All File Changes
v251_preview to v251_preview2 (2011-04-26 to 2011-05-03) v251
- python/ucscgenomics/rafile/OrderedDict.py
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first push to my new branch
- python/ucscgenomics/rafile/RaFile.py
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first push to my new branch
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small changes to cv Validation
- python/ucscgenomics/rafile/cv/CvFile.py
- python/ucscgenomics/rafile/cv/CvRaFile.py
- lines changed 93, context: html, text, full: html, text
small changes to cv Validation
- python/ucscgenomics/rafile/cv/CvRaFile.pyc
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small changes to cv Validation
- python/ucscgenomics/rafile/cv/cvPseudo
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small changes to cv Validation
- python/ucscgenomics/rafile/cv/cvValidate.py
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small changes to cv Validation
- python/ucscgenomics/rafile/cv/cvValidate.pyc
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small changes to cv Validation
- python/ucscgenomics/rafile/cv/fakecv.ra
- python/ucscgenomics/rafile/cv/test.py
- python/ucscgenomics/rafile/cv/validatescript.py
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small changes to cv Validation
- python/ucscgenomics/rafile/cvClassDiagram
- python/ucscgenomics/rafile/cvPseudo
- python/ucscgenomics/rafile/cvValidate.py
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- python/ucscgenomics/rafile/testRaFile.py
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- python/ucscgenomics/rafile/testoutput/CommentsDiff.out
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- python/ucscgenomics/rafile/testoutput/DeleteItem.out
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- python/ucscgenomics/rafile/testoutput/ExtraneousWhitespace.out
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- python/ucscgenomics/rafile/testoutput/GetItem.out
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- python/ucscgenomics/rafile/testoutput/InlineCommentsDiff.out
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- python/ucscgenomics/rafile/testoutput/IterEntryItems.out
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- python/ucscgenomics/rafile/testoutput/IterEntryKeys.out
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- python/ucscgenomics/rafile/testoutput/IterEntryValues.out
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- python/ucscgenomics/rafile/testoutput/IterItems.out
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- python/ucscgenomics/rafile/testoutput/IterKeys.out
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- python/ucscgenomics/rafile/testoutput/IterValues.out
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- python/ucscgenomics/rafile/tests/.IterKeysExpected.ra.swp
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- python/ucscgenomics/rafile/tests/CommentsDiff.ra
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- python/ucscgenomics/rafile/tests/DeleteItem.ra
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- python/ucscgenomics/rafile/tests/FunctionalityCheck.ra
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- python/ucscgenomics/rafile/tests/GetItem.ra
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- python/ucscgenomics/rafile/tests/InlineCommentsDiff.ra
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- python/ucscgenomics/rafile/tests/IterEntryItems.ra
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- python/ucscgenomics/rafile/tests/IterEntryKeys.ra
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- python/ucscgenomics/rafile/tests/IterEntryValues.ra
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- python/ucscgenomics/rafile/tests/IterItems.ra
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- python/ucscgenomics/rafile/tests/IterKeys.ra
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- python/ucscgenomics/rafile/tests/IterValues.ra
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- python/ucscgenomics/rafile/validatescript.py
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first push to my new branch
- src/hg/encode/DAFs/2.0/caltechElements.daf
- lines changed 3, context: html, text, full: html, text
Removing the (Wold) and fixing the validation settings
- src/hg/encode/DAFs/2.0/caltechRnaSeq.daf
- lines changed 3, context: html, text, full: html, text
Added treatment and better validation settings
- lines changed 2, context: html, text, full: html, text
Removing the (Wold) and fixing the validation settings
- src/hg/encode/encodeCharts/important.dates.tab
- lines changed 1, context: html, text, full: html, text
Update data file for Bernard's ENCODE charting
- src/hg/encode/encodeExp/encodeExp.c
- lines changed 90, context: html, text, full: html, text
Add commands to encodeExp lib and tool: copy (for backup), remove (whack experiment from table), deacc (was 'revoke'). Expand 'history' command. Fixes to action and user logging in history table'
- lines changed 51, context: html, text, full: html, text
Add 'why' column to experiment history table. Add 'restore' command to tool (this loads an empty table from a .ra file)
- lines changed 13, context: html, text, full: html, text
Cosmetic fixes to usage. Make defaults safer
- src/hg/encode/encodeExp/tests/expected/accTest.out.ra
- lines changed 21, context: html, text, full: html, text
Add commands to encodeExp lib and tool: copy (for backup), remove (whack experiment from table), deacc (was 'revoke'). Expand 'history' command. Fixes to action and user logging in history table'
- src/hg/encode/encodeExp/tests/expected/copyTest.out.ra
- lines changed 20, context: html, text, full: html, text
Add commands to encodeExp lib and tool: copy (for backup), remove (whack experiment from table), deacc (was 'revoke'). Expand 'history' command. Fixes to action and user logging in history table'
- src/hg/encode/encodeExp/tests/expected/removeTest.out.ra
- lines changed 13, context: html, text, full: html, text
Add commands to encodeExp lib and tool: copy (for backup), remove (whack experiment from table), deacc (was 'revoke'). Expand 'history' command. Fixes to action and user logging in history table'
- src/hg/encode/encodeExp/tests/expected/renameTest.out.ra
- lines changed 20, context: html, text, full: html, text
Add commands to encodeExp lib and tool: copy (for backup), remove (whack experiment from table), deacc (was 'revoke'). Expand 'history' command. Fixes to action and user logging in history table'
- src/hg/encode/encodeExp/tests/expected/restoreTest.out.ra
- lines changed 44, context: html, text, full: html, text
Add 'why' column to experiment history table. Add 'restore' command to tool (this loads an empty table from a .ra file)
- src/hg/encode/encodeExp/tests/input/restoreTest.in.ra
- lines changed 62, context: html, text, full: html, text
Add 'why' column to experiment history table. Add 'restore' command to tool (this loads an empty table from a .ra file)
- src/hg/encode/encodeExp/tests/makefile
- lines changed 27, context: html, text, full: html, text
Add commands to encodeExp lib and tool: copy (for backup), remove (whack experiment from table), deacc (was 'revoke'). Expand 'history' command. Fixes to action and user logging in history table'
- lines changed 17, context: html, text, full: html, text
Add 'why' column to experiment history table. Add 'restore' command to tool (this loads an empty table from a .ra file)
- src/hg/hgCustom/hgCustom.c
- lines changed 9, context: html, text, full: html, text
More spacing stuff for doctype 4.01.
