All File Changes
v246_base to v247_preview (2011-01-25 to 2011-02-01) v247
- python/ucscgenomics/rafile/raFile.py
- lines changed 124, context: html, text, full: html, text
put read/write into raFile
- python/ucscgenomics/rafile/radict.pyc
- lines changed 0, context: html, text, full: html, text
Renamed compareRandomSample.py to checkRandomLinesExist.py, at Jim's suggestion. Merging in some minor changes to ucscGenes.
- python/ucscgenomics/rafile/test.py
- lines changed 7, context: html, text, full: html, text
put read/write into raFile
- python/ucscgenomics/rafile/write.py
- src/hg/encode/DAFs/2.0/cshlLongElements.daf
- lines changed 76, context: html, text, full: html, text
Building a new daf just for all of the elements files
- src/hg/encode/DAFs/2.0/stanfordHg19Hist.daf
- lines changed 1, context: html, text, full: html, text
Added comment line for Revision History.
- src/hg/encode/DAFs/2.0/stanfordHg19Tfbs.daf
- lines changed 1, context: html, text, full: html, text
Fixed error in DAF. Alignments expected tagAlign files however the type should be bam and match the validation settings.
- src/hg/encode/DAFs/2.0/stanfordNucleosome.daf
- lines changed 2, context: html, text, full: html, text
Changed the composite name from just Nsome to SydhNsome. This will had a lab tag so that the composite will be easily distinguished as other composites have this distintction.
- src/hg/encode/DAFs/2.0/uMassDekker5cSample.ddf
- lines changed 7, context: html, text, full: html, text
Sample DDF for Dekker lab
- src/hg/encode/hgEncodeSubmit/lib/pipeline_background.rb
- lines changed 2, context: html, text, full: html, text
oops need to update project record with final status
- src/hg/hgApi/hgApi.c
- lines changed 9, context: html, text, full: html, text
Reworked searchTracks +/- buttons to use javascript and fixed some bugs seen when files search is enabled as a tab in track search.
- src/hg/hgGateway/hgGateway.c
- lines changed 18, context: html, text, full: html, text
Support for genome browser preview site.
1. Changes browser title in CGIs
2. Prints warning text on hgGateway
3. Prints warning text on home page
1. and 2. activated by HTTP_HOST prefix 'genome-preview', or by setting
test.preview=true in hg.conf
- src/hg/hgNotAvail/hgNotAvail.c
- lines changed 3, context: html, text, full: html, text
Support for genome browser preview site.
1. Changes browser title in CGIs
2. Prints warning text on hgGateway
3. Prints warning text on home page
1. and 2. activated by HTTP_HOST prefix 'genome-preview', or by setting
test.preview=true in hg.conf
- src/hg/hgNotYet/hgNotYet.c
- lines changed 4, context: html, text, full: html, text
Support for genome browser preview site.
1. Changes browser title in CGIs
2. Prints warning text on hgGateway
3. Prints warning text on home page
1. and 2. activated by HTTP_HOST prefix 'genome-preview', or by setting
test.preview=true in hg.conf
- src/hg/hgTables/greatData/supportedAssemblies.txt
- lines changed 1, context: html, text, full: html, text
added danRer7 to list of GREAT genomes (2654)
- src/hg/hgTables/schema.c
- lines changed 8, context: html, text, full: html, text
hgTables' schema page displays the SQL type of each column, whichcan be a very long unbroken string when the column is an enum or
set with many values. That makes the HTML table painfully wide.
So when the SQL type contains single-quoted comma-separated items,
add a space after each comma so that the HTML cell can break the
list into multiple lines to maintain a reasonable width.
- src/hg/hgTrackUi/hgTrackUi.c
- lines changed 263, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): Added new coloring and filtering optionsfor new columns exceptions and bitfields. Fixed remaining hardcoded cart
var names to use track name, keeping backwards compat with old sessions.
Lots of refactoring -- got rid of snp125Extended business (mostly so I
wouldn't have to make a snp132Extended); color is stored in snp->weight
now, and extraName stuff overwrites name. Added new color-sorting in
squish mode so the most interesting SNPs appear at the top. Also added
new trackDb var defaultMaxWeight for the NonUnique subset (so its items
aren't invisible by default).
- lines changed 5, context: html, text, full: html, text
Begin to standardize on cfgByCfgType so that hgTrackUi and hui can use common code.
- src/hg/hgTracks/gvfTrack.c
- lines changed 122, context: html, text, full: html, text
Track #34 (dbVar for human): Added new track type gvf with basichandlers in hgTracks and hgc. dbVar's GVF attributes are recognized,
esp. var_type is used to color items, and items are sorted using
the Parent keyword so that parents appear immediately before their
children, and children are sorted by var_type. Attributes are
displayed in hgc; need to do a bit better for the Start_range and
End_range (e.g. translate "." to "inner start unknown" etc.).
- src/hg/hgTracks/hgTracks.c
- lines changed 9, context: html, text, full: html, text
Fix bug Hiram pointed out and fixed bug where selectingh track search from gateway sometimes landed on configuretracks page instead
- lines changed 1, context: html, text, full: html, text
Support for genome browser preview site.
1. Changes browser title in CGIs
2. Prints warning text on hgGateway
3. Prints warning text on home page
1. and 2. activated by HTTP_HOST prefix 'genome-preview', or by setting
test.preview=true in hg.conf
- src/hg/hgTracks/hgTracks.h
- lines changed 3, context: html, text, full: html, text
Track #34 (dbVar for human): Added new track type gvf with basichandlers in hgTracks and hgc. dbVar's GVF attributes are recognized,
esp. var_type is used to color items, and items are sorted using
the Parent keyword so that parents appear immediately before their
children, and children are sorted by var_type. Attributes are
displayed in hgc; need to do a bit better for the Start_range and
End_range (e.g. translate "." to "inner start unknown" etc.).
- src/hg/hgTracks/mainMain.c
- lines changed 1, context: html, text, full: html, text
Support for genome browser preview site.
1. Changes browser title in CGIs
2. Prints warning text on hgGateway
3. Prints warning text on home page
1. and 2. activated by HTTP_HOST prefix 'genome-preview', or by setting
test.preview=true in hg.conf
- lines changed 1, context: html, text, full: html, text
add hgt.setWidth to exlcudeVars
- src/hg/hgTracks/makefile
- lines changed 4, context: html, text, full: html, text
clean up garbage on a successful make
- lines changed 1, context: html, text, full: html, text
no need to remove RENDERO which causes a remake of all objects
- lines changed 1, context: html, text, full: html, text
Track #34 (dbVar for human): Added new track type gvf with basichandlers in hgTracks and hgc. dbVar's GVF attributes are recognized,
esp. var_type is used to color items, and items are sorted using
the Parent keyword so that parents appear immediately before their
children, and children are sorted by var_type. Attributes are
displayed in hgc; need to do a bit better for the Start_range and
End_range (e.g. translate "." to "inner start unknown" etc.).
- src/hg/hgTracks/searchTracks.c
- lines changed 26, context: html, text, full: html, text
Reworked searchTracks +/- buttons to use javascript and fixed some bugs seen when files search is enabled as a tab in track search.
