
- lines changed 1, context: html, text, full: html, text
correct spelling of Chip-seq to ChIP-seq
- lines changed 34, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period
- lines changed 2, context: html, text, full: html, text
Edited links that were causing 'More ..'s than directories in cgi-bin' messages in broken links report
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release3.html
- lines changed 77, context: html, text, full: html, text
Removed rel='nofollow' tag from mm9 files (redmine #7533)
- lines changed 34, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period
- lines changed 2, context: html, text, full: html, text
Edited links that were causing 'More ..'s than directories in cgi-bin' messages in broken links report
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.html
- lines changed 45, context: html, text, full: html, text
Removed rel='nofollow' tag from mm9 files (redmine #7533)
- lines changed 8, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period
- lines changed 2, context: html, text, full: html, text
Edited links that were causing 'More ..'s than directories in cgi-bin' messages in broken links report
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.release2.html
- lines changed 24, context: html, text, full: html, text
Removed rel='nofollow' tag from mm9 files (redmine #7533)
- lines changed 8, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period
- lines changed 2, context: html, text, full: html, text
Edited links that were causing 'More ..'s than directories in cgi-bin' messages in broken links report
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.html
- lines changed 147, context: html, text, full: html, text
Removed rel='nofollow' tag from mm9 files (redmine #7533)
- lines changed 16, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period
- lines changed 2, context: html, text, full: html, text
Edited links that were causing 'More ..'s than directories in cgi-bin' messages in broken links report
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.release2.html
- lines changed 1, context: html, text, full: html, text
Fixed a typo that steve found during code review, redmine# 7655
- lines changed 2, context: html, text, full: html, text
Edited links that were causing 'More ..'s than directories in cgi-bin' messages in broken links report
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.html
- lines changed 37, context: html, text, full: html, text
Removed rel='nofollow' tag from mm9 files (redmine #7533)
- lines changed 24, context: html, text, full: html, text
Fixed for Redmine #111
3. Description Section, third paragraph changed "are" to "is"
6. Capatalized bowtie
7. Removed comman after "Since"
8. Added "the" to downloads page link
11. Fixed spacing issue in references links, by moving "</a>." to same line as article title
- lines changed 1, context: html, text, full: html, text
Added a to make sentence readable. Redmine #111.
- lines changed 2, context: html, text, full: html, text
Moved the out of the link for the downloads page. Redmine #111.
- lines changed 1, context: html, text, full: html, text
Added first name to reference of Hardison in Contact section. Redmine #111.
- lines changed 3, context: html, text, full: html, text
Edited links that were causing 'More ..'s than directories in cgi-bin' messages in broken links report
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.ra
- lines changed 22, context: html, text, full: html, text
Removed G1E H3k4me1 experiment due to peaks being suspect. Moved experiment to release 2. Redmine #111.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.release2.html
- lines changed 3, context: html, text, full: html, text
Edited links that were causing 'More ..'s than directories in cgi-bin' messages in broken links report
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.release2.ra
- lines changed 52, context: html, text, full: html, text
Removed G1E H3k4me1 experiment due to peaks being suspect. Moved experiment to release 2. Redmine #111.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.html
- lines changed 120, context: html, text, full: html, text
Removed rel='nofollow' tag from mm9 files (redmine #7533)
- lines changed 26, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period
- lines changed 3, context: html, text, full: html, text
Edited links that were causing 'More ..'s than directories in cgi-bin' messages in broken links report
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.release2.html
- lines changed 3, context: html, text, full: html, text
Edited links that were causing 'More ..'s than directories in cgi-bin' messages in broken links report
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHist.html
- lines changed 65, context: html, text, full: html, text
Removed rel='nofollow' tag from mm9 files (redmine #7533)
- lines changed 10, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period
- lines changed 3, context: html, text, full: html, text
