All File Changes
v265_preview2 to v265_base (2012-03-20 to 2012-03-27) v265
- python/users/README
- lines changed 4, context: html, text, full: html, text
Adding a directory where users can create programs they don't feel are yet ready for other people to user.
- src/hg/checkTableCoords/tests/input/bed12CTCBad.bed
- lines changed 2, context: html, text, full: html, text
removing invalid score value "."
- src/hg/checkTableCoords/tests/input/bed8CTCBad.bed
- lines changed 2, context: html, text, full: html, text
removing invalid score value "."
- src/hg/encode/DAFs/3.0/mm9/wgEncodePsuRnaSeq.daf
- lines changed 89, context: html, text, full: html, text
First pass at DAF for track. Redmine #107.
- src/hg/encode/DAFs/3.0/mm9/wgEncodeUwRnaSeq.daf
- lines changed 6, context: html, text, full: html, text
Updated DAF to not have required views.
- src/hg/encode/encodeReport/gencodeStats
- lines changed 52, context: html, text, full: html, text
Added code to report numbers of transcripts and genes for 2-way pseudogenes. Corrected the code to get automatic only. Added code to account for the PAR region genes and transcripts which have duplicated ids on chrX and chrY.
- src/hg/encode/encodeValidate/doEncodeValidate.pl
- lines changed 6, context: html, text, full: html, text
Removing freePass fileTypes that we should not be accepting anyway
- lines changed 12, context: html, text, full: html, text
added in checks for bedRnaElement
- lines changed 12, context: html, text, full: html, text
Revert "added in checks for bedRnaElement"
This reverts commit 50c00c11eca89cde855e23932882f8f8493c1ef8.
- lines changed 12, context: html, text, full: html, text
adding back in bedRnaElements checks for columns 7-9
- src/hg/encode/qaAddTrackReferences/qaAddTrackReferences
- lines changed 28, context: html, text, full: html, text
made a bypass for the pmc pathway, because ncbi changed how the xml is delivered in version 1.0 xml's. I need to rewrite the parsing mechanism to account for this, but this works for now.
- src/hg/hgApi/hgApi.c
- lines changed 46, context: html, text, full: html, text
remove experimental and unused trackList cmd and associated code
- lines changed 71, context: html, text, full: html, text
follow-up on code review by Jim; added some doc and use warnAbortHandler
- lines changed 11, context: html, text, full: html, text
use cgiString to simplify code
- lines changed 1, context: html, text, full: html, text
commit tim's code to stop using trackHash in compositeMetadataToggle; this fixes #7376
- lines changed 7, context: html, text, full: html, text
encodeExperiment table 'production copy' lives on preview server. API call looks there if table not found on localhost.
- src/hg/hgTables/bam.c
- lines changed 1, context: html, text, full: html, text
Replacing a hash that gives a tdb for a track name with one that gives tdb for a table name. Addresses redmine 7222.
- src/hg/hgTables/bigBed.c
- lines changed 1, context: html, text, full: html, text
Replacing a hash that gives a tdb for a track name with one that gives tdb for a table name. Addresses redmine 7222.
- src/hg/hgTables/bigWig.c
- lines changed 3, context: html, text, full: html, text
Replacing a hash that gives a tdb for a track name with one that gives tdb for a table name. Addresses redmine 7222.
- src/hg/hgTables/compositeTrack.c
- lines changed 2, context: html, text, full: html, text
commit tim's code to stop using trackHash in compositeMetadataToggle; this fixes #7376
- src/hg/hgTables/hgTables.c
- lines changed 18, context: html, text, full: html, text
Replacing a hash that gives a tdb for a track name with one that gives tdb for a table name. Addresses redmine 7222.
- src/hg/hgTables/hgTables.h
- lines changed 1, context: html, text, full: html, text
Oops forgot to include this .h file in the fix for #7222
- src/hg/hgTables/schema.c
- lines changed 11, context: html, text, full: html, text
Replacing a hash that gives a tdb for a track name with one that gives tdb for a table name. Addresses redmine 7222.
- src/hg/hgTables/sumStats.c
- lines changed 1, context: html, text, full: html, text
Replacing a hash that gives a tdb for a track name with one that gives tdb for a table name. Addresses redmine 7222.
- src/hg/hgTables/vcf.c
- lines changed 1, context: html, text, full: html, text
Replacing a hash that gives a tdb for a track name with one that gives tdb for a table name. Addresses redmine 7222.
- src/hg/hgTrackUi/hgTrackUi.c
- lines changed 2, context: html, text, full: html, text
make individual sequences for publications track clickable, show alignments, correct mouseOvers // Also changs text that is shown for PDF Output in hgTracks (see email with Ann/Donna/Brian)
- lines changed 3, context: html, text, full: html, text
commit tim's code to stop using trackHash in compositeMetadataToggle; this fixes #7376
- lines changed 2, context: html, text, full: html, text
changing track configs according to tims instructions
- lines changed 22, context: html, text, full: html, text
make subtrack config work following tims suggestions, try to make psl track description clearer
- src/hg/hgTracks/gvfTrack.c
- lines changed 8, context: html, text, full: html, text
Track #7090 (ISCA update): Adding abbreviations for several morevariant origin terms from John Lopez (NCBI).