- src/hg/hgTracks/simpleTracks.c
- lines changed 3, context: html, text, full: html, text
filterBy setting should allow spaces by wrapping strings in quotes. Beds should be filterable by filterBy
- lines changed 2, context: html, text, full: html, text
Newline char? From where?
- lines changed 1, context: html, text, full: html, text
make bedLogR be supported like a normal bed file
- lines changed 4, context: html, text, full: html, text
Track #34 (dbVar for human): Added new track type gvf with basichandlers in hgTracks and hgc. dbVar's GVF attributes are recognized,
esp. var_type is used to color items, and items are sorted using
the Parent keyword so that parents appear immediately before their
children, and children are sorted by var_type. Attributes are
displayed in hgc; need to do a bit better for the Start_range and
End_range (e.g. translate "." to "inner start unknown" etc.).
- src/hg/hgTracks/variation.c
- lines changed 471, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): Added new coloring and filtering optionsfor new columns exceptions and bitfields. Fixed remaining hardcoded cart
var names to use track name, keeping backwards compat with old sessions.
Lots of refactoring -- got rid of snp125Extended business (mostly so I
wouldn't have to make a snp132Extended); color is stored in snp->weight
now, and extraName stuff overwrites name. Added new color-sorting in
squish mode so the most interesting SNPs appear at the top. Also added
new trackDb var defaultMaxWeight for the NonUnique subset (so its items
aren't invisible by default).
- src/hg/hgTracks/variation.h
- lines changed 5, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): Added new coloring and filtering optionsfor new columns exceptions and bitfields. Fixed remaining hardcoded cart
var names to use track name, keeping backwards compat with old sessions.
Lots of refactoring -- got rid of snp125Extended business (mostly so I
wouldn't have to make a snp132Extended); color is stored in snp->weight
now, and extraName stuff overwrites name. Added new color-sorting in
squish mode so the most interesting SNPs appear at the top. Also added
new trackDb var defaultMaxWeight for the NonUnique subset (so its items
aren't invisible by default).
- src/hg/hgc/gvfClick.c
- lines changed 55, context: html, text, full: html, text
Track #34 (dbVar for human): Added new track type gvf with basichandlers in hgTracks and hgc. dbVar's GVF attributes are recognized,
esp. var_type is used to color items, and items are sorted using
the Parent keyword so that parents appear immediately before their
children, and children are sorted by var_type. Attributes are
displayed in hgc; need to do a bit better for the Start_range and
End_range (e.g. translate "." to "inner start unknown" etc.).
- src/hg/hgc/hgc.c
- lines changed 2, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): Added new coloring and filtering optionsfor new columns exceptions and bitfields. Fixed remaining hardcoded cart
var names to use track name, keeping backwards compat with old sessions.
Lots of refactoring -- got rid of snp125Extended business (mostly so I
wouldn't have to make a snp132Extended); color is stored in snp->weight
now, and extraName stuff overwrites name. Added new color-sorting in
squish mode so the most interesting SNPs appear at the top. Also added
new trackDb var defaultMaxWeight for the NonUnique subset (so its items
aren't invisible by default).
- lines changed 4, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): minor prettying up of near-genefunctional annotation.
- lines changed 46, context: html, text, full: html, text
Feature #1638 (Add "this SNP also maps to" text to hgdpGeo track).
- lines changed 4, context: html, text, full: html, text
Track #34 (dbVar for human): Added new track type gvf with basichandlers in hgTracks and hgc. dbVar's GVF attributes are recognized,
esp. var_type is used to color items, and items are sorted using
the Parent keyword so that parents appear immediately before their
children, and children are sorted by var_type. Attributes are
displayed in hgc; need to do a bit better for the Start_range and
End_range (e.g. translate "." to "inner start unknown" etc.).
- src/hg/hgc/hgc.h
- lines changed 4, context: html, text, full: html, text
Feature #1638 (Add "this SNP also maps to" text to hgdpGeo track).
- lines changed 3, context: html, text, full: html, text
Track #34 (dbVar for human): Added new track type gvf with basichandlers in hgTracks and hgc. dbVar's GVF attributes are recognized,
esp. var_type is used to color items, and items are sorted using
the Parent keyword so that parents appear immediately before their
children, and children are sorted by var_type. Attributes are
displayed in hgc; need to do a bit better for the Start_range and
End_range (e.g. translate "." to "inner start unknown" etc.).
- src/hg/hgc/hgdpClick.c
- lines changed 9, context: html, text, full: html, text
Feature #1638 (Add "this SNP also maps to" text to hgdpGeo track).
- src/hg/hgc/makefile
- lines changed 1, context: html, text, full: html, text
Track #34 (dbVar for human): Added new track type gvf with basichandlers in hgTracks and hgc. dbVar's GVF attributes are recognized,
esp. var_type is used to color items, and items are sorted using
the Parent keyword so that parents appear immediately before their
children, and children are sorted by var_type. Attributes are
displayed in hgc; need to do a bit better for the Start_range and
End_range (e.g. translate "." to "inner start unknown" etc.).
- src/hg/htdocs/ENCODE/cellTypes.html
- lines changed 2, context: html, text, full: html, text
Expand iframe to remove scrollbars
- src/hg/htdocs/ENCODE/contacts.html
- src/hg/htdocs/goldenPath/pubs.html
- src/hg/htdocs/images/floretPreview.jpg
- lines changed 0, context: html, text, full: html, text
Hiram trimmed white borders
- src/hg/htdocs/indexIntro.html
- lines changed 12, context: html, text, full: html, text
Support for genome browser preview site.
1. Changes browser title in CGIs
2. Prints warning text on hgGateway
3. Prints warning text on home page
1. and 2. activated by HTTP_HOST prefix 'genome-preview', or by setting
test.preview=true in hg.conf
- lines changed 2, context: html, text, full: html, text
Response to feedback from Donna -- bold the warning about preview site
- lines changed 23, context: html, text, full: html, text
Moved warning paragraph, responding to feedback from Jim
- src/hg/inc/bed8Attrs.h
- lines changed 67, context: html, text, full: html, text
Track #34 (dbVar for human): Added new track type gvf with basichandlers in hgTracks and hgc. dbVar's GVF attributes are recognized,
esp. var_type is used to color items, and items are sorted using
the Parent keyword so that parents appear immediately before their
children, and children are sorted by var_type. Attributes are
displayed in hgc; need to do a bit better for the Start_range and
End_range (e.g. translate "." to "inner start unknown" etc.).
- src/hg/inc/genePred.h
- lines changed 3, context: html, text, full: html, text
modified refSeqGet to return results in predictiable order to minimize test failures when database changes
- src/hg/inc/hdb.h
- lines changed 14, context: html, text, full: html, text
Support for genome browser preview site.
1. Changes browser title in CGIs
2. Prints warning text on hgGateway
3. Prints warning text on home page
1. and 2. activated by HTTP_HOST prefix 'genome-preview', or by setting
test.preview=true in hg.conf
- src/hg/inc/hui.h
- lines changed 3, context: html, text, full: html, text
Made cfgByCfgType() public so that hgTrackUi can standardize to this call.