- src/hg/hgFileSearch/hgFileSearch.c
- lines changed 2, context: html, text, full: html, text
Added scrollbars to dropdpwnchecklist.
- lines changed 1, context: html, text, full: html, text
Fixed spacing issue due to DOCTYPE 4.01.
- src/hg/hgFileUi/hgFileUi.c
- lines changed 5, context: html, text, full: html, text
Further refinement to spacing in hgTrackUi and added this fix to hgFileUi
- src/hg/hgGateway/hgGateway.c
- lines changed 10, context: html, text, full: html, text
Fix for missing box around suybmit controls.
- src/hg/hgLiftOver/hgLiftOver.c
- lines changed 8, context: html, text, full: html, text
Changed HDB stuff in hgLiftOver a bit to reduce database calls. This has not helped speed up the CGI though yet
- lines changed 1, context: html, text, full: html, text
Removed filtering chainlist bits just to get the CGI at a usable speed
- lines changed 51, context: html, text, full: html, text
Updated CGI to use new library function and deleted bits associated with having a variable data format.
- lines changed 33, context: html, text, full: html, text
A bit more persistence for settings. They would reset after running the program. now settings reset if page is refreshed and the chain changes.
- src/hg/hgSession/hgSession.c
- lines changed 7, context: html, text, full: html, text
Updated several places to reflect the actual expiration times of custom tracks and BLAT results that are saved in sessions (redmine #3462).
- lines changed 1, context: html, text, full: html, text
Small changes to wording on user-generated tracks saved in sessions. Thanks, Angie. (Redmine #3462)
- src/hg/hgTables/bedList.c
- lines changed 3, context: html, text, full: html, text
Adjusting spacing due to DOCTYPE 4.01.
- src/hg/hgTables/filterFields.c
- lines changed 2, context: html, text, full: html, text
Adjusting spacing due to DOCTYPE 4.01.
- src/hg/hgTables/great.c
- lines changed 1, context: html, text, full: html, text
Adjusting spacing due to DOCTYPE 4.01.
- src/hg/hgTables/identifiers.c
- lines changed 2, context: html, text, full: html, text
Adjusting spacing due to DOCTYPE 4.01.
- src/hg/hgTables/schema.c
- lines changed 8, context: html, text, full: html, text
Adjusting spacing due to DOCTYPE 4.01.
- src/hg/hgTables/seqOut.c
- lines changed 1, context: html, text, full: html, text
Adjusting spacing due to DOCTYPE 4.01.
- lines changed 1, context: html, text, full: html, text
One more for hgTables - spacing because of doctype 4.01.
- src/hg/hgTrackUi/hgTrackUi.c
- lines changed 6, context: html, text, full: html, text
Changed sectionTtile size and spacing before Description in hgTrackUi, for doctype 4.01.
- lines changed 1, context: html, text, full: html, text
Further refinement to spacing in hgTrackUi and added this fix to hgFileUi
- src/hg/hgTracks/config.c
- lines changed 3, context: html, text, full: html, text
Fixed spacing issues due to DOCTYPE 4.01.
- src/hg/hgTracks/container.c
- lines changed 3, context: html, text, full: html, text
Making it so that only visible subtracks are used in the autoScale calcs.
- src/hg/hgTracks/hgTracks.c
- lines changed 16, context: html, text, full: html, text
Converted the group blue bars to use CSS.
- lines changed 1, context: html, text, full: html, text
Title in groups' blue toggle bar was not centering
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Tweak to match 4.01 spacing to 3.2 spacing.
- lines changed 2, context: html, text, full: html, text
Fixed spacing issues due to DOCTYPE 4.01.
- src/hg/hgTracks/multiWig.c
- lines changed 3, context: html, text, full: html, text
Making it so that only visible subtracks are used in the autoScale calcs.
- lines changed 13, context: html, text, full: html, text
Fixing Katrina's 7) Rainbow tracks: when Display mode is set to 'dense' and the Overlay method is set to 'none,' in hgTracks the labels are shifted down, resulting in partially cutting-off the bottom-most label.
- src/hg/hgTracks/searchTracks.c
- lines changed 1, context: html, text, full: html, text
Added scrollbars to dropdownchecklist multi-selects
- lines changed 1, context: html, text, full: html, text
Fixed spacing issues due to DOCTYPE 4.01.
- lines changed 5, context: html, text, full: html, text
Added support for generic AJAX retrieval of static html (such as help pages). This can result in a popup, or having the text fill a predefined div withing the calling page.
- src/hg/hgTracks/variation.c
- lines changed 2, context: html, text, full: html, text
Bug #3765 (buffer overflow error in Common SNP (132)): plugged up hole in snp125ValidFilter logic that allowed use of NULL var.
- src/hg/hgTracks/vcfTrack.c
- lines changed 302, context: html, text, full: html, text
Feature #3711 (vcfTabix: center-weighted haplotype sorting for display of phased genotypes):Now using hacTree to cluster haplotypes as David suggested, instead of sorting by genotypes
which was a mess. Performance could be improved: the tree from hacTree ends up very lopsided
when there are many identical haplotypes, so perhaps hacTree could optionally begin by sorting
items (if a cmp function is passed in) and pre-clustering runs of identical items. When there
are a lot of identicals, that would reduce the initial number of items that we generate all
possible pairs from. Might also consider general balanced insertion schemes.