- src/hg/hgTracks/hgTracks.c
- lines changed 1, context: html, text, full: html, text
give blat track priority 101 to force it after any tracks which have priority == 0 in trackDb (priority 0 is automatically converted to 100) - see #7343
- lines changed 28, context: html, text, full: html, text
make individual sequences for publications track clickable, show alignments, correct mouseOvers // Also changs text that is shown for PDF Output in hgTracks (see email with Ann/Donna/Brian)
- src/hg/hgTracks/hgTracks.h
- lines changed 3, context: html, text, full: html, text
make individual sequences for publications track clickable, show alignments, correct mouseOvers // Also changs text that is shown for PDF Output in hgTracks (see email with Ann/Donna/Brian)
- src/hg/hgTracks/searchTracks.c
- lines changed 2, context: html, text, full: html, text
commit tim's code to stop using trackHash in compositeMetadataToggle; this fixes #7376
- src/hg/hgTracks/simpleTracks.c
- lines changed 149, context: html, text, full: html, text
creating a authorYear label on the fly for pubBlat tracks
- lines changed 181, context: html, text, full: html, text
make individual sequences for publications track clickable, show alignments, correct mouseOvers // Also changs text that is shown for PDF Output in hgTracks (see email with Ann/Donna/Brian)
- lines changed 4, context: html, text, full: html, text
mark pubsMarker items as bed5 so the article count is correct; fix some indentation
- lines changed 14, context: html, text, full: html, text
changing track configs according to tims instructions
- lines changed 5, context: html, text, full: html, text
temporary hack to pubs track name/type confusion, need to find better solution
- src/hg/hgc/hgc.c
- lines changed 1, context: html, text, full: html, text
make individual sequences for publications track clickable, show alignments, correct mouseOvers // Also changs text that is shown for PDF Output in hgTracks (see email with Ann/Donna/Brian)
- lines changed 1, context: html, text, full: html, text
commit tim's code to stop using trackHash in compositeMetadataToggle; this fixes #7376
- src/hg/hgc/peakClusters.c
- lines changed 2, context: html, text, full: html, text
commit tim's code to stop using trackHash in compositeMetadataToggle; this fixes #7376
- src/hg/hgc/pubs.c
- lines changed 44, context: html, text, full: html, text
creating a authorYear label on the fly for pubBlat tracks
- lines changed 187, context: html, text, full: html, text
make individual sequences for publications track clickable, show alignments, correct mouseOvers // Also changs text that is shown for PDF Output in hgTracks (see email with Ann/Donna/Brian)
- lines changed 3, context: html, text, full: html, text
changing track configs according to tims instructions
- lines changed 1, context: html, text, full: html, text
add separators to pubs hgc, some minor comment changes in jksql
- src/hg/htdocs/ENCODE/dataMatrix/dataMatrix.css
- lines changed 1, context: html, text, full: html, text
Restore vertical headers on IE to bottom->top directionality. More readable, and layout is quicker. At the expense of more jagged font.
- src/hg/htdocs/ENCODE/dataMatrix/encodeDataSummaryInclude.html
- lines changed 2, context: html, text, full: html, text
New titles for Data Summary tables, thanks Jeff L
- src/hg/htdocs/ENCODE/downloads.html
- lines changed 5, context: html, text, full: html, text
adding UMass 5C to the list, redmne#225
- lines changed 1, context: html, text, full: html, text
adding Chromatin super track link, redmne# 2606
- src/hg/htdocs/goldenPath/pubs.html
- src/hg/inc/annoStreamDb.h
- lines changed 14, context: html, text, full: html, text
Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter,
annoRow, annoStreamer, annoGrator, and annoFormatter define the core
interfaces for passing data and configuration to and from components.
The annoGrator superclass can join annoRows on position and pass
forward all rows of secondary source. The annoGratorQuery module
orchestrates the passing of annoRows between the primary source,
annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and
annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join
columns of two database tables such as hg19's pgNA12878 and knownGene
into tab-separated output.
- src/hg/inc/hui.h
- lines changed 5, context: html, text, full: html, text
commit tim's code to stop using trackHash in compositeMetadataToggle; this fixes #7376
- src/hg/inc/jksql.h
- lines changed 5, context: html, text, full: html, text
Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter,
annoRow, annoStreamer, annoGrator, and annoFormatter define the core
interfaces for passing data and configuration to and from components.
The annoGrator superclass can join annoRows on position and pass
forward all rows of secondary source. The annoGratorQuery module
orchestrates the passing of annoRows between the primary source,
annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and
annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join
columns of two database tables such as hg19's pgNA12878 and knownGene
into tab-separated output.