- src/hg/inc/mdb.h
- lines changed 5, context: html, text, full: html, text
Made mdbUpdate -recreate faster by doing minimal error checking and loading with all insert statements.
- lines changed 6, context: html, text, full: html, text
Added -validate option to mdbPrint, which will validate mdb vars against cv.ra.
- lines changed 3, context: html, text, full: html, text
By Cricket's request, added -composite as an special case option for commonly queried var
- lines changed 3, context: html, text, full: html, text
In mdb validate, vars that are not defined in cv should be considered invalid if and only if -validateFull requested. On the otherhand, mdbUpdate -test will consider those vars as invalid.
- src/hg/inc/snp125.h
- lines changed 5, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): Added new coloring and filtering optionsfor new columns exceptions and bitfields. Fixed remaining hardcoded cart
var names to use track name, keeping backwards compat with old sessions.
Lots of refactoring -- got rid of snp125Extended business (mostly so I
wouldn't have to make a snp132Extended); color is stored in snp->weight
now, and extraName stuff overwrites name. Added new color-sorting in
squish mode so the most interesting SNPs appear at the top. Also added
new trackDb var defaultMaxWeight for the NonUnique subset (so its items
aren't invisible by default).
- src/hg/inc/snp125Ui.h
- lines changed 36, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): Added new coloring and filtering optionsfor new columns exceptions and bitfields. Fixed remaining hardcoded cart
var names to use track name, keeping backwards compat with old sessions.
Lots of refactoring -- got rid of snp125Extended business (mostly so I
wouldn't have to make a snp132Extended); color is stored in snp->weight
now, and extraName stuff overwrites name. Added new color-sorting in
squish mode so the most interesting SNPs appear at the top. Also added
new trackDb var defaultMaxWeight for the NonUnique subset (so its items
aren't invisible by default).
- src/hg/js/hgTracks.js
- lines changed 194, context: html, text, full: html, text
Reworked searchTracks +/- buttons to use javascript and fixed some bugs seen when files search is enabled as a tab in track search.
- lines changed 1, context: html, text, full: html, text
fix show details for zoomInMore to use the correct icon
- lines changed 3, context: html, text, full: html, text
remove dead code which uses toggle.png
- src/hg/lib/bamFile.c
- lines changed 2, context: html, text, full: html, text
put out BAM tags with htmTextOut so '<' and such are not interpreted as HTML codes #2543
- src/hg/lib/bed8Attrs.as
- lines changed 15, context: html, text, full: html, text
Track #34 (dbVar for human): Added new track type gvf with basichandlers in hgTracks and hgc. dbVar's GVF attributes are recognized,
esp. var_type is used to color items, and items are sorted using
the Parent keyword so that parents appear immediately before their
children, and children are sorted by var_type. Attributes are
displayed in hgc; need to do a bit better for the Start_range and
End_range (e.g. translate "." to "inner start unknown" etc.).
- src/hg/lib/bed8Attrs.c
- lines changed 211, context: html, text, full: html, text
Track #34 (dbVar for human): Added new track type gvf with basichandlers in hgTracks and hgc. dbVar's GVF attributes are recognized,
esp. var_type is used to color items, and items are sorted using
the Parent keyword so that parents appear immediately before their
children, and children are sorted by var_type. Attributes are
displayed in hgc; need to do a bit better for the Start_range and
End_range (e.g. translate "." to "inner start unknown" etc.).
- src/hg/lib/bed8Attrs.sql
- lines changed 23, context: html, text, full: html, text
Track #34 (dbVar for human): Added new track type gvf with basichandlers in hgTracks and hgc. dbVar's GVF attributes are recognized,
esp. var_type is used to color items, and items are sorted using
the Parent keyword so that parents appear immediately before their
children, and children are sorted by var_type. Attributes are
displayed in hgc; need to do a bit better for the Start_range and
End_range (e.g. translate "." to "inner start unknown" etc.).
- src/hg/lib/customFactory.c
- lines changed 1, context: html, text, full: html, text
do not close if it did not open
- src/hg/lib/fileUi.c
- lines changed 2, context: html, text, full: html, text
Found files needs to be in div.filesFound for javascript to work.
- src/hg/lib/genePred.c
- lines changed 13, context: html, text, full: html, text
modified refSeqGet to return results in predictiable order to minimize test failures when database changes
- src/hg/lib/hdb.c
- lines changed 32, context: html, text, full: html, text
Support for genome browser preview site.
1. Changes browser title in CGIs
2. Prints warning text on hgGateway
3. Prints warning text on home page
1. and 2. activated by HTTP_HOST prefix 'genome-preview', or by setting
test.preview=true in hg.conf
- src/hg/lib/hui.c
- lines changed 6, context: html, text, full: html, text
filterBy setting should allow spaces by wrapping strings in quotes. Beds should be filterable by filterBy
- lines changed 4, context: html, text, full: html, text
Made cfgByCfgType() public so that hgTrackUi can standardize to this call.
- src/hg/lib/makefile
- lines changed 1, context: html, text, full: html, text
Track #34 (dbVar for human): Added new track type gvf with basichandlers in hgTracks and hgc. dbVar's GVF attributes are recognized,
esp. var_type is used to color items, and items are sorted using
the Parent keyword so that parents appear immediately before their
children, and children are sorted by var_type. Attributes are
displayed in hgc; need to do a bit better for the Start_range and
End_range (e.g. translate "." to "inner start unknown" etc.).
- src/hg/lib/mdb.c
- lines changed 74, context: html, text, full: html, text
Made mdbUpdate -recreate faster by doing minimal error checking and loading with all insert statements.
- lines changed 195, context: html, text, full: html, text
Added -validate option to mdbPrint, which will validate mdb vars against cv.ra.
- lines changed 6, context: html, text, full: html, text
In mdbObjsValidate() added verbose=2 print of vars that are not defined in cv.ra.
- lines changed 33, context: html, text, full: html, text
By Cricket's request, added -composite as an special case option for commonly queried var
- lines changed 8, context: html, text, full: html, text
In mdb validate, vars that are not defined in cv should be considered invalid if and only if -validateFull requested. On the otherhand, mdbUpdate -test will consider those vars as invalid.
- src/hg/lib/snp125.c
- lines changed 30, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): Added new coloring and filtering optionsfor new columns exceptions and bitfields. Fixed remaining hardcoded cart
var names to use track name, keeping backwards compat with old sessions.
Lots of refactoring -- got rid of snp125Extended business (mostly so I
wouldn't have to make a snp132Extended); color is stored in snp->weight
now, and extraName stuff overwrites name. Added new color-sorting in
squish mode so the most interesting SNPs appear at the top. Also added
new trackDb var defaultMaxWeight for the NonUnique subset (so its items
aren't invisible by default).
- src/hg/lib/snp125Ui.c
- lines changed 177, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): Added new coloring and filtering optionsfor new columns exceptions and bitfields. Fixed remaining hardcoded cart
var names to use track name, keeping backwards compat with old sessions.
Lots of refactoring -- got rid of snp125Extended business (mostly so I
wouldn't have to make a snp132Extended); color is stored in snp->weight
now, and extraName stuff overwrites name. Added new color-sorting in
squish mode so the most interesting SNPs appear at the top. Also added
new trackDb var defaultMaxWeight for the NonUnique subset (so its items
aren't invisible by default).