Edited links that were causing 'More ..'s than directories in cgi-bin' messages in broken links report
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHist.release2.html
- lines changed 68, context: html, text, full: html, text
Removed rel='nofollow' tag from mm9 files (redmine #7533)
- lines changed 10, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period
- lines changed 3, context: html, text, full: html, text
Edited links that were causing 'More ..'s than directories in cgi-bin' messages in broken links report
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhRnaSeq.html
- lines changed 50, context: html, text, full: html, text
Removed rel='nofollow' tag from mm9 files (redmine #7533)
- lines changed 6, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period
- lines changed 2, context: html, text, full: html, text
Edited links that were causing 'More ..'s than directories in cgi-bin' messages in broken links report
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.html
- lines changed 92, context: html, text, full: html, text
Removed rel='nofollow' tag from mm9 files (redmine #7533)
- lines changed 10, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period
- lines changed 3, context: html, text, full: html, text
Edited links that were causing 'More ..'s than directories in cgi-bin' messages in broken links report
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.release3.html
- lines changed 93, context: html, text, full: html, text
Removed rel='nofollow' tag from mm9 files (redmine #7533)
- lines changed 1, context: html, text, full: html, text
update release note with number of total and new experiments, easy to see when the #autogenerated label is still there
- lines changed 10, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period
- lines changed 3, context: html, text, full: html, text
Edited links that were causing 'More ..'s than directories in cgi-bin' messages in broken links report
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.release3.ra
- lines changed 26, context: html, text, full: html, text
give different color scheme for different subtracks
- lines changed 95, context: html, text, full: html, text
set different color for different tfbs, set same color for input.
- lines changed 114, context: html, text, full: html, text
change color back to the scheme the consortium aggreed on #3990
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDgf.html
- lines changed 12, context: html, text, full: html, text
Removed rel='nofollow' tag from mm9 files (redmine #7533)
- lines changed 4, context: html, text, full: html, text
Put '</a>.' on same line as article titles because there was an extra space between the article title and the period
- lines changed 4, context: html, text, full: html, text
Edited links that were causing 'More ..'s than directories in cgi-bin' messages in broken links report
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.html
- lines changed 3, context: html, text, full: html, text
Edited links that were causing 'More ..'s than directories in cgi-bin' messages in broken links report
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.release2.html
- lines changed 3, context: html, text, full: html, text
Edited links that were causing 'More ..'s than directories in cgi-bin' messages in broken links report
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwRnaSeq.html
- lines changed 3, context: html, text, full: html, text
Edited links that were causing 'More ..'s than directories in cgi-bin' messages in broken links report
- src/hg/makeDb/trackDb/tagTypes.tab
- src/hg/makeDb/trackDb/tasmanianDevil/sarHar1/description.html
- lines changed 5, context: html, text, full: html, text
added GNU-licence photo from Wikipedia
- src/hg/makeDb/trackDb/transMap.html
- lines changed 33, context: html, text, full: html, text
In order to fix broken links, regenerated journal links with qaAddTrackReferences
- src/hg/makeDb/trackDb/transMapAlnMRna.html
- lines changed 32, context: html, text, full: html, text
In order to fix broken links, regenerated journal links with qaAddTrackReferences
- src/hg/makeDb/trackDb/transMapAlnRefSeq.html
- lines changed 32, context: html, text, full: html, text
In order to fix broken links, regenerated journal links with qaAddTrackReferences
- src/hg/makeDb/trackDb/transMapAlnSplicedEst.html
- lines changed 32, context: html, text, full: html, text
In order to fix broken links, regenerated journal links with qaAddTrackReferences
- src/hg/makeDb/trackDb/transMapAlnUcscGenes.html
- lines changed 32, context: html, text, full: html, text
In order to fix broken links, regenerated journal links with qaAddTrackReferences
- src/hg/makeDb/trackDb/wgEncodeNhgriBip.html
- lines changed 48, context: html, text, full: html, text
Removed rel='nofollow' tag (redmine #7533)
- src/hg/oneShot/encodeExpToCvDb/doIt
- lines changed 1, context: html, text, full: html, text
Some of this module to help turn encodeExp table into something in cvDb relational database is working.
