All File Changes
v247_preview2 to v247_base (2011-02-08 to 2011-02-14) v247
- python/ucscgenomics/rafile/orderedDict.py
- python/ucscgenomics/rafile/raEntry.py
- python/ucscgenomics/rafile/raFile.py
- python/ucscgenomics/rafile/testinput.ra
- src/hg/altSplice/altSplice/tests/expected/testLoci.psl
- lines changed 1, context: html, text, full: html, text
Added test case for genePredToPsl
- src/hg/altSplice/altSplice/tests/input/testChrom.sizes
- lines changed 1, context: html, text, full: html, text
Added test case for genePredToPsl
- src/hg/altSplice/altSplice/tests/makefile
- lines changed 9, context: html, text, full: html, text
Added test case for genePredToPsl
- src/hg/encode/DAFs/2.0/cshlLongElements.daf
- lines changed 19, context: html, text, full: html, text
Added the headers for all Transcriptome DAFs, added Elements views
- src/hg/encode/DAFs/2.0/cshlLongRnaSeq.daf
- lines changed 13, context: html, text, full: html, text
Added the headers for all Transcriptome DAFs, added Elements views
- src/hg/encode/DAFs/2.0/cshlShortRnaSeq.daf
- lines changed 37, context: html, text, full: html, text
Added the headers for all Transcriptome DAFs, added Elements views
- src/hg/encode/DAFs/2.0/gisRnaElements.daf
- lines changed 42, context: html, text, full: html, text
Added the headers for all Transcriptome DAFs, added Elements views
- src/hg/encode/DAFs/2.0/gisRnaPet.daf
- lines changed 26, context: html, text, full: html, text
Added the headers for all Transcriptome DAFs, added Elements views
- src/hg/encode/DAFs/2.0/rikenCageSolexa.daf
- lines changed 33, context: html, text, full: html, text
Added the headers for all Transcriptome DAFs, added Elements views
- src/hg/encode/DAFs/2.0/rikenElements.daf
- lines changed 39, context: html, text, full: html, text
Added the headers for all Transcriptome DAFs, added Elements views
- src/hg/encode/encodeMkGeoPkg/README.txt
- lines changed 9, context: html, text, full: html, text
Added documentation for database and release options
- src/hg/encode/encodeMkGeoPkg/encodeMkGeoPkg
- lines changed 31, context: html, text, full: html, text
Removed references to wgEncodeHaibTfbsEcc1GRV0416102Etoh02AlnRep* replaced with wgEncodeHaibTfbsEcc1GrV0416102Etoh02AlnRep*
- lines changed 31, context: html, text, full: html, text
Accidently commited older version of this file. Adding back newest revisions.
- src/hg/encode/encodeValidate/config/expVars.ra
- lines changed 1, context: html, text, full: html, text
Corrected wgEncodeHaibMethylArray
- lines changed 4, context: html, text, full: html, text
Added wgEncodeGisChiaPet entry
- src/hg/encode/validateFiles/validateFiles.c
- lines changed 2, context: html, text, full: html, text
Feature #27 (table browser support for BAM): addition of BAM supportwithout enough #ifdef USE_BAM's led to compile errors without USE_BAM=1.
Fix: add stub routines to bamFile.c so that the compile won't break,
but informative error message will be printed if bamFile routines are
called. I was hoping that this would obviate most of the #ifdef USE_BAM's
currently in the tree, but actually most of those prevent CGIs from
getting into trouble by offering BAM functionality when it isn't
compiled in. So I left most current #ifdef USE_BAM's in place, but
when future new code doesn't #ifdef, at least the compile won't break.
- src/hg/hgApi/hgApi.c
- lines changed 32, context: html, text, full: html, text
support codonToPos and exonToPos
- lines changed 5, context: html, text, full: html, text
use return json for codonToPos and exonToPos
- src/hg/hgFileUi/hgFileUi.c
- lines changed 1, context: html, text, full: html, text
fine tuning the data last updated printouts
- src/hg/hgHubConnect/hgHubConnect.c
- lines changed 4, context: html, text, full: html, text
Making terminology about importing tracks and data hubs more consistent.
- src/hg/hgTables/bam.c
- lines changed 4, context: html, text, full: html, text
Feature #27 (table browser support for BAM): addition of BAM supportwithout enough #ifdef USE_BAM's led to compile errors without USE_BAM=1.
Fix: add stub routines to bamFile.c so that the compile won't break,
but informative error message will be printed if bamFile routines are
called. I was hoping that this would obviate most of the #ifdef USE_BAM's
currently in the tree, but actually most of those prevent CGIs from
getting into trouble by offering BAM functionality when it isn't
compiled in. So I left most current #ifdef USE_BAM's in place, but
when future new code doesn't #ifdef, at least the compile won't break.
- lines changed 62, context: html, text, full: html, text
Adding example lines to BAM schema page in table browser. Pushing forward on getting identifiers to work there, but still a ways to go. (It no longer bombs at the paste identifiers page, but it does shortly thereafter.)
- lines changed 24, context: html, text, full: html, text
add intersections, identifier filtering, and file length limits to BAM output
- src/hg/hgTables/filterFields.c
- lines changed 3, context: html, text, full: html, text
add intersections, identifier filtering, and file length limits to BAM output
- src/hg/hgTables/hgTables.c
- lines changed 18, context: html, text, full: html, text
Adding example lines to BAM schema page in table browser. Pushing forward on getting identifiers to work there, but still a ways to go. (It no longer bombs at the paste identifiers page, but it does shortly thereafter.)