- src/hg/lib/trackDbCustom.c
- lines changed 2, context: html, text, full: html, text
Track #34 (dbVar for human): Added new track type gvf with basichandlers in hgTracks and hgc. dbVar's GVF attributes are recognized,
esp. var_type is used to color items, and items are sorted using
the Parent keyword so that parents appear immediately before their
children, and children are sorted by var_type. Attributes are
displayed in hgc; need to do a bit better for the Start_range and
End_range (e.g. translate "." to "inner start unknown" etc.).
- src/hg/makeDb/doc/calJac3.txt
- lines changed 31, context: html, text, full: html, text
Add multiz 13 way maf files for download
- src/hg/makeDb/doc/encodeDccHg19/broadHistoneBernstein.hg19.txt
- lines changed 439, context: html, text, full: html, text
Check in some of this freeze work
- src/hg/makeDb/doc/encodeDccHg19/openChromCrawford.hg19.txt
- lines changed 746, context: html, text, full: html, text
Check in some of this freeze work
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeCaltechRnaSeq.release1.notes
- lines changed 153, context: html, text, full: html, text
redid the notes file to reflect only signals for this release
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeCshlShort.release2.notes
- lines changed 897, context: html, text, full: html, text
These are the notes files I've done over the last week.
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibGenotype.release1.notes
- lines changed 116, context: html, text, full: html, text
These are the notes files I've done over the last week.
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibMethylRrbs.release2.notes
- lines changed 18, context: html, text, full: html, text
These are the notes files I've done over the last week.
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeRikenCage.release2.notes
- lines changed 847, context: html, text, full: html, text
These are the notes files I've done over the last week.
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeSunyAlbanyGeneSt.release1.notes
- lines changed 40, context: html, text, full: html, text
These are the notes files I've done over the last week.
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeSunyRipSeq.release1.notes
- lines changed 200, context: html, text, full: html, text
These are the notes files I've done over the last week.
- src/hg/makeDb/doc/felCat4.txt
- lines changed 53, context: html, text, full: html, text
multiz/phastCons/phyloP for felCat4
- src/hg/makeDb/doc/hg18.txt
- lines changed 13, context: html, text, full: html, text
Update item names in numtSeq track
- lines changed 38, context: html, text, full: html, text
Track #34 (dbVar for human): Fetched ISCA Retrospective dataset fromdbVar and loaded as bed8 plus attributes. Next step: recognize the
new bed8Attrs track type and make a nice track handler.
- lines changed 1, context: html, text, full: html, text
Track #34 (dbVar for human): oops, forgot to subtract 1 from starts.
- src/hg/makeDb/doc/hg19.txt
- lines changed 49, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): Got rid of a couple of the new exceptionsthat were basically echoes of bitfield column values (GenotypeConflict and
ClusterNonOverlappingAlleles). Initially I thought it would be nice to
include those in exceptions for easier filtering, but it's easy enough to
filter on bitfields as well as exceptions. Moreover, it's nice to keep
exceptions UCSC-only, and bitfields dbSNP-only; otherwise it's hard to
explain why we have separate columns for those. Reloaded snp132,
snp132ExceptionDesc, and subsets snp132{Common,Patient,NonUnique,Misc}.
- lines changed 6, context: html, text, full: html, text
Fixing up the HapMap SNPs lift to hg19
- lines changed 1, context: html, text, full: html, text
Track #34 (dbVar for human): Fetched ISCA Retrospective dataset fromdbVar and loaded as bed8 plus attributes. Next step: recognize the
new bed8Attrs track type and make a nice track handler.
- lines changed 4, context: html, text, full: html, text
fixed problem with coverage track
- src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
- lines changed 7, context: html, text, full: html, text
Renamed compareRandomSample.py to checkRandomLinesExist.py, at Jim's suggestion. Merging in some minor changes to ucscGenes.
- lines changed 23, context: html, text, full: html, text
Added a bit more testing, revised the access of the exoniphy table to account for the fact that it no longer has a numeric ID. Fortunately, it doesn't look like that ID was used for anything
- src/hg/makeDb/hgLoadWiggle/makefile
- lines changed 15, context: html, text, full: html, text
add sizeof and hgWiggle to userApp build
- src/hg/makeDb/mdbUpdate/mdbPrint.c
- lines changed 30, context: html, text, full: html, text
Added -validate option to mdbPrint, which will validate mdb vars against cv.ra.
- lines changed 10, context: html, text, full: html, text
By Cricket's request, added -composite as an special case option for commonly queried var
- lines changed 7, context: html, text, full: html, text
In mdb validate, vars that are not defined in cv should be considered invalid if and only if -validateFull requested. On the otherhand, mdbUpdate -test will consider those vars as invalid.
- src/hg/makeDb/mdbUpdate/mdbUpdate.c
- lines changed 3, context: html, text, full: html, text
Made mdbUpdate -recreate faster by doing minimal error checking and loading with all insert statements.
- lines changed 17, context: html, text, full: html, text
By Cricket's request, added -composite as an special case option for commonly queried var
- lines changed 7, context: html, text, full: html, text
Added validation to -test option of mdbUpdate
- lines changed 4, context: html, text, full: html, text
In mdb validate, vars that are not defined in cv should be considered invalid if and only if -validateFull requested. On the otherhand, mdbUpdate -test will consider those vars as invalid.
- lines changed 3, context: html, text, full: html, text
Clarified the invalids message for mdbUpdate
- src/hg/makeDb/schema/all.joiner
- lines changed 1, context: html, text, full: html, text
Response to Q/A and code review. 1. dimensionA setting 2. Clarify hg18 vs. hg19 methods. 3. Add to all.joiner
- lines changed 8, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): updated all.joiner: added newsubset tracks, removed nonexistent table snp132Exceptions.
- src/hg/makeDb/trackDb/cat/felCat4/cons6way.html
- lines changed 409, context: html, text, full: html, text
cons6way track fpr felCat4
- src/hg/makeDb/trackDb/cat/felCat4/trackDb.ra
- lines changed 143, context: html, text, full: html, text
cons6way track fpr felCat4
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 19, context: html, text, full: html, text
Addressing Katrina's code review feedback
- lines changed 10, context: html, text, full: html, text
Changing the genders of several cell lines, in response to feedback from Terry Furey at Duke via Tim
- lines changed 19, context: html, text, full: html, text
Updated the validation documents for a slew of Myers lab antibodies
- lines changed 1, context: html, text, full: html, text
Added a stub cell growth 'protocol' for the prostate tissue. There was no cell growth protocol previously because no cells were grown: the RNA was purchased from a vendor. But, we need to have a protocol in place for the GEO submissions.
- lines changed 23, context: html, text, full: html, text
Updated the validation types of several Myers lab antibodies
- lines changed 8, context: html, text, full: html, text
Set the genders of several cell lines to Both, following word from Terry Furey that these cell lines consist of a mixture of both male and female cells
- lines changed 126, context: html, text, full: html, text
Fixed typeOfTerm 'validate' settings and added 'priority' to typeOfTerm stanzas. No provisional tags have been added. If Melissa disapproves of the changes then they can be backed out. However, I need them in for mdbPrint -validate to work.