Another issue: with the current alpha of 0.5, the signal vanishes once you get a certain
distance away from the center variant. Make alpha depend on #variants? Or just make it larger?
- src/hg/hgc/peakClusters.c
- lines changed 196, context: html, text, full: html, text
Making it so that the DNase clusters can get their metadata from an associated table rather than rummaging through groups and trackDb, following same pattern did for factorSource tracks. It turns out the ENCODE tracks change so much, having one depend on another just is an invitation to problems.
- lines changed 177, context: html, text, full: html, text
More work on DNAse and TFBS cluster tracks' details page. Making newer system, where a minimal amount of metadata is in an associated table that goes with the track, include full metadata if the input track is still available. Making older system just omit a row in the table rather than crashing if the input track has gone missing.
- src/hg/hgc/rnaFoldClick.c
- lines changed 32, context: html, text, full: html, text
Added RNA picture plotted by VARNA for EvoFold.
- src/hg/htdocs/ENCODE/downloads.html
- lines changed 16, context: html, text, full: html, text
adding SUNY RIP GeneST and new supertrack section for RNA Binding Proteins; moved SUNY Tiling to new section
- src/hg/htdocs/ENCODE/index.html
- src/hg/htdocs/evoFold/hg18
- lines changed 1, context: html, text, full: html, text
Added two symbolic links (hg18 and hg19) under /usr/local/apache/htdocs/evoFold.
- src/hg/htdocs/evoFold/hg19
- lines changed 1, context: html, text, full: html, text
Added two symbolic links (hg18 and hg19) under /usr/local/apache/htdocs/evoFold.
- src/hg/htdocs/goldenPath/help/customTrackText.html
- lines changed 2, context: html, text, full: html, text
Updated several places to reflect the actual expiration times of custom tracks and BLAT results that are saved in sessions (redmine #3462).
- src/hg/htdocs/goldenPath/help/hgGenomeHelp.html
- lines changed 4, context: html, text, full: html, text
Updated several places to reflect the actual expiration times of custom tracks and BLAT results that are saved in sessions (redmine #3462).
- src/hg/htdocs/goldenPath/help/hgSessionHelp.html
- lines changed 9, context: html, text, full: html, text
Updated several places to reflect the actual expiration times of custom tracks and BLAT results that are saved in sessions (redmine #3462).
- lines changed 9, context: html, text, full: html, text
Small changes to wording on user-generated tracks saved in sessions. Thanks, Angie. (Redmine #3462)
- src/hg/htdocs/goldenPath/help/hgTracksHelp.html
- lines changed 4, context: html, text, full: html, text
Updated several places to reflect the actual expiration times of custom tracks and BLAT results that are saved in sessions (redmine #3462).
- src/hg/htdocs/images/phylo/calJac3_13way.gif
- src/hg/htdocs/images/phylo/calJac3_13way.png
- src/hg/htdocs/style/HGStyle.css
- lines changed 6, context: html, text, full: html, text
Converted the group blue bars to use CSS.
- src/hg/inc/customPp.h
- lines changed 3, context: html, text, full: html, text
beginning to get some measurements, watch out for divide by zero
- src/hg/inc/customTrack.h
- lines changed 3, context: html, text, full: html, text
begin experiment with progress meter
- src/hg/inc/encode/encodeExp.h
- lines changed 12, context: html, text, full: html, text
Add commands to encodeExp lib and tool: copy (for backup), remove (whack experiment from table), deacc (was 'revoke'). Expand 'history' command. Fixes to action and user logging in history table'
- src/hg/inc/hdb.h
- lines changed 8, context: html, text, full: html, text
Changed HDB stuff in hgLiftOver a bit to reduce database calls. This has not helped speed up the CGI though yet
- src/hg/inc/hui.h
- lines changed 3, context: html, text, full: html, text
Fixing it so that 16 as the max smoothing window appears only one place.
- src/hg/inc/jksql.h
- lines changed 3, context: html, text, full: html, text
Add commands to encodeExp lib and tool: copy (for backup), remove (whack experiment from table), deacc (was 'revoke'). Expand 'history' command. Fixes to action and user logging in history table'
- src/hg/inc/liftOver.h
- lines changed 9, context: html, text, full: html, text
Added one function to liftOver library code that accepts either bed or position data
- src/hg/js/ajax.js
- lines changed 108, context: html, text, full: html, text
Added support for generic AJAX retrieval of static html (such as help pages). This can result in a popup, or having the text fill a predefined div withing the calling page.
- src/hg/js/hgTracks.js
- lines changed 1, context: html, text, full: html, text
Added scrollbars to dropdownchecklist multi-selects
- src/hg/js/hui.js
- lines changed 1, context: html, text, full: html, text
Added scrollbars to dropdownchecklist multi-selects
- src/hg/js/ui.dropdownchecklist.js
- lines changed 2, context: html, text, full: html, text
Fix ugly mess due to DOCTYPE 4.01 transitional redmine 2864 and 3759
- src/hg/js/utils.js
- lines changed 16, context: html, text, full: html, text
Added scrollbars to dropdownchecklist multi-selects
- lines changed 12, context: html, text, full: html, text
Fine tuned filterBy scrolling height for special case of track search simple tab blocking position detection.
- lines changed 1, context: html, text, full: html, text
Setting filterby max height when number of options is small should not be done.
- src/hg/lib/clusterInputDnase.as
- lines changed 10, context: html, text, full: html, text
Adding more metadata fields to the DNase inputs table.
- src/hg/lib/clusterInputDnase.sql
- lines changed 16, context: html, text, full: html, text
Adding more metadata fields to the DNase inputs table.