- src/hg/hgTables/hgTables.h
- lines changed 3, context: html, text, full: html, text
Adding example lines to BAM schema page in table browser. Pushing forward on getting identifiers to work there, but still a ways to go. (It no longer bombs at the paste identifiers page, but it does shortly thereafter.)
- lines changed 3, context: html, text, full: html, text
add intersections, identifier filtering, and file length limits to BAM output
- src/hg/hgTables/identifiers.c
- lines changed 8, context: html, text, full: html, text
Starting to work on getting qName based identifiers to work for BAM files.
- lines changed 2, context: html, text, full: html, text
add intersections, identifier filtering, and file length limits to BAM output
- src/hg/hgTables/intersect.c
- lines changed 3, context: html, text, full: html, text
Making hub tracks had intersection show up.
- lines changed 2, context: html, text, full: html, text
add intersections, identifier filtering, and file length limits to BAM output
- src/hg/hgTables/mainPage.c
- lines changed 9, context: html, text, full: html, text
add intersections, identifier filtering, and file length limits to BAM output
- src/hg/hgTables/wiggle.c
- lines changed 4, context: html, text, full: html, text
add intersections, identifier filtering, and file length limits to BAM output
- src/hg/hgTrackUi/hgTrackUi.c
- lines changed 23, context: html, text, full: html, text
proper display of data last updated time for trackUi information
- lines changed 6, context: html, text, full: html, text
do not try to do printUpdateTime for composites
- lines changed 2, context: html, text, full: html, text
fine tuning the data last updated printouts
- src/hg/hgTracks/hgTracks.c
- lines changed 4, context: html, text, full: html, text
Got dropdownchecklist to work within hgTracks popup cfg
- lines changed 7, context: html, text, full: html, text
Fixed bug screwing up track search tab switching. It seems that ui.code.js does not play well with the tabs widget.
- src/hg/hgTracks/simpleTracks.c
- lines changed 73, context: html, text, full: html, text
Fine tuned omimGeneClass3 methods.
- lines changed 86, context: html, text, full: html, text
Added method for omimAvSnp.
- lines changed 16, context: html, text, full: html, text
Slight code changes to allow a trackDb setting-controlled mouseover text for next-exon buttons
- src/hg/hgTracks/snakeTrack.c
- lines changed 13, context: html, text, full: html, text
fix a bug where blocks were being dropped
- src/hg/hgc/bamClick.c
- lines changed 2, context: html, text, full: html, text
Feature #27 (table browser support for BAM): addition of BAM supportwithout enough #ifdef USE_BAM's led to compile errors without USE_BAM=1.
Fix: add stub routines to bamFile.c so that the compile won't break,
but informative error message will be printed if bamFile routines are
called. I was hoping that this would obviate most of the #ifdef USE_BAM's
currently in the tree, but actually most of those prevent CGIs from
getting into trouble by offering BAM functionality when it isn't
compiled in. So I left most current #ifdef USE_BAM's in place, but
when future new code doesn't #ifdef, at least the compile won't break.
- src/hg/hgc/bigBedClick.c
- lines changed 2, context: html, text, full: html, text
consolidate the display of data last updated printout for hgc clicks, now working for most bbi types
- lines changed 3, context: html, text, full: html, text
proper display of data last updated time for trackUi information
- src/hg/hgc/hgc.c
- lines changed 34, context: html, text, full: html, text
consolidate the display of data last updated printout for hgc clicks, now working for most bbi types
- lines changed 18, context: html, text, full: html, text
fine tuning the data last updated printouts
- lines changed 17, context: html, text, full: html, text
I take that back, do not need specific conditions on date time printout for Encode
- lines changed 1, context: html, text, full: html, text
do not need to check for dbTrack on custom track date time outputs
- lines changed 6, context: html, text, full: html, text
Fine tuned details page for omimAvSnp.
- src/hg/hgc/wiggleClick.c
- lines changed 5, context: html, text, full: html, text
consolidate the display of data last updated printout for hgc clicks, now working for most bbi types
- lines changed 6, context: html, text, full: html, text
I take that back, do not need specific conditions on date time printout for Encode
- src/hg/htdocs/ENCODE/downloads.html
- lines changed 10, context: html, text, full: html, text
adding Histone Mod section and Broad Histone (hg19) track to the downloads page
- lines changed 5, context: html, text, full: html, text
added SUNY Tiling, hg19, redmine #38
- lines changed 6, context: html, text, full: html, text
adding UW Histone and removing PI from SUNY Tiling for Vanessa
- src/hg/htdocs/ENCODE/index.html
- lines changed 1, context: html, text, full: html, text
Fix link to personal browser
- lines changed 1, context: html, text, full: html, text
removed period on bulleted item since it isn't a complete sentence, redmine issue #1163
- src/hg/htdocs/ENCODE/terms.html
- lines changed 5, context: html, text, full: html, text
added proper punctuation, removed unnecessary breaking spaces, redmine issue #1163
- lines changed 10, context: html, text, full: html, text
added capitilization to bulleted items, bolded journal volume, redmine issue #1163
- src/hg/htdocs/goldenPath/help/hgTracksHelp.html
- lines changed 16, context: html, text, full: html, text
Added a few code review mods suggested by Greg.