- src/hg/inc/versionInfo.h
- src/hg/js/ajax.js
- lines changed 7, context: html, text, full: html, text
use request.responseText when available in the errorHandler
- src/hg/js/encodeChipMatrix.js
- lines changed 8, context: html, text, full: html, text
Better method of suppressing extra search dropdowns from URL
- lines changed 10, context: html, text, full: html, text
Suppress mouseOver on X axis (Column headers) under IE8 as QA noted this results in a flashing effect
- src/hg/js/encodeDataMatrix.js
- lines changed 4, context: html, text, full: html, text
Changes responding to QA (redmine #5149, issues note 27). 1. Save user-selected search type in cookie so it persists across pages. 2. Include ChIP-seq in cell-based experiment table on data summary page. 3. encode URL passed to hgEncodeVocab so cells having terms with weird chars (e.g. +) will work. Also, override extra search dropdowns (until figure out how to remove mdbVar cart vars by URL)
- lines changed 7, context: html, text, full: html, text
Better method of suppressing extra search dropdowns from URL
- lines changed 12, context: html, text, full: html, text
Suppress mouseOver on X axis (Column headers) under IE8 as QA noted this results in a flashing effect
- src/hg/js/encodeDataSummary.js
- lines changed 13, context: html, text, full: html, text
Changes responding to QA (redmine #5149, issues note 27). 1. Save user-selected search type in cookie so it persists across pages. 2. Include ChIP-seq in cell-based experiment table on data summary page. 3. encode URL passed to hgEncodeVocab so cells having terms with weird chars (e.g. +) will work. Also, override extra search dropdowns (until figure out how to remove mdbVar cart vars by URL)
- lines changed 7, context: html, text, full: html, text
Better method of suppressing extra search dropdowns from URL
- src/hg/js/encodeMatrix.js
- lines changed 26, context: html, text, full: html, text
Changes responding to QA (redmine #5149, issues note 27). 1. Save user-selected search type in cookie so it persists across pages. 2. Include ChIP-seq in cell-based experiment table on data summary page. 3. encode URL passed to hgEncodeVocab so cells having terms with weird chars (e.g. +) will work. Also, override extra search dropdowns (until figure out how to remove mdbVar cart vars by URL)
- lines changed 22, context: html, text, full: html, text
Add fix for lack of persistence in search type radio button setting when floating header is activated
- lines changed 1, context: html, text, full: html, text
Fix for floating header break -- mistakenly overrode fadein rather than fadeout with fix for lost search radio buttons
- lines changed 3, context: html, text, full: html, text
Fix again so both serarch button persistence and floating header operate correctly. Setting radio button on fadeIn handles it (custom fadeOut didn't hide the floater properly).
- src/hg/js/encodeProject.js
- lines changed 6, context: html, text, full: html, text
Suppress mouseOver on X axis (Column headers) under IE8 as QA noted this results in a flashing effect
- src/hg/js/hgTracks.js
- lines changed 3, context: html, text, full: html, text
trim really long titles in right click menu items
- lines changed 3, context: html, text, full: html, text
fix inconsistency in max length
- src/hg/lib/annoStreamDb.c
- lines changed 187, context: html, text, full: html, text
Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter,
annoRow, annoStreamer, annoGrator, and annoFormatter define the core
interfaces for passing data and configuration to and from components.
The annoGrator superclass can join annoRows on position and pass
forward all rows of secondary source. The annoGratorQuery module
orchestrates the passing of annoRows between the primary source,
annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and
annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join
columns of two database tables such as hg19's pgNA12878 and knownGene
into tab-separated output.
- src/hg/lib/hui.c
- lines changed 47, context: html, text, full: html, text
commit tim's code to stop using trackHash in compositeMetadataToggle; this fixes #7376
- src/hg/lib/jksql.c
- lines changed 29, context: html, text, full: html, text
workaround for mysql5.0 bug in warnings reported during load data infile
- lines changed 10, context: html, text, full: html, text
add separators to pubs hgc, some minor comment changes in jksql
- lines changed 9, context: html, text, full: html, text
mysql load data file warnings abort - adding some caution about changing stuff, so for now warning detection activates only on hgwdev, hgwbeta, hgwalpha but not RR or mirrors (yet)
- src/hg/lib/makefile
- lines changed 1, context: html, text, full: html, text
Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter,
annoRow, annoStreamer, annoGrator, and annoFormatter define the core
interfaces for passing data and configuration to and from components.
The annoGrator superclass can join annoRows on position and pass
forward all rows of secondary source. The annoGratorQuery module
orchestrates the passing of annoRows between the primary source,
annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and
annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join
columns of two database tables such as hg19's pgNA12878 and knownGene
into tab-separated output.
- src/hg/lib/pubsArticle.sql
- lines changed 4, context: html, text, full: html, text
changed table names in sql files as hiram code review, redmine #7363
- src/hg/lib/pubsBlat.sql
- lines changed 6, context: html, text, full: html, text
changed table names in sql files as hiram code review, redmine #7363
- src/hg/lib/pubsMarkerAnnot.sql
- lines changed 1, context: html, text, full: html, text
changed table names in sql files as hiram code review, redmine #7363
- src/hg/lib/pubsMarkerBand.sql
- lines changed 1, context: html, text, full: html, text
changed table names in sql files as hiram code review, redmine #7363
- src/hg/lib/pubsMarkerGene.sql
- lines changed 1, context: html, text, full: html, text
changed table names in sql files as hiram code review, redmine #7363
- src/hg/lib/pubsMarkerSnp.sql
- lines changed 1, context: html, text, full: html, text
changed table names in sql files as hiram code review, redmine #7363
- src/hg/lib/pubsSequence.sql
- lines changed 8, context: html, text, full: html, text
changed table names in sql files as hiram code review, redmine #7363
- src/hg/lib/pubsSequenceAnnot.sql
- lines changed 2, context: html, text, full: html, text
changed table names in sql files as hiram code review, redmine #7363
- src/hg/lib/t2g.sql
- lines changed 19, context: html, text, full: html, text
changed table names in sql files as hiram code review, redmine #7363
- src/hg/lib/tests/annoGratorTester.c
- lines changed 117, context: html, text, full: html, text
Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter,
annoRow, annoStreamer, annoGrator, and annoFormatter define the core
interfaces for passing data and configuration to and from components.
The annoGrator superclass can join annoRows on position and pass
forward all rows of secondary source. The annoGratorQuery module
orchestrates the passing of annoRows between the primary source,
annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and
annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join
columns of two database tables such as hg19's pgNA12878 and knownGene
into tab-separated output.