- src/hg/oneShot/encodeExpToCvDb/encodeExpToCvDb.c
- lines changed 169, context: html, text, full: html, text
Some of this module to help turn encodeExp table into something in cvDb relational database is working.
- lines changed 187, context: html, text, full: html, text
Creating tab separated file and django model for an 'experiment' table based on hgFixed.encodeExps and hg19.metaDb
- lines changed 93, context: html, text, full: html, text
Further work, mostly making it generate series table too.
- src/hg/oneShot/encodeExpToCvDb/exp.sql
- lines changed 36, context: html, text, full: html, text
Sort of a pain to get Django to generate this, so committing it.
- src/hg/oneShot/encodeExpToCvDb/makefile
- lines changed 18, context: html, text, full: html, text
Some of this module to help turn encodeExp table into something in cvDb relational database is working.
- src/hg/oneShot/encodeExpToCvDb/results.sql
- src/hg/oneShot/encodeExpToCvDb/series.sql
- lines changed 8, context: html, text, full: html, text
Further work, mostly making it generate series table too.
- src/hg/oneShot/testCvToSql/README
- lines changed 2, context: html, text, full: html, text
A little README for the testCvToSql dir.
- src/hg/oneShot/testCvToSql/splitAntibody.ra
- lines changed 7, context: html, text, full: html, text
Adding some scripting to post-process cv database tab and model files.
- src/hg/oneShot/testCvToSql/splitAntibody.sql
- lines changed 34, context: html, text, full: html, text
Adding a few more files will want to reuse come the true conversion.
- src/hg/oneShot/testCvToSql/splitAntibodyModel.py
- lines changed 47, context: html, text, full: html, text
Adding some scripting to post-process cv database tab and model files.
- lines changed 31, context: html, text, full: html, text
Adding a few more files will want to reuse come the true conversion.
- src/hg/oneShot/testCvToSql/testCvToSql.c
- lines changed 141, context: html, text, full: html, text
Making it do direct SQL create table output. Adding prefix for tables for django
- lines changed 18, context: html, text, full: html, text
Adding missing parenthesis to Django output. Adding admin section to Django output.
- lines changed 36, context: html, text, full: html, text
Separating django output into separate files.
- lines changed 5, context: html, text, full: html, text
Fixing it so have control over table name so Django doesn't stomp camelCasing word separators.
- lines changed 246, context: html, text, full: html, text
Simplifying things a bit - removing table splitting parts.
- lines changed 2, context: html, text, full: html, text
Changing class level comment to be in doc string format.
- src/hg/oneShot/testCvToSql/tryIt
- lines changed 37, context: html, text, full: html, text
Adding some scripting to post-process cv database tab and model files.
- src/hg/patCount/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Another batch of makefile changes to add -lm"
This reverts commit b515245139885e85616db56a4cfd1c6321a84e80.
- src/hg/protein/spToDb/spDb.sql
- lines changed 16, context: html, text, full: html, text
Moving featureId so easier to do foreign key constraints.
- src/hg/scanRa/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Another batch of makefile changes to add -lm"
This reverts commit b515245139885e85616db56a4cfd1c6321a84e80.
- src/hg/splitFa/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Another batch of makefile changes to add -lm"
This reverts commit b515245139885e85616db56a4cfd1c6321a84e80.
- src/hg/utils/automation/Encode.pm
- lines changed 4, context: html, text, full: html, text
Fixed ENCODE freeze date.
- src/hg/utils/automation/HgDb.pm
- lines changed 10, context: html, text, full: html, text
support db in profiles (used for central profiles)
- src/hg/utils/automation/doCpgIslands.pl
- lines changed 156, context: html, text, full: html, text
masking and cpg operation are now kluster jobs to take care of the gigantic contig count genomes
- lines changed 1, context: html, text, full: html, text
correctly specify paraHub for the doCpg script
- lines changed 11, context: html, text, full: html, text
add run time calculation
- lines changed 2, context: html, text, full: html, text
add featureBits measurement of result
- src/hg/utils/automation/geoMirrorNode.pl
- lines changed 63, context: html, text, full: html, text
this is a script to test sanity of entries in geoIpNode (#3103)
- src/hg/utils/verticalSplitSqlTable/makefile
- lines changed 21, context: html, text, full: html, text
Starting program that will split a table into two vertically.