- src/hg/lib/customFactory.c
- lines changed 34, context: html, text, full: html, text
begin experiment with progress meter
- lines changed 68, context: html, text, full: html, text
beginning to get some measurements, watch out for divide by zero
- src/hg/lib/customPp.c
- lines changed 8, context: html, text, full: html, text
beginning to get some measurements, watch out for divide by zero
- src/hg/lib/customTrack.c
- lines changed 3, context: html, text, full: html, text
begin experiment with progress meter
- src/hg/lib/encode/encodeExp.c
- lines changed 229, context: html, text, full: html, text
Add commands to encodeExp lib and tool: copy (for backup), remove (whack experiment from table), deacc (was 'revoke'). Expand 'history' command. Fixes to action and user logging in history table'
- lines changed 33, context: html, text, full: html, text
Add 'why' column to experiment history table. Add 'restore' command to tool (this loads an empty table from a .ra file)
- src/hg/lib/fileUi.c
- lines changed 1, context: html, text, full: html, text
Added scrollbars to dropdownchecklist multi-selects
- src/hg/lib/hdb.c
- lines changed 27, context: html, text, full: html, text
Changed HDB stuff in hgLiftOver a bit to reduce database calls. This has not helped speed up the CGI though yet
- lines changed 1, context: html, text, full: html, text
Removed filtering chainlist bits just to get the CGI at a usable speed
- src/hg/lib/jksql.c
- lines changed 13, context: html, text, full: html, text
Add commands to encodeExp lib and tool: copy (for backup), remove (whack experiment from table), deacc (was 'revoke'). Expand 'history' command. Fixes to action and user logging in history table'
- src/hg/lib/jsHelper.c
- lines changed 1, context: html, text, full: html, text
Changed sectionTtile size and spacing before Description in hgTrackUi, for doctype 4.01.
- src/hg/lib/liftOver.c
- lines changed 51, context: html, text, full: html, text
Added one function to liftOver library code that accepts either bed or position data
- lines changed 1, context: html, text, full: html, text
Fix for something caught only by Ubuntu gcc's more conservative warnings:lineFileOpen's second argument is a bool, but a quoted string was passed in.
- src/hg/lib/mdb.c
- lines changed 20, context: html, text, full: html, text
Fixed multi-selects searches where values contained spaces. Redmine 3763. Also added sql locking for mdb updates. This is mostly overkill, since updates are always run on a sandbox mdb.
- src/hg/lib/metaDb.sql
- lines changed 4, context: html, text, full: html, text
toook out the now missing 'txt' field
- src/hg/lib/web.c
- lines changed 4, context: html, text, full: html, text
If browser is IE and not version 8, then revert to DOCTYPE 3.2.
- lines changed 1, context: html, text, full: html, text
Make that exclusions of IE < 8.
- src/hg/makeDb/doc/anoCar2.txt
- lines changed 48, context: html, text, full: html, text
finished lastz runs for anoCar2 on mm9 and xenTro2
- lines changed 111, context: html, text, full: html, text
running lastz galGal3 and ornAna1
- lines changed 37, context: html, text, full: html, text
completed gasAcu1 and ornAna1 lastz
- src/hg/makeDb/doc/calJac3.txt
- lines changed 198, context: html, text, full: html, text
Finished Multiz rework.
- src/hg/makeDb/doc/galGal3.txt
- src/hg/makeDb/doc/gasAcu1.txt
- lines changed 20, context: html, text, full: html, text
lastz to lizard anoCar2 done
- src/hg/makeDb/doc/hg18.txt
- lines changed 158, context: html, text, full: html, text
Created .png picture files for hg18 and hg19 EvoFold tracks.
- src/hg/makeDb/doc/hg19.txt
- lines changed 5, context: html, text, full: html, text
Adding more metadata fields to the DNase inputs table.
- lines changed 1, context: html, text, full: html, text
More work on DNAse and TFBS cluster tracks' details page. Making newer system, where a minimal amount of metadata is in an associated table that goes with the track, include full metadata if the input track is still available. Making older system just omit a row in the table rather than crashing if the input track has gone missing.
- lines changed 15, context: html, text, full: html, text
Renaming Caltech RNA components of wgEncodeReg to start with their parent track name, wgEncodeRegTxn, to keep it consistent with everything else and keep various scripts working. Adjusting default visibilities and view limits on rainbows. Defining sourceObj metadata tag and adding it to pooled Caltech RNAs.
- lines changed 157, context: html, text, full: html, text
Created .png picture files for hg18 and hg19 EvoFold tracks.
- src/hg/makeDb/doc/melGal1.txt
- lines changed 1, context: html, text, full: html, text
fix datte for Human Proteins
- src/hg/makeDb/doc/mm9.txt
- lines changed 7, context: html, text, full: html, text
finished lastz runs for anoCar2 on mm9 and xenTro2
- lines changed 204, context: html, text, full: html, text
Initial Nuclear Lamina for mm9
- src/hg/makeDb/doc/ornAna1.txt
- lines changed 20, context: html, text, full: html, text
lastz to lizard anoCar2 done
- src/hg/makeDb/doc/xenTro2.txt
- lines changed 20, context: html, text, full: html, text
finished lastz runs for anoCar2 on mm9 and xenTro2
- src/hg/makeDb/genbank/etc/hgwbeta.dbs
- lines changed 1, context: html, text, full: html, text
Added lizard (anoCar2) assembly to list
- src/hg/makeDb/hgBedsToBedExps/hgBedsToBedExps.c
- lines changed 1, context: html, text, full: html, text
Changing strand from '+' to '.' since it really is unknown.
- src/hg/makeDb/schema/all.joiner
- src/hg/makeDb/trackDb/README
- lines changed 8, context: html, text, full: html, text
Updating inputTrackTable description and depreciating inputTracksSubgroupDisplay, which proved too fragile of a method.