- lines changed 3, context: html, text, full: html, text
A touch up to some of the validate settings
- lines changed 1, context: html, text, full: html, text
One mre tweek to rank validation
- lines changed 8, context: html, text, full: html, text
Added project into typeOfTerms for mdbPrint -validate purposes.
- src/hg/makeDb/trackDb/cv/beta/cv.ra
- lines changed 192, context: html, text, full: html, text
Copying a bunch of changes from alpha to beta
- src/hg/makeDb/trackDb/cv/public/cv.ra
- lines changed 821, context: html, text, full: html, text
releasing changes I just reviewed on beta/cv.ra to public - no review necessary
- src/hg/makeDb/trackDb/drosophila/droAna2/gap.html
- lines changed 1, context: html, text, full: html, text
Updated link to Eisen Lab
- src/hg/makeDb/trackDb/drosophila/droAna2/gold.html
- lines changed 1, context: html, text, full: html, text
Updated link to Eisen Lab
- src/hg/makeDb/trackDb/drosophila/droEre1/gap.html
- lines changed 1, context: html, text, full: html, text
Updated link to Eisen Lab
- src/hg/makeDb/trackDb/drosophila/droGri1/gap.html
- lines changed 1, context: html, text, full: html, text
Updated link to Eisen Lab
- src/hg/makeDb/trackDb/drosophila/droMoj2/gap.html
- lines changed 1, context: html, text, full: html, text
Updated link to Eisen Lab
- src/hg/makeDb/trackDb/drosophila/droVir2/gap.html
- lines changed 1, context: html, text, full: html, text
Updated link to Eisen Lab
- src/hg/makeDb/trackDb/human/agilentCghAlpha.html
- lines changed 1, context: html, text, full: html, text
minor grammar mistake being fixed: http://redmine.soe.ucsc.edu/issues/2596
- src/hg/makeDb/trackDb/human/hapmapSnps.html
- lines changed 193, context: html, text, full: html, text
Fixing up the HapMap SNPs lift to hg19
- src/hg/makeDb/trackDb/human/hg18/hapmapSnps.html
- lines changed 193, context: html, text, full: html, text
Fixing up the HapMap SNPs lift to hg19
- src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
- lines changed 2, context: html, text, full: html, text
added hyphen to Promoter-Associated and changed Promoted to Promoter in shortLabel
- lines changed 9, context: html, text, full: html, text
added hyphen to Promoter-Associated and changed Promoted to Promoter in shortLabel
- src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadHmm.ra
- lines changed 16, context: html, text, full: html, text
Broad HMM is modeling with one l. Can use filterBy on name.
- lines changed 14, context: html, text, full: html, text
Getting cfg settings for bed9 requires 'bed 9 .'
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
- lines changed 1, context: html, text, full: html, text
added metadata for Suny Rip-seq
- lines changed 2, context: html, text, full: html, text
Add reference to metaData for Uchicago.
- lines changed 1, context: html, text, full: html, text
Added the new Methyl27 data with its metaData
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
- lines changed 5832, context: html, text, full: html, text
added metadata for V2 files
- lines changed 83, context: html, text, full: html, text
added missing metadata for sub 3473
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
- lines changed 12, context: html, text, full: html, text
made the dataTypes all RnaSeq to be consistent
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
- lines changed 224, context: html, text, full: html, text
made the dataTypes all RnaSeq to be consistent
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaSeq.ra
- lines changed 5, context: html, text, full: html, text
changed the views to RawData from RawData3
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibGenotype.ra
- lines changed 22, context: html, text, full: html, text
added troubled submission into metaData for Kate's reporting
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethyl27.ra
- lines changed 1475, context: html, text, full: html, text
Added the new Methyl27 data with its metaData
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
- lines changed 4, context: html, text, full: html, text
added the metadata for Haib RRBS
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibRnaSeq.ra
- lines changed 25, context: html, text, full: html, text
adding a Haib Rna Seq to the hg19
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
- lines changed 4013, context: html, text, full: html, text
Added 14 submissions for the Jan 2011 Freeze.
- lines changed 880, context: html, text, full: html, text
Added 16 submissions for Jan 2011 freeze.
- lines changed 41, context: html, text, full: html, text
Fixed naming of files, and tables for incorrectly tagged antibodyies for Mef2asc13268 -> Mef2csc13268 and Foxa1sc6554 -> Foxa2sc6554
- lines changed 34, context: html, text, full: html, text
Fixed the standardization of dataType ChipSeq from ChIPseq -> ChipSeq. Also replaced controlId None with correct controlId
- lines changed 20, context: html, text, full: html, text
Changed lower case values of Sl -> SL to be consistent.
- lines changed 6, context: html, text, full: html, text
Removed all refrences to controlId None. Replaced using controlId provided by other fileTypes from the same experiment.
- lines changed 89, context: html, text, full: html, text
Patched up metaData file with missing metaData and fixed mislabelled metaData.
- lines changed 200, context: html, text, full: html, text
Updated meta-data with correct controlId and labExpId using known experiments and excel sheet provided by preti found in redmine issue #420.
- lines changed 8, context: html, text, full: html, text
Fixed meta-data for experimetns with known controlId and expLabId's.
- lines changed 27, context: html, text, full: html, text
Added controlId and labExpId for raw data files that I was not able to correctly identify using experimental variables.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
- lines changed 8, context: html, text, full: html, text
Fixed dataTypes, updated cross-gender bam's labVersion, revoked FAIRE/NHBE
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
- lines changed 29, context: html, text, full: html, text
Fixing some ambiguous genders
- lines changed 45, context: html, text, full: html, text
Fixed dataTypes, updated cross-gender bam's labVersion, revoked FAIRE/NHBE
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
- lines changed 8, context: html, text, full: html, text
Fixed inconsistent labs from cv. Changed UCDavis -> UCD, UCD(Farnham) -> UCD and UNC(Lieb) -> UNC.
- lines changed 11, context: html, text, full: html, text
Fixing some ambiguous genders
- lines changed 117, context: html, text, full: html, text
Fixed dataTypes, updated cross-gender bam's labVersion, revoked FAIRE/NHBE
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
- lines changed 119, context: html, text, full: html, text
changed Clusters to Signals, fixed supertrack setting, and maxWindowsToDraw according to Vanessa's wishes
- lines changed 169, context: html, text, full: html, text
Fixed the comment in issue#41, the broken link, the Alignments description, the title of the track, the missing meta data, the Clusters being called signals
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyRipSeq.ra
- lines changed 951, context: html, text, full: html, text
added metadata for Suny Rip-seq
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
- lines changed 7, context: html, text, full: html, text
Fixed the standardization of dataType ChipSeq from ChIPseq -> ChipSeq.
- lines changed 7, context: html, text, full: html, text
Corrected lab UCD(Farnham) -> UCD.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
- lines changed 131, context: html, text, full: html, text
Removed reference for submission 3249. Cell line used was incorrect and will reload data with newly registered HEK293 variant.
- lines changed 26, context: html, text, full: html, text
For submission 2093, the control used was incorrect. Changed IgG-Yale control to Standard Controls. This involved renaming files and tables and meta-data terms. THe ZZZ3 antibody was incorrect labeled in the trackDb as ZZZ3i, removed i to become ZZZ3.