- lines changed 6, context: html, text, full: html, text
Vertical table splitter seems to work.
- lines changed 26, context: html, text, full: html, text
Moving out of hg since no need for MySQL.
- src/hg/utils/verticalSplitSqlTable/tests/expected/cvDb_abTarget.as
- lines changed 9, context: html, text, full: html, text
Vertical table splitter seems to work.
- lines changed 9, context: html, text, full: html, text
Moving out of hg since no need for MySQL.
- src/hg/utils/verticalSplitSqlTable/tests/expected/cvDb_abTarget.tab
- lines changed 81, context: html, text, full: html, text
Vertical table splitter seems to work.
- lines changed 81, context: html, text, full: html, text
Moving out of hg since no need for MySQL.
- src/hg/utils/verticalSplitSqlTable/tests/expected/cvDb_antibody.as
- lines changed 17, context: html, text, full: html, text
Vertical table splitter seems to work.
- lines changed 17, context: html, text, full: html, text
Moving out of hg since no need for MySQL.
- src/hg/utils/verticalSplitSqlTable/tests/expected/cvDb_antibody.tab
- lines changed 100, context: html, text, full: html, text
Vertical table splitter seems to work.
- lines changed 100, context: html, text, full: html, text
Moving out of hg since no need for MySQL.
- src/hg/utils/verticalSplitSqlTable/tests/expected/mergeErrs.txt
- lines changed 29, context: html, text, full: html, text
Vertical table splitter seems to work.
- lines changed 29, context: html, text, full: html, text
Moving out of hg since no need for MySQL.
- src/hg/utils/verticalSplitSqlTable/tests/in/antibody.as
- lines changed 20, context: html, text, full: html, text
Starting program that will split a table into two vertically.
- lines changed 20, context: html, text, full: html, text
Moving out of hg since no need for MySQL.
- src/hg/utils/verticalSplitSqlTable/tests/in/antibody.split
- lines changed 7, context: html, text, full: html, text
Starting program that will split a table into two vertically.
- lines changed 1, context: html, text, full: html, text
Vertical table splitter seems to work.
- lines changed 7, context: html, text, full: html, text
Moving out of hg since no need for MySQL.
- src/hg/utils/verticalSplitSqlTable/tests/in/antibody.tab
- lines changed 100, context: html, text, full: html, text
Vertical table splitter seems to work.
- lines changed 100, context: html, text, full: html, text
Moving out of hg since no need for MySQL.
- src/hg/utils/verticalSplitSqlTable/verticalSplitSqlTable.c
- lines changed 176, context: html, text, full: html, text
Starting program that will split a table into two vertically.
- lines changed 187, context: html, text, full: html, text
Vertical table splitter seems to work.
- lines changed 5, context: html, text, full: html, text
Improving usage statement.
- lines changed 1, context: html, text, full: html, text
Improving usage statement.
- lines changed 349, context: html, text, full: html, text
Moving out of hg since no need for MySQL.
- src/inc/annoFilter.h
- lines changed 5, context: html, text, full: html, text
Feature #6152 (Variant Annotation Tool): enhancement to filter logic:filters can be for inclusion or exclusion when the condition is met,
based on the new filter->isExclude. When a filter is set to rightJoin
and it is for inclusion, annoGratorIntegrate propagates rightJoin
failure if no rows overlap since the condition for inclusion has not
been met.
- src/inc/annoGrator.h
- lines changed 4, context: html, text, full: html, text
Feature #6152 (Variant Annotation Tool): enhancement to filter logic:filters can be for inclusion or exclusion when the condition is met,
based on the new filter->isExclude. When a filter is set to rightJoin
and it is for inclusion, annoGratorIntegrate propagates rightJoin
failure if no rows overlap since the condition for inclusion has not
been met.