- src/hg/lib/tests/annoGratorTests.mk
- lines changed 22, context: html, text, full: html, text
Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter,
annoRow, annoStreamer, annoGrator, and annoFormatter define the core
interfaces for passing data and configuration to and from components.
The annoGrator superclass can join annoRows on position and pass
forward all rows of secondary source. The annoGratorQuery module
orchestrates the passing of annoRows between the primary source,
annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and
annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join
columns of two database tables such as hg19's pgNA12878 and knownGene
into tab-separated output.
- src/hg/lib/tests/expected/annoGrator/pgSnpDbToTabOut.txt
- lines changed 4, context: html, text, full: html, text
Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter,
annoRow, annoStreamer, annoGrator, and annoFormatter define the core
interfaces for passing data and configuration to and from components.
The annoGrator superclass can join annoRows on position and pass
forward all rows of secondary source. The annoGratorQuery module
orchestrates the passing of annoRows between the primary source,
annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and
annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join
columns of two database tables such as hg19's pgNA12878 and knownGene
into tab-separated output.
- src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToTabOutShort.txt
- lines changed 4, context: html, text, full: html, text
Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter,
annoRow, annoStreamer, annoGrator, and annoFormatter define the core
interfaces for passing data and configuration to and from components.
The annoGrator superclass can join annoRows on position and pass
forward all rows of secondary source. The annoGratorQuery module
orchestrates the passing of annoRows between the primary source,
annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and
annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join
columns of two database tables such as hg19's pgNA12878 and knownGene
into tab-separated output.
- src/hg/lib/tests/makefile
- lines changed 8, context: html, text, full: html, text
Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter,
annoRow, annoStreamer, annoGrator, and annoFormatter define the core
interfaces for passing data and configuration to and from components.
The annoGrator superclass can join annoRows on position and pass
forward all rows of secondary source. The annoGratorQuery module
orchestrates the passing of annoRows between the primary source,
annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and
annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join
columns of two database tables such as hg19's pgNA12878 and knownGene
into tab-separated output.
- src/hg/makeDb/doc/cavPor3.txt
- lines changed 21, context: html, text, full: html, text
lastz runs done for susScr2 vicPac1 turTru1 tupBel1 equCab2 oryCun2 cavPor3
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeDukeAffyExon.release3.notes
- lines changed 324, context: html, text, full: html, text
updated notes for duke affy exon
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeOpenChromDnase.release2.notes
- src/hg/makeDb/doc/equCab2.txt
- lines changed 21, context: html, text, full: html, text
lastz runs done for susScr2 vicPac1 turTru1 tupBel1 equCab2 oryCun2 cavPor3
- src/hg/makeDb/doc/hg19.txt
- lines changed 6, context: html, text, full: html, text
trackDb override for ENCODE Pilot regions (lifted from hg18)
- src/hg/makeDb/doc/makeEnsembl.txt
- lines changed 18, context: html, text, full: html, text
fixup chrM coordinates on hg19
- src/hg/makeDb/doc/mm10.txt
- lines changed 21, context: html, text, full: html, text
lastz runs done for susScr2 vicPac1 turTru1 tupBel1 equCab2 oryCun2 cavPor3
- lines changed 25, context: html, text, full: html, text
finished lastz for ailMel1 pteVam1 loxAfr3 canFam3 felCat4
- lines changed 291, context: html, text, full: html, text
starting lastz for dasNov2 myoLuc2 bosTau7 oviAri1 proCap1
- lines changed 304, context: html, text, full: html, text
starting lastz runs on sorAra1 eriEur1 ochPri2 echTel1 and macEug2
- lines changed 5, context: html, text, full: html, text
finished with bosTau7 lastz
- lines changed 113, context: html, text, full: html, text
completed proCap1 sorAra1 eriEur1 echTel1 macEug2 ochPri2
- src/hg/makeDb/doc/oryCun2.txt
- lines changed 21, context: html, text, full: html, text
lastz runs done for susScr2 vicPac1 turTru1 tupBel1 equCab2 oryCun2 cavPor3
- src/hg/makeDb/doc/rn5.txt
- lines changed 86, context: html, text, full: html, text
window masker done, gaps done, repeat masker almost done
- lines changed 129, context: html, text, full: html, text
done with masking and created lineage specific repeats
- src/hg/makeDb/doc/susScr2.txt
- lines changed 21, context: html, text, full: html, text
lastz runs done for susScr2 vicPac1 turTru1 tupBel1 equCab2 oryCun2 cavPor3
- src/hg/makeDb/doc/tupBel1.txt
- lines changed 21, context: html, text, full: html, text
lastz runs done for susScr2 vicPac1 turTru1 tupBel1 equCab2 oryCun2 cavPor3
- src/hg/makeDb/doc/turTru1.txt
- lines changed 21, context: html, text, full: html, text
lastz runs done for susScr2 vicPac1 turTru1 tupBel1 equCab2 oryCun2 cavPor3
- src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes13.csh
- lines changed 1427, context: html, text, full: html, text
starting on mm10 ucsc genes (#7045)
- src/hg/makeDb/doc/vicPac1.txt
- lines changed 21, context: html, text, full: html, text
lastz runs done for susScr2 vicPac1 turTru1 tupBel1 equCab2 oryCun2 cavPor3
- src/hg/makeDb/doc/windowMasker.txt
- lines changed 35, context: html, text, full: html, text
documentating windowmasker binary build
- src/hg/makeDb/genbank/etc/rr-dbload
- lines changed 28, context: html, text, full: html, text
restored accidently removed file
- src/hg/makeDb/hgBedsToBedExps/hgBedsToBedExps.c
- lines changed 2, context: html, text, full: html, text
Fixing a bug Bob noticed where in wgEncodeRegTfbsClustered the score sometimes was larger than the max of the components visible on the details page.