- lines changed 5, context: html, text, full: html, text
Changed wording on next/preveious item navigation instructions as per redmine #2760.
- src/hg/htdocs/license/index.html
- lines changed 3, context: html, text, full: html, text
Changed licensing contact to Wil.
- src/hg/htdocs/staff.html
- lines changed 46, context: html, text, full: html, text
Added new folks, moved others to the alumni section.
- src/hg/inc/bamFile.h
- lines changed 22, context: html, text, full: html, text
Feature #27 (table browser support for BAM): addition of BAM supportwithout enough #ifdef USE_BAM's led to compile errors without USE_BAM=1.
Fix: add stub routines to bamFile.c so that the compile won't break,
but informative error message will be printed if bamFile routines are
called. I was hoping that this would obviate most of the #ifdef USE_BAM's
currently in the tree, but actually most of those prevent CGIs from
getting into trouble by offering BAM functionality when it isn't
compiled in. So I left most current #ifdef USE_BAM's in place, but
when future new code doesn't #ifdef, at least the compile won't break.
- lines changed 11, context: html, text, full: html, text
Adding example lines to BAM schema page in table browser. Pushing forward on getting identifiers to work there, but still a ways to go. (It no longer bombs at the paste identifiers page, but it does shortly thereafter.)
- src/hg/inc/genePred.h
- lines changed 9, context: html, text, full: html, text
add utility routines for zoomToCodon and zoomToExon
- src/hg/inc/hdb.h
- lines changed 7, context: html, text, full: html, text
consolidate the display of data last updated printout for hgc clicks, now working for most bbi types
- src/hg/inc/hui.h
- lines changed 1, context: html, text, full: html, text
Added support for background colors in filterBy.
- src/hg/inc/trackDb.h
- lines changed 1, context: html, text, full: html, text
fine tuning the data last updated printouts
- lines changed 1, context: html, text, full: html, text
I take that back, do not need specific conditions on date time printout for Encode
- src/hg/inc/versionInfo.h
- src/hg/js/hgTracks.js
- lines changed 45, context: html, text, full: html, text
Got dropdownchecklist to work within hgTracks popup cfg
- lines changed 8, context: html, text, full: html, text
use return json for codonToPos and exonToPos
- lines changed 22, context: html, text, full: html, text
Fixed another of my bugs found be Larry. The popup box is no longer executing close(), so I forced the cleanup before a rightClick
- src/hg/js/ui.dropdownchecklist.js
- lines changed 4, context: html, text, full: html, text
Added support for background colors in filterBy.
- lines changed 13, context: html, text, full: html, text
Got dropdownchecklist to work within hgTracks popup cfg
- lines changed 19, context: html, text, full: html, text
Fixed some supportColors bugs in dd checklist
- lines changed 3, context: html, text, full: html, text
Fixed bug of mine that Larry caught, where popup cfg tripped over assuming changed val was string.
- src/hg/js/utils.js
- lines changed 14, context: html, text, full: html, text
Got dropdownchecklist to work within hgTracks popup cfg
- lines changed 3, context: html, text, full: html, text
Fixed bug of mine that Larry caught, where popup cfg tripped over assuming changed val was string.
- lines changed 1, context: html, text, full: html, text
No need to handle multi-select array of vals as a special case if array contains only one val
- lines changed 6, context: html, text, full: html, text
Special case for ie so that sort table column headers show that they are sortable.
- src/hg/lib/bamFile.c
- lines changed 142, context: html, text, full: html, text
Feature #27 (table browser support for BAM): addition of BAM supportwithout enough #ifdef USE_BAM's led to compile errors without USE_BAM=1.
Fix: add stub routines to bamFile.c so that the compile won't break,
but informative error message will be printed if bamFile routines are
called. I was hoping that this would obviate most of the #ifdef USE_BAM's
currently in the tree, but actually most of those prevent CGIs from
getting into trouble by offering BAM functionality when it isn't
compiled in. So I left most current #ifdef USE_BAM's in place, but
when future new code doesn't #ifdef, at least the compile won't break.
- lines changed 90, context: html, text, full: html, text
Adding example lines to BAM schema page in table browser. Pushing forward on getting identifiers to work there, but still a ways to go. (It no longer bombs at the paste identifiers page, but it does shortly thereafter.)
- lines changed 2, context: html, text, full: html, text
MLQ #2810 (error compiling uscs genome browser): fixing a couplefunction declarations in USE_BAM=0 code, that would have been
caught by compiling with the environment variable USE_BAM=0.
- src/hg/lib/customFactory.c
- lines changed 2, context: html, text, full: html, text
Fix for confusing error message when type is given as pgSnp but the data lines are not correct (redmine #2791)
- lines changed 24, context: html, text, full: html, text
Added further information to error messages for pgSnp custom tracks redmine #2791
- src/hg/lib/genePred.c
- lines changed 98, context: html, text, full: html, text
add utility routines for zoomToCodon and zoomToExon
- src/hg/lib/hdb.c
- lines changed 9, context: html, text, full: html, text
Making link to table browser for hub tracks preload the hub track.