- src/inc/annoStreamer.h
- lines changed 4, context: html, text, full: html, text
Feature #6152 (Variant Annotation Tool): enhancement to filter logic:filters can be for inclusion or exclusion when the condition is met,
based on the new filter->isExclude. When a filter is set to rightJoin
and it is for inclusion, annoGratorIntegrate propagates rightJoin
failure if no rows overlap since the condition for inclusion has not
been met.
- src/inc/asParse.h
- lines changed 3, context: html, text, full: html, text
Adding asColumnFind function.
- src/inc/basicBed.h
- lines changed 1, context: html, text, full: html, text
keeping .as score as uint for many reasons. stuck with int for bed struct still in support of old CTs
- src/inc/common.h
- lines changed 3, context: html, text, full: html, text
Adding trimLastChar function.
- src/inc/dystring.h
- lines changed 2, context: html, text, full: html, text
Feature #1652 (Variant Annotation Tool): First draft of UI: mostactions trigger an ajax call that sends a JSON description of the
query (and what changed); the response is a JSON description of one
or more page sections, with new HTML content to reflect the change.
There is a lot of code lifted verbatim from hgTables that I intend
to libify when the dust settles a bit (search for "verbatim").
Things that work: group -> track -> table selection; reordering
updates notion of which source is primary (needed for filters);
removed sections are reset, and newly displayed sections always appear
at bottom; all buttons do something, even if it's not yet useful. :)
To do: query execution, position input, output format change handling,
output field selection, and filters.
- src/inc/linefile.h
- lines changed 6, context: html, text, full: html, text
remove -lm dependency on linefile; also enables others to use callback methods to support other types
- src/index/indexfa/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/index/indexgl/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/index/ixali/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/index/ixword1/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/index/ixword3/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/index/makepgo/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/index/stToXao/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/lib/annoFilter.c
- lines changed 30, context: html, text, full: html, text
Feature #6152 (Variant Annotation Tool): enhancement to filter logic:filters can be for inclusion or exclusion when the condition is met,
based on the new filter->isExclude. When a filter is set to rightJoin
and it is for inclusion, annoGratorIntegrate propagates rightJoin
failure if no rows overlap since the condition for inclusion has not
been met.
- src/lib/annoGrator.c
- lines changed 27, context: html, text, full: html, text
Feature #6152 (Variant Annotation Tool): enhancement to filter logic:filters can be for inclusion or exclusion when the condition is met,
based on the new filter->isExclude. When a filter is set to rightJoin
and it is for inclusion, annoGratorIntegrate propagates rightJoin
failure if no rows overlap since the condition for inclusion has not
been met.
- src/lib/asParse.c
- lines changed 11, context: html, text, full: html, text
Adding asColumnFind function.
- lines changed 8, context: html, text, full: html, text
Dealing with a name conflict I just introduced between lib and hg/lib.
- src/lib/basicBed.c
- lines changed 1, context: html, text, full: html, text
keeping .as score as uint for many reasons. stuck with int for bed struct still in support of old CTs
- src/lib/common.c
- lines changed 8, context: html, text, full: html, text
Adding trimLastChar function.
- src/lib/lineFileOnBigBed.c
- lines changed 110, context: html, text, full: html, text
remove -lm dependency on linefile; also enables others to use callback methods to support other types
- src/lib/linefile.c
- lines changed 79, context: html, text, full: html, text
remove -lm dependency on linefile; also enables others to use callback methods to support other types
- src/lib/makefile
- lines changed 1, context: html, text, full: html, text
remove -lm dependency on linefile; also enables others to use callback methods to support other types
- src/lib/obscure.c
- lines changed 1, context: html, text, full: html, text
Fixing an old typo in comment.