- lines changed 54, context: html, text, full: html, text
Updated table, filename and track names for wgEncodeSydhTfbsK562bKap1Ucd experiments to be K562b instead of K562.
- lines changed 525, context: html, text, full: html, text
MdbPrint to verify integrity of magic number.
- lines changed 1057, context: html, text, full: html, text
Added 9 submissions for the Jan 2011 freeze.
- lines changed 175, context: html, text, full: html, text
Fixed the standardization of dataType ChipSeq from ChIPseq -> ChipSeq.
- lines changed 61, context: html, text, full: html, text
Fixed inconsistent labs from cv. Changed UCDavis -> UCD, UCD(Farnham) -> UCD and UNC(Lieb) -> UNC.
- lines changed 209, context: html, text, full: html, text
Patched up metaData file and objectnames with actual file names. Now all metaData maps 1:1 to a file.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUchicagoTfbs.ra
- lines changed 1219, context: html, text, full: html, text
Displayed the first set of experiments from the University of Chicago.
- lines changed 1219, context: html, text, full: html, text
Removed all meta-data and tracks to reload data with better meta-data.
- lines changed 1219, context: html, text, full: html, text
Update meta-data and files with correct metaData.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
- lines changed 134, context: html, text, full: html, text
Added replacement peaks (V2) for 5 cell lines. Removed the Version 1 references in trackDb.ra, but not in metaDb.ra.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
- lines changed 161, context: html, text, full: html, text
Added replacement peaks (V2) for 8 cell lines-replicate pairs. Removed the Version 1 references in trackDb.ra, but not in metaDb.ra.
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
- lines changed 1, context: html, text, full: html, text
statging metaDb for SunyTiling, redmine issue #38
- lines changed 1, context: html, text, full: html, text
unstaging Caltech, redmine issue #35
- lines changed 1, context: html, text, full: html, text
restaging CaltechRnaSeq on hgwbeta, redmine issue# 35
- lines changed 3, context: html, text, full: html, text
wgEncodeAffyRnaChip was included twice
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeCaltechRnaSeq.ra
- lines changed 9039, context: html, text, full: html, text
unstaging Caltech, redmine issue #35
- lines changed 14870, context: html, text, full: html, text
restaging CaltechRnaSeq on hgwbeta, redmine issue# 35
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSunyAlbanyTiling.ra
- lines changed 153, context: html, text, full: html, text
statging metaDb for SunyTiling, redmine issue #38
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 30, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): Added hg19 overrides for new tracks snp132{Common,Patient,NonUnique}.
- lines changed 5, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): Added some missing settings forsubset tracks (snpSeq, snpSeqFile) and fixed some visibilities.
- lines changed 3, context: html, text, full: html, text
Fixing up the HapMap SNPs lift to hg19
- lines changed 1, context: html, text, full: html, text
fixed problem with coverage track
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- lines changed 1, context: html, text, full: html, text
Displayed the first set of experiments from the University of Chicago.
- lines changed 1, context: html, text, full: html, text
made Riken have alpha release tags
- lines changed 14, context: html, text, full: html, text
adding a Haib Rna Seq to the hg19
- lines changed 4, context: html, text, full: html, text
Getting the Caltech new data roughly displayed on alpha
- lines changed 2, context: html, text, full: html, text
Added the new Methyl27 data with its metaData
- src/hg/makeDb/trackDb/human/hg19/uMassBrainHistone.html
- lines changed 7, context: html, text, full: html, text
Response to Q/A and code review. 1. dimensionA setting 2. Clarify hg18 vs. hg19 methods. 3. Add to all.joiner
- src/hg/makeDb/trackDb/human/hg19/uMassBrainHistone.ra
- lines changed 1, context: html, text, full: html, text
Response to Q/A and code review. 1. dimensionA setting 2. Clarify hg18 vs. hg19 methods. 3. Add to all.joiner
- src/hg/makeDb/trackDb/human/hg19/wgEncodeBuOrchid.ra
- lines changed 1, context: html, text, full: html, text
removed drag and drop at Tim's request
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.ra
- lines changed 21, context: html, text, full: html, text
Getting the Caltech new data roughly displayed on alpha
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.ra
- lines changed 91, context: html, text, full: html, text
changed short and long labels of incoming data
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.html
- lines changed 51, context: html, text, full: html, text
New description page for Haib CNV
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.ra
- lines changed 192, context: html, text, full: html, text
Changed to have a drop down instead of a matrix
- lines changed 98, context: html, text, full: html, text
trying to display the view settings, not working yet
- lines changed 85, context: html, text, full: html, text
Updated longLabels to new format.
- lines changed 173, context: html, text, full: html, text
Changed back to bed 9 to view
- lines changed 2, context: html, text, full: html, text
Updated labels with treatment for Tamoxifen
- lines changed 86, context: html, text, full: html, text
use bedLogR handler for this
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl27.ra
- lines changed 575, context: html, text, full: html, text
Added the new Methyl27 data with its metaData
- lines changed 67, context: html, text, full: html, text
Fixed longLabels to new format
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.html
- lines changed 154, context: html, text, full: html, text
adding new release for Methyl RRBS with new cell types and release information
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.ra
- lines changed 27, context: html, text, full: html, text
adding new release for Methyl RRBS with new cell types and release information
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylSeq.ra
- lines changed 29, context: html, text, full: html, text
Fixed longLabels to new format
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.ra
- lines changed 830, context: html, text, full: html, text
adding a Haib Rna Seq to the hg19
- lines changed 31, context: html, text, full: html, text
changed gtf to genepred as that is what it is called by the handler
- lines changed 90, context: html, text, full: html, text
Fixed longLabels of file to proper format.
- lines changed 1, context: html, text, full: html, text
resolving merge conflicts
- lines changed 1, context: html, text, full: html, text
resolving merge conflicts
- lines changed 191, context: html, text, full: html, text
Developed ShortLabel and LongLabel Schema for Treatments
- lines changed 13, context: html, text, full: html, text
Fixed ESTRADIOL spelling
- lines changed 101, context: html, text, full: html, text
Added times to treatments
- lines changed 1, context: html, text, full: html, text
Adjusted treatment ordering
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
- lines changed 880, context: html, text, full: html, text
Added 14 submissions for the Jan 2011 Freeze.
- lines changed 432, context: html, text, full: html, text
Added 16 submissions for Jan 2011 freeze.