- lines changed 33, context: html, text, full: html, text
consolidate the display of data last updated printout for hgc clicks, now working for most bbi types
- lines changed 21, context: html, text, full: html, text
proper display of data last updated time for trackUi information
- lines changed 4, context: html, text, full: html, text
fine tuning the data last updated printouts
- src/hg/lib/hui.c
- lines changed 49, context: html, text, full: html, text
Added support for background colors in filterBy.
- lines changed 1, context: html, text, full: html, text
Youch, houd did that get checked in.
- lines changed 9, context: html, text, full: html, text
Got dropdownchecklist to work within hgTracks popup cfg
- lines changed 1, context: html, text, full: html, text
Fixed some supportColors bugs in dd checklist
- lines changed 81, context: html, text, full: html, text
Moved date routines into common, and made expired restriction dates dimmer in hgTrackUi
- src/hg/lib/trackDbCustom.c
- lines changed 4, context: html, text, full: html, text
fine tuning the data last updated printouts
- lines changed 4, context: html, text, full: html, text
I take that back, do not need specific conditions on date time printout for Encode
- src/hg/lib/web.c
- lines changed 2, context: html, text, full: html, text
Making link to table browser for hub tracks preload the hub track.
- src/hg/makeDb/doc/danRer7.txt
- lines changed 19, context: html, text, full: html, text
add description of NCBI incident database build
- src/hg/makeDb/doc/encodeDccHg19/openChromCrawford.hg19.txt
- lines changed 393, context: html, text, full: html, text
Added to the pushQ for Jan 2011 freeze.
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeCshlShort.release2.notes
- lines changed 17, context: html, text, full: html, text
Added a few files to notes
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeOpenChromChip.release1.notes
- lines changed 591, context: html, text, full: html, text
Readying Open Chrom composites for QA
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeOpenChromDnase.release1.notes
- lines changed 714, context: html, text, full: html, text
Readying Open Chrom composites for QA
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeOpenChromFaire.release1.notes
- lines changed 388, context: html, text, full: html, text
Readying Open Chrom composites for QA
- lines changed 17, context: html, text, full: html, text
One more submission, replacing revoked FAIRE NHBE gets in under the wire
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeOpenChromSynth.release1.notes
- lines changed 58, context: html, text, full: html, text
Readying Open Chrom composites for QA
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeRikenCage.release1.notes
- lines changed 29, context: html, text, full: html, text
Dropped tables like wgEncodeRikenCageK562NucleolusTotal
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeYaleRnaSeq.release1.notes
- src/hg/makeDb/doc/hg19.txt
- lines changed 14, context: html, text, full: html, text
Added DECIPHER build description section.
- lines changed 19, context: html, text, full: html, text
add description of NCBI incident database build
- src/hg/makeDb/doc/mm9.txt
- lines changed 19, context: html, text, full: html, text
add description of NCBI incident database build
- src/hg/makeDb/schema/all.joiner
- lines changed 1, context: html, text, full: html, text
Track #671 (BDTNP for dm2): Added bdtnpDnase% to tablesIgnored for fly, thanks Greg.
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 3, context: html, text, full: html, text
Elaborating on some of the comments relating to metaDb validation
- lines changed 2, context: html, text, full: html, text
Addressing code review feedback from Katrina: Issue #2735
- lines changed 3, context: html, text, full: html, text
Accepted some provisional stanzas relating mostly to the CHIA-PET lab / grant
- lines changed 25, context: html, text, full: html, text
In response to Flo Pauli at Hudson Alpha, (1) removed a duplicate antibody entry that DOESN'T appear in metaDb, (2) for two duplicate antibody entries that DO appear in metaDb, changed the comments to indicate the antibody entry that should be used and updated the validation status to reflect that those antibodies were validated, under a different name, and (3) updated the lab affiliationf ro the Farnham/Myers antibody to just be Farnham.
- src/hg/makeDb/trackDb/cv/beta/cv.ra
- lines changed 10, context: html, text, full: html, text
Moving a bunch of changes from alpha to beta while the cv is reasonably stable
- src/hg/makeDb/trackDb/drosophila/bdtnpDnase.html
- lines changed 1, context: html, text, full: html, text
Track #671 (BDTNP for dm2): Corrected the description of regions'default vis (squish not dense), thanks Greg.
- src/hg/makeDb/trackDb/gibbon/nomLeu1/trackDb.ra
- lines changed 2, context: html, text, full: html, text
Override all_mrna and all_est track
- src/hg/makeDb/trackDb/human/decipher.html
- lines changed 18, context: html, text, full: html, text
Luvina's edits since she can't commit yet: some grammar edits and encoding the emails.
- lines changed 2, context: html, text, full: html, text
Changed 'mean ratio' into 'mean log ratio'.
- src/hg/makeDb/trackDb/human/decipherOld.html
- lines changed 67, context: html, text, full: html, text
changing trackDb so that decipher track points to old html. Will change to new html when release hg19. http://redmine.soe.ucsc.edu/issues/2719
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeBroadHmm.ra
- lines changed 10, context: html, text, full: html, text
This data is not restricted. Deleting dateUnrestricted causes a date to be calculated by hgTrackUi CGI.