- src/lib/tests/makefile
- lines changed 15, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/primeMate/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/protDust/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/reformat/fatont4/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/reformat/gb2cdi/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/reformat/gbtofa/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/reformat/geniegff/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/reformat/gffgenes/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/reformat/moresyn/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/scanIntrons/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/tracks/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/utils/addCols/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/utils/asCompare/asCompare.c
- src/utils/aveCols/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/utils/bedToBigBed/bedToBigBed.c
- lines changed 6, context: html, text, full: html, text
improving the help msg for vf b2bb hglb
- src/utils/catUncomment/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/utils/ccCp/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/utils/chopFaLines/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/utils/countChars/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/utils/cpgIslandExt/README
- lines changed 26, context: html, text, full: html, text
UCSC source from CVS source tree 2005 version
- src/utils/cpgIslandExt/cpg.c
- lines changed 174, context: html, text, full: html, text
UCSC source from CVS source tree 2005 version
- src/utils/cpgIslandExt/cpg_lh.c
- lines changed 200, context: html, text, full: html, text
UCSC source from CVS source tree 2005 version
- lines changed 12, context: html, text, full: html, text
fixup compile errors with modern environment
- src/utils/cpgIslandExt/makefile
- lines changed 2, context: html, text, full: html, text
UCSC source from CVS source tree 2005 version
- lines changed 21, context: html, text, full: html, text
fixup compile errors with modern environment
- src/utils/cpgIslandExt/readseq.c
- lines changed 191, context: html, text, full: html, text
UCSC source from CVS source tree 2005 version
- lines changed 2, context: html, text, full: html, text
fixup compile errors with modern environment
- src/utils/cpgIslandExt/readseq.h
- lines changed 9, context: html, text, full: html, text
UCSC source from CVS source tree 2005 version
- src/utils/faNoise/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/utils/faOneRecord/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/utils/faSplit/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/utils/fixCr/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Another batch of makefile changes to add -lm"
This reverts commit b515245139885e85616db56a4cfd1c6321a84e80.
- src/utils/git-reports/git-reports.c
- lines changed 2, context: html, text, full: html, text
fixing problem between htmlEncoding and wanting to preserve newlines in comments
- src/utils/htmlPics/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Another batch of makefile changes to add -lm"
This reverts commit b515245139885e85616db56a4cfd1c6321a84e80.
- src/utils/jkUniq/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Another batch of makefile changes to add -lm"
This reverts commit b515245139885e85616db56a4cfd1c6321a84e80.
- src/utils/makefile
- lines changed 1, context: html, text, full: html, text
Addint verticalSplitSqlTable to makefile.
- src/utils/newProg/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Another batch of makefile changes to add -lm"
This reverts commit b515245139885e85616db56a4cfd1c6321a84e80.
- src/utils/nibFrag/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Another batch of makefile changes to add -lm"
This reverts commit b515245139885e85616db56a4cfd1c6321a84e80.
- src/utils/nibSize/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Another batch of makefile changes to add -lm"
This reverts commit b515245139885e85616db56a4cfd1c6321a84e80.
- src/utils/qa/makeUniProtFile.csh
- lines changed 2, context: html, text, full: html, text
Added -e so that the script will exit on errors, and changed the cp at the end to cp -f to force a copy of the file for cases where the existing file is not group writeable.
- lines changed 6, context: html, text, full: html, text
On second thought, changed the copy at the end to a move, so that the new file will have the same ownership as the person who ran the script. Changed the final steps to look at the file in the new location, not the current directory.
- src/utils/qa/weeklybld/buildEnv.csh
- src/utils/replaceTextBetween/makefile
- lines changed 24, context: html, text, full: html, text
Another little text utility seems to work.
- src/utils/replaceTextBetween/replaceTextBetween.c
- lines changed 76, context: html, text, full: html, text
Another little text utility seems to work.
- src/utils/replaceTextBetween/testExpected
- lines changed 1, context: html, text, full: html, text
Another little text utility seems to work.
- src/utils/replaceTextBetween/testExpectedWithEnds
- lines changed 1, context: html, text, full: html, text
Another little text utility seems to work.
- src/utils/replaceTextBetween/testInner
- lines changed 1, context: html, text, full: html, text
Another little text utility seems to work.