- src/hg/makeDb/hgLoadBed/hgLoadBed.c
- lines changed 9, context: html, text, full: html, text
Removing the code to introduce nulls #7330
- lines changed 9, context: html, text, full: html, text
Undoing last commit, needs to be checked in with changes to encodeValidate
- src/hg/makeDb/schema/all.joiner
- lines changed 38, context: html, text, full: html, text
all.joiner corrections for pubs
- lines changed 2, context: html, text, full: html, text
make individual sequences for publications track clickable, show alignments, correct mouseOvers // Also changs text that is shown for PDF Output in hgTracks (see email with Ann/Donna/Brian)
- lines changed 4, context: html, text, full: html, text
all.joiner corrections for publications track
- lines changed 48, context: html, text, full: html, text
Merck tracks all.joiner additions
- lines changed 20, context: html, text, full: html, text
Added tables for polyASeq track to tables ignored.
- lines changed 20, context: html, text, full: html, text
Revert "Added tables for polyASeq track to tables ignored."
This reverts commit 423bd9acec19f88be938ebe8d5f06e6beb2e15f1.
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 15, context: html, text, full: html, text
Added 3 treatments for UW Stam data.
- lines changed 3, context: html, text, full: html, text
Added provisional tags and fixed minor spelling errors.
- lines changed 2, context: html, text, full: html, text
HAEpiC had the wrong vendorId, fixed 7100-7110
- lines changed 1, context: html, text, full: html, text
Sex of U87 has been updated to Male from Unknown
- lines changed 2, context: html, text, full: html, text
Trying to deprecate the level and annotation per Mark request, it is still stuck in hg18, but in hg19 V3 and V4 are pulled
- lines changed 7, context: html, text, full: html, text
CV Fixes from Code Review
- lines changed 1, context: html, text, full: html, text
Fixed error in merge conflict that resulted in making File Type searchable. Redmine #7100.
- lines changed 1, context: html, text, full: html, text
Correcting gender for hMSC-UC
- lines changed 11, context: html, text, full: html, text
removed privacy from the cv, redmine #4143 comment 21
- lines changed 119, context: html, text, full: html, text
Adding childOf var and two approved cell lines
- lines changed 119, context: html, text, full: html, text
Adding in commented out non-NHGRI approved cell lines for easier registration before Freeze
- lines changed 81, context: html, text, full: html, text
Adding beta-estradiol and ZNF Knockout treatments to CV
- lines changed 49, context: html, text, full: html, text
Changed Hardison treatments to match differentiation registration.
- lines changed 2, context: html, text, full: html, text
Fixing a couple of treatment tags
- lines changed 3, context: html, text, full: html, text
Corrected cell registration with treatment for G1E-ER4+E2 to be G1E-ER4. Redmine #7418.
- lines changed 12, context: html, text, full: html, text
Fixed broken links as well as removed GO term from label for type localization.
- lines changed 20, context: html, text, full: html, text
Added read type for PSU RNA-seq data.
- lines changed 15, context: html, text, full: html, text
Added in 3 new views for Mouse Transcriptome data.
- lines changed 18, context: html, text, full: html, text
adding in gencode v10 views
- lines changed 2, context: html, text, full: html, text
Changing HEK293 from cancer to normal, Adding to description that cells contain Adenovirus 5 DNA, from early References
- src/hg/makeDb/trackDb/cv/beta/cv.ra
- lines changed 1, context: html, text, full: html, text
Fixed error in merge conflict that resulted in making File Type searchable. Redmine #7100.
- lines changed 12, context: html, text, full: html, text
Fixed broken links as well as removed GO term from label for type localization.
- src/hg/makeDb/trackDb/cv/public/cv.ra
- lines changed 388, context: html, text, full: html, text
Moved over approved changes to public. Redmine #7355.
- lines changed 12, context: html, text, full: html, text
Fixed broken links as well as removed GO term from label for type localization.
- src/hg/makeDb/trackDb/fugu/fr3/description.html
- lines changed 2, context: html, text, full: html, text
commented out one of the sample queries. It's not working on beta. If it's not working on the RR either then I'll remove it completely.