- src/hg/makeDb/trackDb/human/hg18/trackDb.ra
- lines changed 18, context: html, text, full: html, text
Extend serach scope of NumtS tracks
- src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadHmm.html
- lines changed 130, context: html, text, full: html, text
Got description from Jason Ernst
- lines changed 23, context: html, text, full: html, text
Links to encode vocab should go to common page
- src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadHmm.ra
- lines changed 3, context: html, text, full: html, text
Got description from Jason Ernst
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAffyRnaChip.ra
- lines changed 989, context: html, text, full: html, text
fixed AffyRnaChip extraneous entries
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
- lines changed 6577, context: html, text, full: html, text
fixed numerous extraneous ra entries
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
- lines changed 55, context: html, text, full: html, text
=Added replicate 0 for generation 0 data
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeDukeAffyExon.ra
- lines changed 4, context: html, text, full: html, text
added dateSubmitted where missing
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisChiaPet.ra
- lines changed 6, context: html, text, full: html, text
oops... a few more changes to the replicate numbers
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
- lines changed 20, context: html, text, full: html, text
fixed HaibMethyl and SunyAlbany
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
- lines changed 2, context: html, text, full: html, text
Fixed b7ac3f99154b0b74b9fd59ee4f19a0684371e300 of overridding trackDb for Haib with metaDb.Fixed obj wgEncodeHaibTfbsK562ControlV0416101AlnRep1 that had dateResubmitted instead of dateSubmitted.
- lines changed 97, context: html, text, full: html, text
Removed references to wgEncodeHaibTfbsEcc1GRV0416102Etoh02AlnRep* replaced with wgEncodeHaibTfbsEcc1GrV0416102Etoh02AlnRep*
- lines changed 11, context: html, text, full: html, text
Revised Control Ids (Issue #2774) and (Issue #2773) for incorrect meta-object names for bam files.
- lines changed 2, context: html, text, full: html, text
Adding file index that was previously missing for the bam file.
- lines changed 15, context: html, text, full: html, text
Removed duplicate Antibody designations. Changed IRF4 -> IRF4_(M-17) and EBF -> EBF1_(C-8) to be consistent across all data.
- lines changed 24, context: html, text, full: html, text
Removed reference to obj wgEncodeHaibTfbsHepg2ControlPcr1xRawRep2 which doesn't exist in any submission directory. (Issue 2758).
- lines changed 45, context: html, text, full: html, text
Added 2 missing bam files submission 3505
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
- lines changed 90, context: html, text, full: html, text
fixed numerous extraneous ra entries
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
- lines changed 18, context: html, text, full: html, text
removed entry that had no file attached to it
- lines changed 18, context: html, text, full: html, text
fixed numerous extraneous ra entries
- lines changed 91, context: html, text, full: html, text
Replaced revoked FARE NHBE experiment
- lines changed 16, context: html, text, full: html, text
Dates for last submision were for resubmission
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
- lines changed 99, context: html, text, full: html, text
Added the better downloads page, changed the .html to say Signals instead of Clusters, removed 2 questionable tracks
- lines changed 76, context: html, text, full: html, text
Added replicate 0 as a place holder
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyAlbanyGeneSt.ra
- lines changed 148, context: html, text, full: html, text
fixed HaibMethyl and SunyAlbany
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhNsome.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
- lines changed 538, context: html, text, full: html, text
fixed numerous extraneous ra entries
- lines changed 494, context: html, text, full: html, text
Fixed the accidently deletion of 12 meta-data objects, along with correcting dataVersion to be Jan 2011 Freeze.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
- lines changed 371, context: html, text, full: html, text
Cleaned up meta-data and file mapping. (issue 2758)
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeYaleRnaSeq.ra
- lines changed 160, context: html, text, full: html, text
added the signals back in and changed labels
- lines changed 43, context: html, text, full: html, text
Fixed the fastqs to have the correct metadata
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeRikenCage.ra
- lines changed 1023, context: html, text, full: html, text
recopied alpha version to include the missing meta data that Cricket added, redmine issue# 41
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
- lines changed 1, context: html, text, full: html, text
preparing metadata for release of Broad Histone (Redmine Issue #1550)
- lines changed 1, context: html, text, full: html, text
prepping for the release of SUNY Tiling, hg19, redmine #38
- lines changed 1, context: html, text, full: html, text
preparing trackDb & metaDb for release of UW Histone
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeBroadHistone.ra
- lines changed 21085, context: html, text, full: html, text
preparing metadata for release of Broad Histone (Redmine Issue #1550)
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeSunyAlbanyTiling.ra
- lines changed 153, context: html, text, full: html, text
prepping for the release of SUNY Tiling, hg19, redmine #38
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwHistone.ra
- lines changed 18024, context: html, text, full: html, text
preparing trackDb & metaDb for release of UW Histone
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 1, context: html, text, full: html, text
the test track gc5BaseBw should be release alpha
- lines changed 92, context: html, text, full: html, text
snakes for the MHC region
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- lines changed 1, context: html, text, full: html, text
removing release tags for Broad Histone because I am releasing it to the RR
- lines changed 1, context: html, text, full: html, text
preparing trackDb & metaDb for release of UW Histone
- src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.html
- lines changed 1, context: html, text, full: html, text
changing month of this first release to February
- src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.ra
- lines changed 245, context: html, text, full: html, text
Removing view designation from shortLabels. Personally I find this degree of standardization pitifully bureauocratic
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.ra
- lines changed 95, context: html, text, full: html, text
stop using type bedLogR. We can get most of what we want through the extraFields trackDb setting
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl27.ra
- lines changed 12, context: html, text, full: html, text
Added maxWindowsToDraw and viewUi, sorting the cell-lines by Tier
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
- lines changed 20, context: html, text, full: html, text
Updated the Tag's in trackDb for which protocols were changed. Issue #2731
- lines changed 36760, context: html, text, full: html, text
Fixed obj wgEncodeHaibTfbsK562ControlV0416101AlnRep1 that had dateResubmitted instead of dateSubmitted.