- src/utils/replaceTextBetween/testOuter
- lines changed 1, context: html, text, full: html, text
Another little text utility seems to work.
- src/utils/rmFaDups/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Another batch of makefile changes to add -lm"
This reverts commit b515245139885e85616db56a4cfd1c6321a84e80.
- src/utils/scaffoldFaToAgp/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Another batch of makefile changes to add -lm"
This reverts commit b515245139885e85616db56a4cfd1c6321a84e80.
- src/utils/scrambleFa/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Another batch of makefile changes to add -lm"
This reverts commit b515245139885e85616db56a4cfd1c6321a84e80.
- src/utils/subChar/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Another batch of makefile changes to add -lm"
This reverts commit b515245139885e85616db56a4cfd1c6321a84e80.
- src/utils/textBetween/makefile
- lines changed 18, context: html, text, full: html, text
A handy little text utility, sort of a text PCR.
- src/utils/textBetween/textBetween.c
- lines changed 54, context: html, text, full: html, text
A handy little text utility, sort of a text PCR.
- src/utils/toLower/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Another batch of makefile changes to add -lm"
This reverts commit b515245139885e85616db56a4cfd1c6321a84e80.
- src/utils/toUpper/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Another batch of makefile changes to add -lm"
This reverts commit b515245139885e85616db56a4cfd1c6321a84e80.
- src/utils/undupFa/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Another batch of makefile changes to add -lm"
This reverts commit b515245139885e85616db56a4cfd1c6321a84e80.
- src/utils/upper/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Another batch of makefile changes to add -lm"
This reverts commit b515245139885e85616db56a4cfd1c6321a84e80.
- src/utils/verticalSplitSqlTable/makefile
- lines changed 26, context: html, text, full: html, text
Moving out of hg since no need for MySQL.
- lines changed 2, context: html, text, full: html, text
Fixing up makefile after directory move.
- src/utils/verticalSplitSqlTable/tests/expected/cvDb_abTarget.as
- lines changed 9, context: html, text, full: html, text
Moving out of hg since no need for MySQL.
- src/utils/verticalSplitSqlTable/tests/expected/cvDb_abTarget.tab
- lines changed 81, context: html, text, full: html, text
Moving out of hg since no need for MySQL.
- src/utils/verticalSplitSqlTable/tests/expected/cvDb_antibody.as
- lines changed 17, context: html, text, full: html, text
Moving out of hg since no need for MySQL.
- src/utils/verticalSplitSqlTable/tests/expected/cvDb_antibody.tab
- lines changed 100, context: html, text, full: html, text
Moving out of hg since no need for MySQL.
- src/utils/verticalSplitSqlTable/tests/expected/mergeErrs.txt
- lines changed 29, context: html, text, full: html, text
Moving out of hg since no need for MySQL.
- src/utils/verticalSplitSqlTable/tests/in/antibody.as
- lines changed 20, context: html, text, full: html, text
Moving out of hg since no need for MySQL.
- src/utils/verticalSplitSqlTable/tests/in/antibody.split
- lines changed 7, context: html, text, full: html, text
Moving out of hg since no need for MySQL.
- src/utils/verticalSplitSqlTable/tests/in/antibody.tab
- lines changed 100, context: html, text, full: html, text
Moving out of hg since no need for MySQL.
- src/utils/verticalSplitSqlTable/verticalSplitSqlTable.c
- lines changed 349, context: html, text, full: html, text
Moving out of hg since no need for MySQL.
- lines changed 2, context: html, text, full: html, text
Clarifying usage message.
- src/utils/wordLine/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Another batch of makefile changes to add -lm"
This reverts commit b515245139885e85616db56a4cfd1c6321a84e80.
- src/weblet/counter/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/weblet/hitreport/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- src/xenoAli/bwana/makefile
- lines changed 1, context: html, text, full: html, text
Revert "Added -lm to a bunch of makefiles since Galt's recent change (I think) calls math routines in lib code."
This reverts commit d8d7b36bf9eac1c01e342ec56182caa374d46c3a.
- lines changed: 52952
- files changed: 733