- src/hg/makeDb/trackDb/human/hg18/agilentCgh.html
- lines changed 131, context: html, text, full: html, text
changed around some naming to merge Agilent CGH with the new Affy CytoScan array track
- src/hg/makeDb/trackDb/human/hg18/genotypeArrays.html
- lines changed 131, context: html, text, full: html, text
changed around some naming to merge Agilent CGH with the new Affy CytoScan array track
- src/hg/makeDb/trackDb/human/hg18/trackDb.ra
- lines changed 9, context: html, text, full: html, text
changed around some naming to merge Agilent CGH with the new Affy CytoScan array track
- src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
- lines changed 92, context: html, text, full: html, text
splitting out the methyl27 track from the monolithic trackDb file
- lines changed 9, context: html, text, full: html, text
removed all rep=1 and it's variants, replaced with .patch.ra's
- src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.patch.ra
- lines changed 1257, context: html, text, full: html, text
removed all rep=1 and it's variants, replaced with .patch.ra's
- src/hg/makeDb/trackDb/human/hg18/wgEncodeGisRnaSeq.patch.ra
- lines changed 301, context: html, text, full: html, text
removed all rep=1 and it's variants, replaced with .patch.ra's
- src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethyl27.patch.ra
- lines changed 92, context: html, text, full: html, text
removed all rep=1 and it's variants, replaced with .patch.ra's
- src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethyl27.ra
- lines changed 92, context: html, text, full: html, text
splitting out the methyl27 track from the monolithic trackDb file
- src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethylSeq.patch.ra
- lines changed 324, context: html, text, full: html, text
removed all rep=1 and it's variants, replaced with .patch.ra's
- src/hg/makeDb/trackDb/human/hg19/agilentCgh.html
- lines changed 174, context: html, text, full: html, text
changed around some naming to merge Agilent CGH with the new Affy CytoScan array track
- src/hg/makeDb/trackDb/human/hg19/genotypeArrays.html
- lines changed 174, context: html, text, full: html, text
changed around some naming to merge Agilent CGH with the new Affy CytoScan array track
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeDukeAffyExon.ra
- lines changed 510, context: html, text, full: html, text
replacing tracks with bigBed tracks
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV3.ra
- lines changed 6, context: html, text, full: html, text
Trying to deprecate the level and annotation per Mark request, it is still stuck in hg18, but in hg19 V3 and V4 are pulled
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGencodeV4.ra
- lines changed 8, context: html, text, full: html, text
Trying to deprecate the level and annotation per Mark request, it is still stuck in hg18, but in hg19 V3 and V4 are pulled
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
- lines changed 384, context: html, text, full: html, text
added in new haib tracks
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
- lines changed 39, context: html, text, full: html, text
removed privacy var form open chrom chip, missed last time
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
- lines changed 145, context: html, text, full: html, text
removed privacy from the cv, redmine #4143 comment 21
- lines changed 52, context: html, text, full: html, text
added md5sums, added in replacement bigWig v4, and revoked old one
- lines changed 9, context: html, text, full: html, text
added in metaData from old submission
- lines changed 291, context: html, text, full: html, text
added treatment = None for all stanzas that didn't have it
- lines changed 30, context: html, text, full: html, text
added in some expIds and dccAccessions
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhNsome.ra
- lines changed 25, context: html, text, full: html, text
Fixed truncated file, but loading newer version of the file. Redmine #131.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
- lines changed 15, context: html, text, full: html, text
Moved accession to dccInternalNotes. Redmine #7384.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra
- lines changed 20, context: html, text, full: html, text
testing bigbed for hg19, gencode combine search results GM12878IngelCytosol
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeOpenChromChip.ra
- lines changed 8, context: html, text, full: html, text
staged new freeze dates to openChromChip
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeOpenChromDnase.ra
- lines changed 5166, context: html, text, full: html, text
Staging Open Chrom DNase (Release 2) on beta (redmine #4143)
- lines changed 201, context: html, text, full: html, text
Matt made some changes to the metadata (redmine #4143)
- lines changed 320, context: html, text, full: html, text
Matt made some corrections to the metadata (redmine #4143)
- lines changed 15, context: html, text, full: html, text
Matt made some corrections to the metadata (redmine #4143)
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSydhNsome.ra
- lines changed 108, context: html, text, full: html, text
pushing out V2 of truncated file, redmine 131 note-54, and pushing out other metadata changes: Geo Series added, md5sums added, .bam.bai files added
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
- lines changed 1, context: html, text, full: html, text
Releasing the Chromatin super track and the new UMass 5C, redmine#225 & #2606
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeOpenChromChip.ra
- lines changed 8, context: html, text, full: html, text
Matt updated 'post' freeze dates in the metadata (redmine #6581)
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeSydhNsome.ra
- lines changed 108, context: html, text, full: html, text
pushing out V2 of truncated file, redmine 131 note-54, and pushing out other metadata changes: Geo Series added, md5sums added, .bam.bai files added
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUmassDekker5C.ra
- lines changed 988, context: html, text, full: html, text
Releasing the Chromatin super track and the new UMass 5C, redmine#225 & #2606
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 20, context: html, text, full: html, text
changed around some naming to merge Agilent CGH with the new Affy CytoScan array track
- lines changed 1, context: html, text, full: html, text
add a few species to the turtle skunk alignment
- lines changed 5, context: html, text, full: html, text
trackDb override for ENCODE Pilot regions (lifted from hg18)
- lines changed 1, context: html, text, full: html, text
encode icon for pilot regions
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- lines changed 2, context: html, text, full: html, text
moving the 5C path to beta in preparation of the chromatin supertrack release, redmine#2606 note# 49
- lines changed 3, context: html, text, full: html, text
Releasing the Chromatin super track and the new UMass 5C, redmine#225 & #2606
- lines changed 2, context: html, text, full: html, text
Staging Open Chrom DNase (Release 2) on beta (redmine #4143)
- lines changed 2, context: html, text, full: html, text
removed all rep=1 and it's variants, replaced with .patch.ra's
- src/hg/makeDb/trackDb/human/hg19/wgEncodeChromSuper.html
- lines changed 18, context: html, text, full: html, text
fixed references and html for Chromatin Super Track, redmine# 2606
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.release2.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.release3.ra
- lines changed 262, context: html, text, full: html, text
fixed some trackDb settings for duke affy exon
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.html
- lines changed 170, context: html, text, full: html, text
fixed a lot of html errors in description page
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release2.ra
- lines changed 1, context: html, text, full: html, text
adding in geo accession to hgfilui
- lines changed 3, context: html, text, full: html, text
removed short labels from view parent stanzas
- lines changed 5, context: html, text, full: html, text
qa fixes, viewlimits were off relative to the data, and set peaks to dense
- lines changed 48, context: html, text, full: html, text
reordered matrix, and other qa fixes
- lines changed 4, context: html, text, full: html, text
more alphabetization fixes
- lines changed 1, context: html, text, full: html, text
updated submission id and date
- lines changed 2, context: html, text, full: html, text
last second label changes for length purposes
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.release3.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUmassDekker5C.html
- lines changed 3, context: html, text, full: html, text
had steve make a final pass for the UMass 5C page and made the fixes. Redmine# 225, note# 53
- lines changed 1, context: html, text, full: html, text
added another suggested change from steve for the UMass 5C page and made the fixes. Redmine# 225, note# 53
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.release2.ra
- lines changed 11, context: html, text, full: html, text
testing bigbed for hg19, gencode combine search results GM12878IngelCytosol
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.patch.ra
- lines changed 4562, context: html, text, full: html, text
removed all rep=1 and it's variants, replaced with .patch.ra's
- src/hg/makeDb/trackDb/human/iscaComposite.html
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 9, context: html, text, full: html, text
changed around some naming to merge Agilent CGH with the new Affy CytoScan array track
- lines changed 10, context: html, text, full: html, text
turned off some isca tracks by default and changed viewLimit for the bedGraph subtracks
- src/hg/makeDb/trackDb/merckPolyA.html
- lines changed 1, context: html, text, full: html, text
One minor grammar correction.