- lines changed 36760, context: html, text, full: html, text
Fixed b7ac3f99154b0b74b9fd59ee4f19a0684371e300 of overridding trackDb for Haib with metaDb.Fixed obj wgEncodeHaibTfbsK562ControlV0416101AlnRep1 that had dateResubmitted instead of dateSubmitted.
- lines changed 19, context: html, text, full: html, text
Removed duplicate Antibody designations. Changed IRF4 -> IRF4_(M-17) and EBF -> EBF1_(C-8) to be consistent across all data.
- lines changed 10, context: html, text, full: html, text
Removed reference to obj wgEncodeHaibTfbsHepg2ControlPcr1xRawRep2 which doesn't exist in any submission directory. (Issue 2758).
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.html
- lines changed 17, context: html, text, full: html, text
Spruced up release notes in preparation for QA
- lines changed 1, context: html, text, full: html, text
Links to encode vocab should go to common page
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.ra
- lines changed 2, context: html, text, full: html, text
Touch up settings as recommended by Terry Furey
- lines changed 88, context: html, text, full: html, text
None of these should have had origAssembly set
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.html
- lines changed 16, context: html, text, full: html, text
Spruced up release notes in preparation for QA
- lines changed 1, context: html, text, full: html, text
Links to encode vocab should go to common page
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.ra
- lines changed 3, context: html, text, full: html, text
Touch up settings as recommended by Terry Furey
- lines changed 84, context: html, text, full: html, text
None of these should have had origAssembly set
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.html
- lines changed 17, context: html, text, full: html, text
Spruced up release notes in preparation for QA
- lines changed 1, context: html, text, full: html, text
Links to encode vocab should go to common page
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.ra
- lines changed 75, context: html, text, full: html, text
Touch up settings as recommended by Terry Furey
- lines changed 36, context: html, text, full: html, text
None of these should have had origAssembly set
- lines changed 27, context: html, text, full: html, text
Adding in resubmission of revoked FAIRE NHBE experiment
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.html
- lines changed 221, context: html, text, full: html, text
Open Chromatin Synthesis finally gets description.
- lines changed 15, context: html, text, full: html, text
Spruced up release notes in preparation for QA
- lines changed 8, context: html, text, full: html, text
Touch up settings as recommended by Terry Furey
- lines changed 1, context: html, text, full: html, text
Links to encode vocab should go to common page
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.ra
- lines changed 2, context: html, text, full: html, text
Open Chromatin Synthesis finally gets description.
- lines changed 10, context: html, text, full: html, text
Touch up settings as recommended by Terry Furey
- lines changed 7, context: html, text, full: html, text
And Open Chrom Synth should not be marked by origAssembly either
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.html
- lines changed 1, context: html, text, full: html, text
Added the better downloads page, changed the .html to say Signals instead of Clusters, removed 2 questionable tracks
- lines changed 6, context: html, text, full: html, text
Added release notes and comment about custom tag
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.ra
- lines changed 1, context: html, text, full: html, text
Added the better downloads page, changed the .html to say Signals instead of Clusters, removed 2 questionable tracks
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.ra
- lines changed 46, context: html, text, full: html, text
Added the better downloads page, changed the .html to say Signals instead of Clusters, removed 2 questionable tracks
- lines changed 1, context: html, text, full: html, text
Changed settings for maxWindowsToDraw for Vanessa
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyTiling.html
- lines changed 1, context: html, text, full: html, text
clarified what track the lab was referring to, redmine issue # 38
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyTiling.ra
- lines changed 8, context: html, text, full: html, text
prepping for the release of SUNY Tiling, hg19, redmine #38
- lines changed 1, context: html, text, full: html, text
Changed title to match the new standard
- lines changed 1, context: html, text, full: html, text
removed the Tenebaum name from the label
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSunySwitchgear.html
- lines changed 8, context: html, text, full: html, text
Fixed html tags and contact info
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSuper.ra
- lines changed 1, context: html, text, full: html, text
Touch up settings as recommended by Terry Furey
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhNsome.ra
- lines changed 39, context: html, text, full: html, text
oops.. why do I always forget something?
- lines changed 1, context: html, text, full: html, text
set some rational view limits
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.new.ra
- lines changed 1, context: html, text, full: html, text
Updated priority to 5 to be consistent with Release 1 of track.
- lines changed 42, context: html, text, full: html, text
Updated short and long-labels for new and Version 2 data.
- lines changed 6, context: html, text, full: html, text
Updated Short labels for Sk-N-SH_RA and WERI-Rb-1 to have consistent abbreviations with UW TFBS and UW Histone track.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.ra
- lines changed 1, context: html, text, full: html, text
Updated priority of track to match release 1.