- lines changed 8, context: html, text, full: html, text
Fixed naming of files, and tables for incorrectly tagged antibodyies for Mef2asc13268 -> Mef2csc13268 and Foxa1sc6554 -> Foxa2sc6554
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.ra
- lines changed 33, context: html, text, full: html, text
Fixed dataTypes, updated cross-gender bam's labVersion, revoked FAIRE/NHBE
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.html
- lines changed 9, context: html, text, full: html, text
Fixed the comment in issue#41, the broken link, the Alignments description, the title of the track, the missing meta data, the Clusters being called signals
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.ra
- lines changed 2, context: html, text, full: html, text
Fixed the comment in issue#41, the broken link, the Alignments description, the title of the track, the missing meta data, the Clusters being called signals
- lines changed 12, context: html, text, full: html, text
getting the Riken new data roughly displayed on alpha
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.ra
- lines changed 129, context: html, text, full: html, text
changed Clusters to Signals, fixed supertrack setting, and maxWindowsToDraw according to Vanessa's wishes
- lines changed 2, context: html, text, full: html, text
Fixed the comment in issue#41, the broken link, the Alignments description, the title of the track, the missing meta data, the Clusters being called signals
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyTiling.html
- lines changed 2, context: html, text, full: html, text
fixing typos, redmine issue #41
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
- lines changed 18, context: html, text, full: html, text
Removed reference for submission 3249. Cell line used was incorrect and will reload data with newly registered HEK293 variant.
- lines changed 5, context: html, text, full: html, text
For submission 2093, the control used was incorrect. Changed IgG-Yale control to Standard Controls. This involved renaming files and tables and meta-data terms. THe ZZZ3 antibody was incorrect labeled in the trackDb as ZZZ3i, removed i to become ZZZ3.
- lines changed 9, context: html, text, full: html, text
Updated table, filename and track names for wgEncodeSydhTfbsHepg2Znf274Ucd experiments to be HepG2b instead of HepG2.
- lines changed 8, context: html, text, full: html, text
Updated table, filename and track names for wgEncodeSydhTfbsK562bKap1Ucd experiments to be K562b instead of K562.
- lines changed 198, context: html, text, full: html, text
Added 9 submissions for the Jan 2011 freeze.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.ra
- lines changed 185, context: html, text, full: html, text
Displayed the first set of experiments from the University of Chicago.
- lines changed 118, context: html, text, full: html, text
Removed all meta-data and tracks to reload data with better meta-data.
- lines changed 120, context: html, text, full: html, text
Update meta-data and files with correct metaData.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.new.ra
- lines changed 119, context: html, text, full: html, text
Added replacement peaks (V2) for 5 cell lines. Removed the Version 1 references in trackDb.ra, but not in metaDb.ra.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.ra
- lines changed 146, context: html, text, full: html, text
Added replacement peaks (V2) for 8 cell lines-replicate pairs. Removed the Version 1 references in trackDb.ra, but not in metaDb.ra.
- src/hg/makeDb/trackDb/human/numtSeq.html
- lines changed 131, context: html, text, full: html, text
Update item names in numtSeq track
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 2, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): Added some missing settings forsubset tracks (snpSeq, snpSeqFile) and fixed some visibilities.
- lines changed 9, context: html, text, full: html, text
Track #34 (dbVar for human): Fetched ISCA Retrospective dataset fromdbVar and loaded as bed8 plus attributes. Next step: recognize the
new bed8Attrs track type and make a nice track handler.
- lines changed 1, context: html, text, full: html, text
Track #34 (dbVar for human): Added new track type gvf with basichandlers in hgTracks and hgc. dbVar's GVF attributes are recognized,
esp. var_type is used to color items, and items are sorted using
the Parent keyword so that parents appear immediately before their
children, and children are sorted by var_type. Attributes are
displayed in hgc; need to do a bit better for the Start_range and
End_range (e.g. translate "." to "inner start unknown" etc.).
- src/hg/makeDb/trackDb/marmoset/calJac3/cons13way.html
- lines changed 1, context: html, text, full: html, text
Use assembly names in table
- src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.ra
- lines changed 25, context: html, text, full: html, text
Change shortLabel from 'Vertebrate ...' to '13 way ...'
- lines changed 2, context: html, text, full: html, text
Adjust wig range for phyloP
- src/hg/makeDb/trackDb/snp132.html
- lines changed 169, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): Changed snp132's shortLabel to"All SNPs (132)"; added new coloring/filtering options and field
descriptions to snp132.html.
- lines changed 3, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): Adding another warning about unreliablebitfield. Sending bug report to dbSNP...
- src/hg/makeDb/trackDb/snp132Common.html
- lines changed 365, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): Descriptions for new subset tracks.These are pretty much duplicates of snp132.html, but with brief
descriptions of each subset. Also, default max weight for
snp132NonUnique is 3 (1 for all others).
- lines changed 3, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): Adding another warning about unreliablebitfield. Sending bug report to dbSNP...
- src/hg/makeDb/trackDb/snp132NonUnique.html
- lines changed 366, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): Descriptions for new subset tracks.These are pretty much duplicates of snp132.html, but with brief
descriptions of each subset. Also, default max weight for
snp132NonUnique is 3 (1 for all others).
- lines changed 3, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): Adding another warning about unreliablebitfield. Sending bug report to dbSNP...
- src/hg/makeDb/trackDb/snp132Patient.html
- lines changed 367, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): Descriptions for new subset tracks.These are pretty much duplicates of snp132.html, but with brief
descriptions of each subset. Also, default max weight for
snp132NonUnique is 3 (1 for all others).
- lines changed 3, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): Adding another warning about unreliablebitfield. Sending bug report to dbSNP...
- src/hg/makeDb/trackDb/tagTypes.tab
- lines changed 1, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): Added new coloring and filtering optionsfor new columns exceptions and bitfields. Fixed remaining hardcoded cart
var names to use track name, keeping backwards compat with old sessions.
Lots of refactoring -- got rid of snp125Extended business (mostly so I
wouldn't have to make a snp132Extended); color is stored in snp->weight
now, and extraName stuff overwrites name. Added new color-sorting in
squish mode so the most interesting SNPs appear at the top. Also added
new trackDb var defaultMaxWeight for the NonUnique subset (so its items
aren't invisible by default).
- lines changed 1, context: html, text, full: html, text
adding a Haib Rna Seq to the hg19
- lines changed 1, context: html, text, full: html, text
changed gtf to genepred as that is what it is called by the handler
- lines changed 1, context: html, text, full: html, text
Track #34 (dbVar for human): Added new track type gvf with basichandlers in hgTracks and hgc. dbVar's GVF attributes are recognized,
esp. var_type is used to color items, and items are sorted using
the Parent keyword so that parents appear immediately before their
children, and children are sorted by var_type. Attributes are
displayed in hgc; need to do a bit better for the Start_range and
End_range (e.g. translate "." to "inner start unknown" etc.).
- src/hg/makeDb/trackDb/trackDb.ra
- lines changed 1, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): Added new coloring and filtering optionsfor new columns exceptions and bitfields. Fixed remaining hardcoded cart
var names to use track name, keeping backwards compat with old sessions.
Lots of refactoring -- got rid of snp125Extended business (mostly so I
wouldn't have to make a snp132Extended); color is stored in snp->weight
now, and extraName stuff overwrites name. Added new color-sorting in
squish mode so the most interesting SNPs appear at the top. Also added
new trackDb var defaultMaxWeight for the NonUnique subset (so its items
aren't invisible by default).
- lines changed 1, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): Changed snp132's shortLabel to"All SNPs (132)"; added new coloring/filtering options and field
descriptions to snp132.html.
- lines changed 3, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): Added some missing settings forsubset tracks (snpSeq, snpSeqFile) and fixed some visibilities.