- src/hg/makeDb/trackDb/chicken/trackDb.chainNet.ra
- lines changed 3, context: html, text, full: html, text
set priorities and parameters for all lastz alignments to lizard anoCar2
- src/hg/makeDb/trackDb/chimp/panTro3/trackDb.chainNet.ra
- lines changed 5, context: html, text, full: html, text
adding overrides for ponAbe2 panTro3 chain/net
- src/hg/makeDb/trackDb/chimp/panTro3/trackDb.ra
- lines changed 2, context: html, text, full: html, text
adding overrides for ponAbe2 panTro3 chain/net
- lines changed 1, context: html, text, full: html, text
need blank line following an include statement
- src/hg/makeDb/trackDb/chimp/trackDb.chainNet.ra
- lines changed 6, context: html, text, full: html, text
adding overrides for galGal3 chain/net
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 8, context: html, text, full: html, text
Accepted provisional changes, including the introduction of three new mouse cell types
- lines changed 1, context: html, text, full: html, text
Replaced references to George Stamatoyannopoulous, the father, with John Stamatoyannopoulous, the son and the correct party
- lines changed 6, context: html, text, full: html, text
Added new sequence platform Illumina HiSeq 2000
- lines changed 11, context: html, text, full: html, text
Renaming Caltech RNA components of wgEncodeReg to start with their parent track name, wgEncodeRegTxn, to keep it consistent with everything else and keep various scripts working. Adjusting default visibilities and view limits on rainbows. Defining sourceObj metadata tag and adding it to pooled Caltech RNAs.
- lines changed 11, context: html, text, full: html, text
Adding attic as a type of term and marking it as hidden
- lines changed 1, context: html, text, full: html, text
Correction to dccAccession validation regex, thanks to Cricket's review.
- lines changed 12, context: html, text, full: html, text
Added tier 3 cell line PBMC.
- lines changed 12, context: html, text, full: html, text
Changed the tags for several terms based on feedback from Tim from the code review. Also dropped a term that had been saying should be retired since 12-15-2010
- lines changed 1, context: html, text, full: html, text
Missing type caused hgEncodeVocab to choke
- lines changed 20, context: html, text, full: html, text
Adding grant and lab for Anshul because I need to get his mapability data submitted.
- src/hg/makeDb/trackDb/cv/beta/cv.ra
- lines changed 391, context: html, text, full: html, text
Updating beta with several changes from alpha. Amid these changes are hundreds of updates from the NHGRI, based on curation data from the infamous spreadsheet. At this time, these changes are in the file but commented out
- src/hg/makeDb/trackDb/human/encodeEgaspSuper.html
- lines changed 2, context: html, text, full: html, text
Fixed links to Washington University/Brent Lab
- src/hg/makeDb/trackDb/human/encodeGencodeGeneOct05.html
- lines changed 1, context: html, text, full: html, text
Fixed link to Reymond article
- src/hg/makeDb/trackDb/human/encodeGencodeIntronOct05.html
- lines changed 1, context: html, text, full: html, text
Fixed link to Reymond article
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
- lines changed 2, context: html, text, full: html, text
Changing the expVars to not have localization
- src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
- lines changed 2, context: html, text, full: html, text
Making word before histone mark in rainbow tracks be 'layered' as per Bob's suggestion. Moving ENCODE to end of some short labels.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAffyRnaChip.ra
- lines changed 5122, context: html, text, full: html, text
Adding accession numbers
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
- lines changed 1216, context: html, text, full: html, text
Issue 2019, cleaning up the trackDb to incorporate changes from release 1 and removing all the V1 bigwigs from the metaDB
- lines changed 1487, context: html, text, full: html, text
Renamed Paired to Aligns, renamed fastq V2 to fastq, dropped extra files
- lines changed 248, context: html, text, full: html, text
Removing Ilna from file names and metaData
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
- lines changed 217, context: html, text, full: html, text
Incorporating Julien's changes from the CRG regarding bioRep, labProtocolID, labExpId
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeDukeAffyExon.ra
- lines changed 211, context: html, text, full: html, text
Adding accession numbers
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisDnaPet.ra
- lines changed 42, context: html, text, full: html, text
Added GEO accession numbers
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
- lines changed 306, context: html, text, full: html, text
Incorporating Julien's changes from the CRG regarding bioRep, labProtocolID, labExpId
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaSeq.ra
- lines changed 55, context: html, text, full: html, text
Incorporating Julien's changes from the CRG regarding bioRep, labProtocolID, labExpId
- lines changed 37, context: html, text, full: html, text
Adding accession numbers
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
- lines changed 20, context: html, text, full: html, text
Added final fastq to the mdb
- lines changed 35, context: html, text, full: html, text
Putting items into the attic in both the trackDb and the meatDb
- lines changed 1, context: html, text, full: html, text
removed a spurious "attic" line
- lines changed 85, context: html, text, full: html, text
Track 2254 notes 20 and 21, changed fileSortOrder, dropped bad GSMs, moved auxExp from htr8, fixed some long labels
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
- lines changed 47, context: html, text, full: html, text
Fixed wgEncodeHaibTfbsPanc1ControlPcr1xRawRep2 to be protocol=Pcr1x to protocol=Pcr2x and match metaData for SL523.
- lines changed 17, context: html, text, full: html, text
Updated the CTCF replicate experiments with the correct labExpId. Replicate 1 and Replicate 2 labExpId's were switched.
- lines changed 9, context: html, text, full: html, text
Accidently typed SL1204 and Sl1205 as SL1024 and SL1025 in last commit.