- lines changed 391, context: html, text, full: html, text
Major HTML cleanup, as this page was obviously generated with MS Word's dreadful Save As.. > HTML.
- src/hg/makeDb/trackDb/mouse/agilentCgh.html
- lines changed 95, context: html, text, full: html, text
changed around some naming to merge Agilent CGH with the new Affy CytoScan array track
- src/hg/makeDb/trackDb/mouse/genotypeArrays.html
- lines changed 95, context: html, text, full: html, text
changed around some naming to merge Agilent CGH with the new Affy CytoScan array track
- src/hg/makeDb/trackDb/mouse/mm10/trackDb.chainNet.ra
- lines changed 258, context: html, text, full: html, text
adding placental chain net composite
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuHistone.ra
- lines changed 115, context: html, text, full: html, text
Corrected cell registration with treatment for G1E-ER4+E2 to be G1E-ER4. Redmine #7418.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
- lines changed 109, context: html, text, full: html, text
Removed files referenced for submission 2972 that were never replaced.
- lines changed 131, context: html, text, full: html, text
Corrected cell registration with treatment for G1E-ER4+E2 to be G1E-ER4. Redmine #7418.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwRnaSeq.ra
- lines changed 268, context: html, text, full: html, text
Performed a little renaming in anticipation of data being replaced.
- lines changed 259, context: html, text, full: html, text
Updated object names for Plus and Minus Raw Signal to use the appropriate abbreviations.
- lines changed 388, context: html, text, full: html, text
Replaced Signal data on recomendation from lab. Redmine #4469.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeCaltechHist.ra
- lines changed 65, context: html, text, full: html, text
Copied Venkat's metadata changes to beta and public (redmine #6581)
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeCaltechTfbs.ra
- lines changed 125, context: html, text, full: html, text
Copied Venkat's metadata changes to beta and public (redmine #6581)
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeLicrHistone.ra
- lines changed 12463, context: html, text, full: html, text
Staging LICR Histone (Release 2) on beta (redmine #5393)
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeLicrTfbs.ra
- lines changed 5305, context: html, text, full: html, text
staging LICR TFBS (Release 2) on beta, redmine# 5394
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodePsuHistone.ra
- lines changed 341, context: html, text, full: html, text
Staging PSU Histone (Release 1) on beta (redmine #111)
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeSydhHist.ra
- lines changed 91, context: html, text, full: html, text
Copied Venkat's metadata changes to beta and public (redmine #6581)
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeCaltechHist.ra
- lines changed 65, context: html, text, full: html, text
Copied Venkat's metadata changes to beta and public (redmine #6581)
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeCaltechTfbs.ra
- lines changed 125, context: html, text, full: html, text
Copied Venkat's metadata changes to beta and public (redmine #6581)
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeSydhHist.ra
- lines changed 91, context: html, text, full: html, text
Copied Venkat's metadata changes to beta and public (redmine #6581)
- src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
- lines changed 2, context: html, text, full: html, text
Corrected cell registration with treatment for G1E-ER4+E2 to be G1E-ER4. Redmine #7418.