- src/hg/near/hgMapToGene/hgMapToGene.c
- lines changed 11, context: html, text, full: html, text
At Jim's suggestion, revised mostOverlappingBed so that if there is a bed of compatible gene structure, it will be chosen, but if there isn't such a bed, then some bed will still be chosen
- src/hg/pslCDnaFilter/makefile
- lines changed 1, context: html, text, full: html, text
remove garbage msg files after successful make
- src/hg/snp/snpLoad/snpNcbiToUcsc.c
- lines changed 19, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): Got rid of a couple of the new exceptionsthat were basically echoes of bitfield column values (GenotypeConflict and
ClusterNonOverlappingAlleles). Initially I thought it would be nice to
include those in exceptions for easier filtering, but it's easy enough to
filter on bitfields as well as exceptions. Moreover, it's nice to keep
exceptions UCSC-only, and bitfields dbSNP-only; otherwise it's hard to
explain why we have separate columns for those. Reloaded snp132,
snp132ExceptionDesc, and subsets snp132{Common,Patient,NonUnique,Misc}.
- src/hg/test/makefile
- lines changed 6, context: html, text, full: html, text
remove garbage after successful make to keep git status clean
- src/hg/txGene/txGeneValidation/checkRandomLinesExist.py
- lines changed 40, context: html, text, full: html, text
Renamed compareRandomSample.py to checkRandomLinesExist.py, at Jim's suggestion. Merging in some minor changes to ucscGenes.
- lines changed 8, context: html, text, full: html, text
Made the grep commands in this script prepared for some regular expression characters
- lines changed 2, context: html, text, full: html, text
Removed an extraneous diagnostic statement, and abandoned the idea of escaping special characters. The calling program is responsible for taking care of grep special characters
- src/hg/txGene/txGeneValidation/compareRandomSample.py
- lines changed 40, context: html, text, full: html, text
Renamed compareRandomSample.py to checkRandomLinesExist.py, at Jim's suggestion. Merging in some minor changes to ucscGenes.
- src/hg/txGene/txGeneValidation/makefile
- lines changed 3, context: html, text, full: html, text
Added no-op clean target to txGeneValidation/makefile to get rid ofstderr complaint from make about lack of clean target.
- lines changed 3, context: html, text, full: html, text
don't break when SCRIPTS variable is overridden
- lines changed 6, context: html, text, full: html, text
Revised the makefile to play more nicely by copying the scripts to the directory, and removing its scripts from that directory prior to copying
- src/hg/utils/automation/constructLiftFile.pl
- lines changed 44, context: html, text, full: html, text
example script procedure to run a stand-along lastz/chain procedure on two genomes without UCSC environment
- src/hg/utils/automation/runLastzChain.sh
- lines changed 122, context: html, text, full: html, text
example script procedure to run a stand-along lastz/chain procedure on two genomes without UCSC environment
- src/hg/utils/overlapSelect/makefile
- lines changed 1, context: html, text, full: html, text
remove garbage after successful make to keep git status clean
- src/hg/utils/pslMap/makefile
- lines changed 1, context: html, text, full: html, text
clean up garbage after successful make to keep git status clean
- src/hg/utils/refSeqGet/refSeqGet.c
- lines changed 44, context: html, text, full: html, text
modified refSeqGet to return results in predictiable order to minimize test failures when database changes
- src/hg/utils/refSeqGet/refSeqVerInfo.c
- lines changed 20, context: html, text, full: html, text
modified refSeqGet to return results in predictiable order to minimize test failures when database changes
- src/hg/utils/refSeqGet/refSeqVerInfo.h
- lines changed 2, context: html, text, full: html, text
modified refSeqGet to return results in predictiable order to minimize test failures when database changes
- src/hg/utils/refSeqGet/tests/expected/basicListTest.gp
- lines changed 3, context: html, text, full: html, text
modified refSeqGet to return results in predictiable order to minimize test failures when database changes
- src/hg/utils/refSeqGet/tests/expected/basicListTest.meta
- lines changed 4, context: html, text, full: html, text
modified refSeqGet to return results in predictiable order to minimize test failures when database changes
- src/hg/utils/refSeqGet/tests/expected/basicListTest.psl
- lines changed 4, context: html, text, full: html, text
modified refSeqGet to return results in predictiable order to minimize test failures when database changes
- src/hg/utils/refSeqGet/tests/expected/basicListTest.rna.fa
- lines changed 12, context: html, text, full: html, text
modified refSeqGet to return results in predictiable order to minimize test failures when database changes
- src/hg/utils/refSeqGet/tests/expected/versionedListTest.meta
- lines changed 2, context: html, text, full: html, text
modified refSeqGet to return results in predictiable order to minimize test failures when database changes
- src/hg/utils/refSeqGet/tests/expected/versionedListTest.psl
- lines changed 2, context: html, text, full: html, text
modified refSeqGet to return results in predictiable order to minimize test failures when database changes
- src/hg/utils/refSeqGet/tests/expected/versionedListTest.rna.fa
- lines changed 6, context: html, text, full: html, text
modified refSeqGet to return results in predictiable order to minimize test failures when database changes
- src/hg/utils/refreshNamedSessionCustomTracks/makefile
- lines changed 5, context: html, text, full: html, text
refreshNamedSessionCustomTracks doesn't compile on OS/X due lack of sigtimedwait, so just disable compiling until someone really needs it
- src/hg/utils/refreshNamedSessionCustomTracks/refreshNamedSessionCustomTracks.c
- lines changed 6, context: html, text, full: html, text
proper error message when can not connect and clean up error messages
- lines changed 1, context: html, text, full: html, text
refreshNamedSessionCustomTracks doesn't compile on OS/X due lack of sigtimedwait, so just disable compiling until someone really needs it
- src/inc/common.mk
- lines changed 4, context: html, text, full: html, text
OSTYPE is only an environment variable in tcsh, so explicty create a make variable SYS using uname
- src/inc/memgfx.h
- lines changed 1, context: html, text, full: html, text
using MEMGFX_BIGENDIAN for building on BIGENDIAN machines
- src/lib/memgfx.c
- lines changed 14, context: html, text, full: html, text
using MEMGFX_BIGENDIAN for building on BIGENDIAN machines
- src/lib/ra.c
- lines changed 2, context: html, text, full: html, text
Added -validate option to mdbPrint, which will validate mdb vars against cv.ra.
- src/makefile
- lines changed 1, context: html, text, full: html, text
clean up garbage on a successful make
- lines changed 6, context: html, text, full: html, text
add sizeof and hgWiggle to userApp build
- src/utils/git-reports/git-reports.c
- lines changed 2, context: html, text, full: html, text
include merge commits #2517. We'll probably filter some subset of them out if they're filled with pointless automaticity.
- src/utils/qa/countPerChrom.csh
- lines changed 5, context: html, text, full: html, text
added logic to compute number of items for each x in histogram for casae where only one table is displayed
- lines changed 17, context: html, text, full: html, text
refactored a bit to get output stats into one place regardless of whether one or two tables were processed
- src/utils/qa/weeklybld/buildEnv.csh
- src/utils/sizeof/makefile
- lines changed 2, context: html, text, full: html, text
add sizeof and hgWiggle to userApp build
- lines changed: 62503
- files changed: 324