- lines changed 215, context: html, text, full: html, text
Updated short and long labels to track labeling standards for Jan Freeze Data and New versions of old data.
- lines changed 14, context: html, text, full: html, text
Updated Short labels for Sk-N-SH_RA and WERI-Rb-1 to have consistent abbreviations with UW TFBS and UW Histone track.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.html
- lines changed 3, context: html, text, full: html, text
rearranged second sentence for readability, changed '1%' to 'one percent', cut author list of ref to 10 et al (Redmine Issue #71)
- lines changed 2, context: html, text, full: html, text
Updated FTP link to downloads page and fixed linkto hgdownload instead of hgdownload-test. Fixed typo in link that linked to UWDnase instead of UWHistone downlaods page.
- lines changed 1, context: html, text, full: html, text
clarified the release number of this release
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.ra
- lines changed 1, context: html, text, full: html, text
Updated ViewLimit for signal to be 1:100 instead of 1:10. Matches settings on other UW tracks.
- lines changed 1, context: html, text, full: html, text
Revereted viewLimit from 1:100 -> 1:10 on recomendation for QA.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.ra
- lines changed 8, context: html, text, full: html, text
For consitency updated the abreviation for SK-N-SH_RA from SKNSHRA -> SKRA
- src/hg/makeDb/trackDb/human/hg19/wgEncodeYaleRnaSeq.html
- lines changed 0, context: html, text, full: html, text
added the signals back in and changed labels
- src/hg/makeDb/trackDb/human/hg19/wgEncodeYaleRnaSeq.ra
- lines changed 114, context: html, text, full: html, text
Changed labels and added new polyA- AMA50 experiment
- lines changed 80, context: html, text, full: html, text
added the signals back in and changed labels
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 26, context: html, text, full: html, text
Hid some OMIM tracks to avoid clotting the display.
- lines changed 1, context: html, text, full: html, text
changing trackDb so that decipher track points to old html. Will change to new html when release hg19. http://redmine.soe.ucsc.edu/issues/2719
- src/hg/makeDb/trackDb/ncbiIncidentDb.html
- lines changed 23, context: html, text, full: html, text
update and expand this description
- src/hg/makeDb/trackDb/tagTypes.tab
- lines changed 2, context: html, text, full: html, text
Slight code changes to allow a trackDb setting-controlled mouseover text for next-exon buttons
- src/hg/makeDb/trackDb/zebrafish/danRer5/affyConsensusAndTargetZonWildType.html
- lines changed 2, context: html, text, full: html, text
Corrected Affy product link
- src/hg/makeDb/trackDb/zebrafish/danRer7/danRer7multipleChainNet.html
- lines changed 1, context: html, text, full: html, text
Added the word THE for better grammar.
- src/hg/oneShot/freen/freen.c
- lines changed 6, context: html, text, full: html, text
Adding example lines to BAM schema page in table browser. Pushing forward on getting identifiers to work there, but still a ways to go. (It no longer bombs at the paste identifiers page, but it does shortly thereafter.)
- src/hg/qaPushQ/pushQ.c
- lines changed 638, context: html, text, full: html, text
enlarging limit from 1 TB to 100TB on form submit for pushQ
- src/hg/qaPushQ/pushQ.h
- lines changed 196, context: html, text, full: html, text
enlarging limit from 1 TB to 100TB on form submit for pushQ
- src/hg/qaPushQ/qaPushQ.c
- lines changed 1, context: html, text, full: html, text
enlarging limit from 1 TB to 100TB on form submit for pushQ
- src/hg/utils/automation/Encode.pm
- src/hg/utils/automation/gwUploadFile
- lines changed 121, context: html, text, full: html, text
Mark says python libraries are .py not scripts
- lines changed 33, context: html, text, full: html, text
better try and except clauses and exception exits
- src/hg/utils/automation/gwUploadFile.py
- lines changed 4, context: html, text, full: html, text
have import functioning from specified directory
- lines changed 121, context: html, text, full: html, text
Mark says python libraries are .py not scripts
- src/hg/utils/automation/ncbiIncidentUpdate.sh
- lines changed 83, context: html, text, full: html, text
working scripts for automatic NCBI Incident DB update procedure
- src/hg/utils/automation/ncbiRunIncidentUpdate.sh
- lines changed 30, context: html, text, full: html, text
working scripts for automatic NCBI Incident DB update procedure
- src/inc/bbiFile.h
- lines changed 3, context: html, text, full: html, text
consolidate the display of data last updated printout for hgc clicks, now working for most bbi types
- src/inc/bigBed.h
- lines changed 1, context: html, text, full: html, text
consolidate the display of data last updated printout for hgc clicks, now working for most bbi types
- src/inc/common.h
- lines changed 4, context: html, text, full: html, text
Moved date routines into common, and made expired restriction dates dimmer in hgTrackUi
- src/inc/htmshell.h
- lines changed 3, context: html, text, full: html, text
Added routine to strip html tags from text. This shouuld be used on strings that become tooltip titles.