- lines changed 117, context: html, text, full: html, text
Revoked SL305 Peaks and SL3988 experiment on request by the lab.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeMapability.ra
- lines changed 19, context: html, text, full: html, text
Adding accession numbers
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromSynth.ra
- lines changed 1, context: html, text, full: html, text
Added composite as an expVars as per Kate request
- lines changed 15, context: html, text, full: html, text
Experimentified and accessioned Open Chrom Synth
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeReg.ra
- lines changed 7, context: html, text, full: html, text
Fixing compositeTrack tag.
- lines changed 72, context: html, text, full: html, text
Adding metadata for high level DNase and TFBS tracks.
- lines changed 28, context: html, text, full: html, text
Renaming Caltech RNA components of wgEncodeReg to start with their parent track name, wgEncodeRegTxn, to keep it consistent with everything else and keep various scripts working. Adjusting default visibilities and view limits on rainbows. Defining sourceObj metadata tag and adding it to pooled Caltech RNAs.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
- lines changed 424, context: html, text, full: html, text
Incorporating Julien's changes from the CRG regarding bioRep, labProtocolID, labExpId
- lines changed 24, context: html, text, full: html, text
Changed Pooled when in fact, it was not pooled, only one rep was available
- lines changed 1513, context: html, text, full: html, text
Added clusters and replacements Gm12878 data
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunySwitchgear.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwAffyExonArray.ra
- lines changed 271, context: html, text, full: html, text
Adding accession numbers
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSunyAlbanyGeneSt.ra
- lines changed 49, context: html, text, full: html, text
staging metadata changes on beta
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwDnase.ra
- lines changed 5977, context: html, text, full: html, text
staging UW DNaseI (release 2), redmine #2397
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
- lines changed 1, context: html, text, full: html, text
preparing for release of SUNY RIP GeneST, redmine issue #37
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeSunyAlbanyGeneSt.ra
- lines changed 483, context: html, text, full: html, text
preparing for release of SUNY RIP GeneST, redmine issue #37
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- lines changed 2, context: html, text, full: html, text
preparing for release of SUNY RIP GeneST, redmine issue #37
- lines changed 2, context: html, text, full: html, text
staging UW DNaseI (release 2), redmine #2397
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.ra
- lines changed 19, context: html, text, full: html, text
Issue 2019, cleaning up the trackDb to incorporate changes from release 1 and removing all the V1 bigwigs from the metaDB
- lines changed 64, context: html, text, full: html, text
Renamed Paired to Aligns, renamed fastq V2 to fastq, dropped extra files
- lines changed 104, context: html, text, full: html, text
Removing Ilna from file names and metaData
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra
- lines changed 1, context: html, text, full: html, text
Added a new fileSortOrder to be consistent with other transcriptome tracks
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.new.ra
- lines changed 1, context: html, text, full: html, text
Changed fileSortOrder to match in all files
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.ra
- lines changed 1, context: html, text, full: html, text
Changed fileSortOrder to match in all files
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.ra
- lines changed 1, context: html, text, full: html, text
Changed fileSortOrder to match in all files
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.ra
- lines changed 1, context: html, text, full: html, text
Hiding genometype track by default.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.ra
- lines changed 90, context: html, text, full: html, text
Putting items into the attic in both the trackDb and the meatDb
- lines changed 53, context: html, text, full: html, text
Track 2254 notes 20 and 21, changed fileSortOrder, dropped bad GSMs, moved auxExp from htr8, fixed some long labels
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
- lines changed 2, context: html, text, full: html, text
Fixed wgEncodeHaibTfbsPanc1ControlPcr1xRawRep2 to be protocol=Pcr1x to protocol=Pcr2x and match metaData for SL523.
- lines changed 26, context: html, text, full: html, text
Revoked SL305 Peaks and SL3988 experiment on request by the lab.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.html
- lines changed 55, context: html, text, full: html, text
made changes to help clarify filterBy and Dsp.Conv & Config, redmine issue #2881
- lines changed 9, context: html, text, full: html, text
Fixed some pValue language as per Terry Furey's email.
- lines changed 26, context: html, text, full: html, text
Terry has updated the ocCode/color definitions with proper p-value meanings.
- lines changed 1, context: html, text, full: html, text
Open Chrom blue is only OC types 2 and 3.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.ra
- lines changed 11, context: html, text, full: html, text
made changes to help clarify filterBy and Dsp.Conv & Config, redmine issue #2881
- lines changed 6, context: html, text, full: html, text
Adjustments as per Terry's request.
- lines changed 1, context: html, text, full: html, text
Open Chrom blue is only OC types 2 and 3.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
- lines changed 6, context: html, text, full: html, text
Making word before histone mark in rainbow tracks be 'layered' as per Bob's suggestion. Moving ENCODE to end of some short labels.
- lines changed 3, context: html, text, full: html, text
Making it so that the DNase clusters can get their metadata from an associated table rather than rummaging through groups and trackDb, following same pattern did for factorSource tracks. It turns out the ENCODE tracks change so much, having one depend on another just is an invitation to problems.