- src/inc/maf.h
- lines changed 7, context: html, text, full: html, text
add functions to clone mafAli objects
- src/inc/obscure.h
- lines changed 3, context: html, text, full: html, text
adding printVmPeak() function to allow checking of maximum memory usage
- src/inc/udc.h
- lines changed 3, context: html, text, full: html, text
consolidate the display of data last updated printout for hgc clicks, now working for most bbi types
- src/lib/bbiRead.c
- lines changed 6, context: html, text, full: html, text
consolidate the display of data last updated printout for hgc clicks, now working for most bbi types
- src/lib/common.c
- lines changed 73, context: html, text, full: html, text
Moved date routines into common, and made expired restriction dates dimmer in hgTrackUi
- src/lib/htmshell.c
- lines changed 26, context: html, text, full: html, text
Added routine to strip html tags from text. This shouuld be used on strings that become tooltip titles.
- src/lib/maf.c
- lines changed 41, context: html, text, full: html, text
add functions to clone mafAli objects
- src/lib/net.c
- lines changed 13, context: html, text, full: html, text
adding detection of incorrect 200 response when expecting 206 partial content, should help detect earlier and explain the problem to users
- src/lib/obscure.c
- lines changed 24, context: html, text, full: html, text
adding printVmPeak() function to allow checking of maximum memory usage
- src/lib/udc.c
- lines changed 15, context: html, text, full: html, text
consolidate the display of data last updated printout for hgc clicks, now working for most bbi types
- lines changed 1, context: html, text, full: html, text
Improving out of data comment.
- lines changed 1, context: html, text, full: html, text
adding detection of incorrect 200 response when expecting 206 partial content, should help detect earlier and explain the problem to users
- src/product/ex.hg.conf
- lines changed 8, context: html, text, full: html, text
Added some clarifying comments about central.domain and central.cookie inthe context of multiple mirror hosts. Removed bogus setting
backupcentral.domain -- it is never used by the code. In retrospect, I
think central.cookie and central.domain should have been named
cookie.name and cookie.domain because they are distinct from the central
database mysql profile. It's important that multiple central databases
used by hosts in the same domain get separate cookie names, but having
the central.* prefix on both db and cookie hasn't made that obvious in
the past. :)
- src/utils/bedGraphToBigWig/bedGraphToBigWig.c
- lines changed 3, context: html, text, full: html, text
adding printVmPeak() function to allow checking of maximum memory usage
- src/utils/bedGraphToBigWig/makefile
- lines changed 5, context: html, text, full: html, text
adding printVmPeak() function to allow checking of maximum memory usage
- src/utils/bedToBigBed/bedToBigBed.c
- lines changed 2, context: html, text, full: html, text
adding printVmPeak() debug call to each of the big* commands
- src/utils/bedToBigBed/makefile
- lines changed 1, context: html, text, full: html, text
adding printVmPeak() debug call to each of the big* commands
- src/utils/bigBedInfo/bigBedInfo.c
- lines changed 2, context: html, text, full: html, text
adding printVmPeak() debug call to each of the big* commands
- src/utils/bigBedInfo/makefile
- lines changed 5, context: html, text, full: html, text
adding printVmPeak() debug call to each of the big* commands
- src/utils/bigBedSummary/bigBedSummary.c
- lines changed 3, context: html, text, full: html, text
adding printVmPeak() debug call to each of the big* commands
- src/utils/bigBedSummary/makefile
- lines changed 3, context: html, text, full: html, text
adding printVmPeak() debug call to each of the big* commands
- src/utils/bigBedToBed/bigBedToBed.c
- lines changed 3, context: html, text, full: html, text
adding printVmPeak() debug call to each of the big* commands
- src/utils/bigBedToBed/makefile
- lines changed 3, context: html, text, full: html, text
adding printVmPeak() debug call to each of the big* commands
- src/utils/bigWigInfo/bigWigInfo.c
- lines changed 2, context: html, text, full: html, text
adding printVmPeak() debug call to each of the big* commands
- src/utils/bigWigInfo/makefile
- lines changed 7, context: html, text, full: html, text
adding printVmPeak() debug call to each of the big* commands
- src/utils/bigWigSummary/bigWigSummary.c
- lines changed 3, context: html, text, full: html, text
adding printVmPeak() debug call to each of the big* commands
- src/utils/bigWigSummary/makefile
- lines changed 3, context: html, text, full: html, text
adding printVmPeak() debug call to each of the big* commands
- src/utils/bigWigToBedGraph/bigWigToBedGraph.c
- lines changed 3, context: html, text, full: html, text
adding printVmPeak() debug call to each of the big* commands
- src/utils/bigWigToBedGraph/makefile
- lines changed 3, context: html, text, full: html, text
adding printVmPeak() debug call to each of the big* commands
- src/utils/bigWigToWig/bigWigToWig.c
- lines changed 3, context: html, text, full: html, text
adding printVmPeak() debug call to each of the big* commands
- src/utils/decipher/buildDecipher
- lines changed 8, context: html, text, full: html, text
Updated buildDecipher from hg18 to hg19.
- src/utils/decipher/checkDecipher.sh
- lines changed 3, context: html, text, full: html, text
Updated checkDecipher.sh to accomodate new DECIPHER release.
- src/utils/qa/weeklybld/buildEnv.csh
- src/utils/wigToBigWig/makefile
- lines changed 4, context: html, text, full: html, text
adding printVmPeak() function to allow checking of maximum memory usage
- src/utils/wigToBigWig/wigToBigWig.c
- lines changed 3, context: html, text, full: html, text
adding printVmPeak() function to allow checking of maximum memory usage
- lines changed: 134449
- files changed: 303