- lines changed 23, context: html, text, full: html, text
Renaming Caltech RNA components of wgEncodeReg to start with their parent track name, wgEncodeRegTxn, to keep it consistent with everything else and keep various scripts working. Adjusting default visibilities and view limits on rainbows. Defining sourceObj metadata tag and adding it to pooled Caltech RNAs.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTxn.html
- lines changed 3, context: html, text, full: html, text
Adding text about the pooling and normalization in the description of RNA seq.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.ra
- lines changed 1, context: html, text, full: html, text
Changed fileSortOrder to match in all files
- lines changed 358, context: html, text, full: html, text
Added clusters and replacements Gm12878 data
- lines changed 3, context: html, text, full: html, text
Added replicated pooled so that make works, did not mean to check this in in the first place
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.ra
- lines changed 2, context: html, text, full: html, text
Commented out the p-value after discussion with Katrina. Issue 37
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.ra
- lines changed 7, context: html, text, full: html, text
Fixed short label length for 4-hydroxytamoxifen experiments. Changed short label abbreviation of treatment from OHTAM -> OHT
- src/hg/makeDb/trackDb/human/trackDb.chainNet.ra
- lines changed 3, context: html, text, full: html, text
set priorities and parameters for all lastz alignments to lizard anoCar2
- src/hg/makeDb/trackDb/lizard/anoCar2/description.html
- lines changed 13, context: html, text, full: html, text
fixup sample search terms
- src/hg/makeDb/trackDb/lizard/anoCar2/trackDb.chainNet.ra
- lines changed 6, context: html, text, full: html, text
adding chain net overrides
- lines changed 6, context: html, text, full: html, text
set priorities and parameters for all lastz alignments to lizard anoCar2
- src/hg/makeDb/trackDb/lizard/anoCar2/trackDb.ra
- lines changed 2, context: html, text, full: html, text
adding chain net overrides
- src/hg/makeDb/trackDb/loadTracks
- lines changed 2, context: html, text, full: html, text
Changing some /cluster/data to the newer /hive/data/genomes since /cluster/data is just now a symbolic link to /hive/data/genomes the last few years, and the /cluster file system was being flaky.
- src/hg/makeDb/trackDb/makefile.metaDb
- lines changed 1, context: html, text, full: html, text
add makefile to the list of dependencies so changing the makefile will rebuild the metaDb
- src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.ra
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
- lines changed 911, context: html, text, full: html, text
Added 7 input experiments previously missing for this track.
- lines changed 443, context: html, text, full: html, text
Added 7 new submissions. Updating track long labels and defautl tracks on.
- lines changed 443, context: html, text, full: html, text
Added Spleen Inputs and experiments to TFBS and Histone tracks.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
- lines changed 599, context: html, text, full: html, text
Added 7 new submissions. Updating track long labels and defautl tracks on.
- lines changed 131, context: html, text, full: html, text
Added Spleen Inputs and experiments to TFBS and Histone tracks.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
- lines changed 731, context: html, text, full: html, text
Added 6 new experiments.
- src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
- lines changed 80, context: html, text, full: html, text
Nuclear Lamina tracks for mm9
- lines changed 4, context: html, text, full: html, text
Default display to full for all LaminB1 tracks
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.ra
- lines changed 64, context: html, text, full: html, text
Added 7 input experiments previously missing for this track.
- lines changed 93, context: html, text, full: html, text
Updated Notes and configuration for the track. Updated Long and Short labels to follow labelling standards and added fileSortOrder option.
- lines changed 46, context: html, text, full: html, text
Added 7 new submissions. Updating track long labels and defautl tracks on.
- lines changed 46, context: html, text, full: html, text
Added Spleen Inputs and experiments to TFBS and Histone tracks.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.ra
- lines changed 92, context: html, text, full: html, text
Updated Notes and configuration for the track. Updated Long and Short labels to follow labelling standards and added fileSortOrder option.
- lines changed 64, context: html, text, full: html, text
Added 7 new submissions. Updating track long labels and defautl tracks on.
- lines changed 9, context: html, text, full: html, text
Added Spleen Inputs and experiments to TFBS and Histone tracks.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.newR2.ra
- lines changed 91, context: html, text, full: html, text
Added 6 new experiments.
- src/hg/makeDb/trackDb/mouse/trackDb.chainNet.ra
- lines changed 3, context: html, text, full: html, text
set priorities and parameters for all lastz alignments to lizard anoCar2
- src/hg/makeDb/trackDb/platypus/trackDb.chainNet.ra
- lines changed 3, context: html, text, full: html, text
set priorities and parameters for all lastz alignments to lizard anoCar2
- src/hg/makeDb/trackDb/stickleback/trackDb.chainNet.ra
- lines changed 3, context: html, text, full: html, text
set priorities and parameters for all lastz alignments to lizard anoCar2
- src/hg/makeDb/trackDb/trackDb.chainNet.ra
- lines changed 51, context: html, text, full: html, text
set priorities and parameters for all lastz alignments to lizard anoCar2
- src/hg/makeDb/trackDb/xenTro/trackDb.chainNet.ra
- lines changed 3, context: html, text, full: html, text
set priorities and parameters for all lastz alignments to lizard anoCar2
- src/hg/oneShot/doEvoFold/doEvoFold.c
- lines changed 81, context: html, text, full: html, text
Added one shot program doEvoFold for track EvoFold build.
- src/hg/oneShot/doEvoFold/makefile
- lines changed 14, context: html, text, full: html, text
Added one shot program doEvoFold for track EvoFold build.
- src/hg/oneShot/freen/freen.c
- lines changed 15, context: html, text, full: html, text
Freen tests new ra handling a bit.
- src/hg/ratStuff/mafAddIRows/mafAddIRows.c
- lines changed 14, context: html, text, full: html, text
make mafAddIRows barf if you give it a maf with more than one target sequence. #3494
- src/hg/utils/phyloTrees/chainNet.pl
- src/inc/common.h
- lines changed 1, context: html, text, full: html, text
Added new lib module hacTree (Hierarchical Agglomerative Clustering),which takes an slList of items and a couple user-defined functions,
and returns a binary tree of clusters, with the leaf nodes containing
the original input items. The user-defined functions do the interesting
parts: computing distance between two items and/or clusters, and
merging two items and/or clusters into a new cluster.
This is motivated by work on Feature #3711 (vcfTabix: center-weighted
haplotype sorting for display of phased genotypes), but I'm hoping
it might have other uses.
- src/inc/hacTree.h
- lines changed 69, context: html, text, full: html, text
Added new lib module hacTree (Hierarchical Agglomerative Clustering),which takes an slList of items and a couple user-defined functions,
and returns a binary tree of clusters, with the leaf nodes containing
the original input items. The user-defined functions do the interesting
parts: computing distance between two items and/or clusters, and
merging two items and/or clusters into a new cluster.
This is motivated by work on Feature #3711 (vcfTabix: center-weighted
haplotype sorting for display of phased genotypes), but I'm hoping
it might have other uses.
- src/inc/ra.h
- lines changed 3, context: html, text, full: html, text
Adding raTagVals function.
- src/inc/udc.h
- lines changed 5, context: html, text, full: html, text
beginning to get some measurements, watch out for divide by zero
- src/lib/common.c
- lines changed 1, context: html, text, full: html, text
Added new lib module hacTree (Hierarchical Agglomerative Clustering),which takes an slList of items and a couple user-defined functions,
and returns a binary tree of clusters, with the leaf nodes containing
the original input items. The user-defined functions do the interesting
parts: computing distance between two items and/or clusters, and
merging two items and/or clusters into a new cluster.
This is motivated by work on Feature #3711 (vcfTabix: center-weighted
haplotype sorting for display of phased genotypes), but I'm hoping
it might have other uses.
- lines changed 74, context: html, text, full: html, text
Removed old version of function that Galt replaced, when he found a bug in my code.
- src/lib/hacTree.c
- lines changed 114, context: html, text, full: html, text
Added new lib module hacTree (Hierarchical Agglomerative Clustering),which takes an slList of items and a couple user-defined functions,
and returns a binary tree of clusters, with the leaf nodes containing
the original input items. The user-defined functions do the interesting
parts: computing distance between two items and/or clusters, and
merging two items and/or clusters into a new cluster.
This is motivated by work on Feature #3711 (vcfTabix: center-weighted
haplotype sorting for display of phased genotypes), but I'm hoping
it might have other uses.
- src/lib/htmshell.c
- lines changed 6, context: html, text, full: html, text
If browser is IE and not version 8, then revert to DOCTYPE 3.2.
- lines changed 1, context: html, text, full: html, text
Make that exclusions of IE < 8.
- src/lib/makefile
- lines changed 1, context: html, text, full: html, text
Added new lib module hacTree (Hierarchical Agglomerative Clustering),which takes an slList of items and a couple user-defined functions,
and returns a binary tree of clusters, with the leaf nodes containing
the original input items. The user-defined functions do the interesting
parts: computing distance between two items and/or clusters, and
merging two items and/or clusters into a new cluster.
This is motivated by work on Feature #3711 (vcfTabix: center-weighted
haplotype sorting for display of phased genotypes), but I'm hoping
it might have other uses.
- src/lib/ra.c
- lines changed 19, context: html, text, full: html, text
Adding raTagVals function.
- lines changed 1, context: html, text, full: html, text
Jim pointed out one location where continuation lines were not supported properly.
- src/lib/tests/expected/hacTreeTest.out
- lines changed 49, context: html, text, full: html, text
Added new lib module hacTree (Hierarchical Agglomerative Clustering),which takes an slList of items and a couple user-defined functions,
and returns a binary tree of clusters, with the leaf nodes containing
the original input items. The user-defined functions do the interesting
parts: computing distance between two items and/or clusters, and
merging two items and/or clusters into a new cluster.
This is motivated by work on Feature #3711 (vcfTabix: center-weighted
haplotype sorting for display of phased genotypes), but I'm hoping
it might have other uses.
- lines changed 15, context: html, text, full: html, text
Better hacTree test: instead of using a dumb contrived example, useDavid's clustering example from email.
- src/lib/tests/hacTreeTest.c
- lines changed 205, context: html, text, full: html, text
Added new lib module hacTree (Hierarchical Agglomerative Clustering),which takes an slList of items and a couple user-defined functions,
and returns a binary tree of clusters, with the leaf nodes containing
the original input items. The user-defined functions do the interesting
parts: computing distance between two items and/or clusters, and
merging two items and/or clusters into a new cluster.
This is motivated by work on Feature #3711 (vcfTabix: center-weighted
haplotype sorting for display of phased genotypes), but I'm hoping
it might have other uses.
- lines changed 68, context: html, text, full: html, text
Better hacTree test: instead of using a dumb contrived example, useDavid's clustering example from email.
- src/lib/tests/input/hacTreeTest.txt
- lines changed 7, context: html, text, full: html, text
Added new lib module hacTree (Hierarchical Agglomerative Clustering),which takes an slList of items and a couple user-defined functions,
and returns a binary tree of clusters, with the leaf nodes containing
the original input items. The user-defined functions do the interesting
parts: computing distance between two items and/or clusters, and
merging two items and/or clusters into a new cluster.
This is motivated by work on Feature #3711 (vcfTabix: center-weighted
haplotype sorting for display of phased genotypes), but I'm hoping
it might have other uses.
- lines changed 7, context: html, text, full: html, text
Better hacTree test: instead of using a dumb contrived example, useDavid's clustering example from email.
- src/lib/tests/makefile
- lines changed 12, context: html, text, full: html, text
Added new lib module hacTree (Hierarchical Agglomerative Clustering),which takes an slList of items and a couple user-defined functions,
and returns a binary tree of clusters, with the leaf nodes containing
the original input items. The user-defined functions do the interesting
parts: computing distance between two items and/or clusters, and
merging two items and/or clusters into a new cluster.
This is motivated by work on Feature #3711 (vcfTabix: center-weighted
haplotype sorting for display of phased genotypes), but I'm hoping
it might have other uses.
- src/lib/udc.c
- lines changed 22, context: html, text, full: html, text
beginning to get some measurements, watch out for divide by zero
- src/product/README.building.source
- lines changed 3, context: html, text, full: html, text
Emphasize the need to set environment variables when using other libraries
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed: 28709
- files changed: 301