- lines changed 2, context: html, text, full: html, text
Staging LICR Histone (Release 2) on beta (redmine #5393)
- lines changed 2, context: html, text, full: html, text
staging LICR TFBS (Release 2) on beta, redmine# 5394
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release2.html
- lines changed 6, context: html, text, full: html, text
fixed Jacob's point 3, 6, 7
- lines changed 1, context: html, text, full: html, text
fixed Jacob't point 4, #5393
- lines changed 75, context: html, text, full: html, text
fix those old references not using the same format as those generated by qaAddTrackReferences
- lines changed 12, context: html, text, full: html, text
fixed points raised by Katrina in #6476 note 54 which are similar to these two tracks and by Jacob see #5393, note 130
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.release2.ra
- lines changed 2, context: html, text, full: html, text
clean up description, references, config
- lines changed 2, context: html, text, full: html, text
fixed points raised by Katrina in #6476 note 54 which are similar to these two tracks and by Jacob see #5393, note 130
- lines changed 1, context: html, text, full: html, text
correcting matrix cheked box see Jacob's point 2 note 131 in #5393
- lines changed 14, context: html, text, full: html, text
fix long labels according to Katrina's suggestions in LicrRnaSeq where the length fit in with the limitation of 86 chr maximum
- lines changed 15, context: html, text, full: html, text
change immortalized to immortal cells
- lines changed 125, context: html, text, full: html, text
fix long label to <=80, see Steve's note 140 #5393
- lines changed 119, context: html, text, full: html, text
fixt longLabel changed 8wks to 8w
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.release2.html
- lines changed 2, context: html, text, full: html, text
fixing Katrina's points 5, 15 in notes 78, ticket #6476
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.release2.ra
- lines changed 1, context: html, text, full: html, text
change viewLimit from 0:50 to 2:50 to see whether this could eliminate the problem in dense mode, see Katrina's point 12 in note 72 of ticket #6476
- lines changed 1, context: html, text, full: html, text
change viewLimit back to 0:50 as the previous did not have any effects
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.release2.html
- lines changed 91, context: html, text, full: html, text
fixed points raised by Katrina in #6476 note 54 which are similar to these two tracks and by Jacob see #5393, note 130
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.release2.ra
- lines changed 2, context: html, text, full: html, text
fixed points raised by Katrina in #6476 note 54 which are similar to these two tracks and by Jacob see #5393, note 130
- lines changed 1, context: html, text, full: html, text
correcting matrix cheked box see Jacob's point 2 note 131 in #5393
- lines changed 98, context: html, text, full: html, text
fixed long labels according to Katrina's point 1, note 54, #6476 for LicrRnaSeq, which are similar
- lines changed 5, context: html, text, full: html, text
fixed longLabel to <=80 chr long
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.ra
- lines changed 24, context: html, text, full: html, text
Corrected cell registration with treatment for G1E-ER4+E2 to be G1E-ER4. Redmine #7418.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.patch.ra
- lines changed 499, context: html, text, full: html, text
Corrected cell registration with treatment for G1E-ER4+E2 to be G1E-ER4. Redmine #7418.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.release2.ra
- lines changed 7, context: html, text, full: html, text
Fixed tags to be alphanumeric since only numeric tags break javascript. Redmine #4468.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwRnaSeq.ra
- lines changed 46, context: html, text, full: html, text
Performed a little renaming in anticipation of data being replaced.
- lines changed 108, context: html, text, full: html, text
Updated object names for Plus and Minus Raw Signal to use the appropriate abbreviations.
- lines changed 429, context: html, text, full: html, text
Replaced Signal data on recomendation from lab. Redmine #4469.
- src/hg/makeDb/trackDb/mouse/trackDb.ra
- lines changed 5, context: html, text, full: html, text
changed around some naming to merge Agilent CGH with the new Affy CytoScan array track
- src/hg/makeDb/trackDb/pubs.html
- lines changed 3, context: html, text, full: html, text
creating a authorYear label on the fly for pubBlat tracks
- lines changed 17, context: html, text, full: html, text
make subtrack config work following tims suggestions, try to make psl track description clearer
- src/hg/makeDb/trackDb/rat/agilentCgh.html
- lines changed 95, context: html, text, full: html, text
changed around some naming to merge Agilent CGH with the new Affy CytoScan array track
- src/hg/makeDb/trackDb/rat/genotypeArrays.html
- lines changed 95, context: html, text, full: html, text
changed around some naming to merge Agilent CGH with the new Affy CytoScan array track
- src/hg/makeDb/trackDb/rat/trackDb.ra
- lines changed 5, context: html, text, full: html, text
changed around some naming to merge Agilent CGH with the new Affy CytoScan array track
- src/hg/makeDb/trackDb/rhesus/rheMac3/ctgPos2.html
- lines changed 16, context: html, text, full: html, text
Scaffold track (ctgPos2) of rhemac3
- src/hg/makeDb/trackDb/tagTypes.tab
- lines changed 1, context: html, text, full: html, text
make individual sequences for publications track clickable, show alignments, correct mouseOvers // Also changs text that is shown for PDF Output in hgTracks (see email with Ann/Donna/Brian)
- lines changed 3, context: html, text, full: html, text
changing track configs according to tims instructions
- src/hg/makeDb/trackDb/trackDb.ra
- lines changed 15, context: html, text, full: html, text
make individual sequences for publications track clickable, show alignments, correct mouseOvers // Also changs text that is shown for PDF Output in hgTracks (see email with Ann/Donna/Brian)
- lines changed 36, context: html, text, full: html, text
make subtrack config work following tims suggestions, try to make psl track description clearer
- src/hg/utils/automation/unigene.csh
- lines changed 2, context: html, text, full: html, text
updating this to go to me instead of brooke
- src/inc/annoColumn.h
- lines changed 26, context: html, text, full: html, text
Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter,
annoRow, annoStreamer, annoGrator, and annoFormatter define the core
interfaces for passing data and configuration to and from components.
The annoGrator superclass can join annoRows on position and pass
forward all rows of secondary source. The annoGratorQuery module
orchestrates the passing of annoRows between the primary source,
annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and
annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join
columns of two database tables such as hg19's pgNA12878 and knownGene
into tab-separated output.
- src/inc/annoFilter.h
- lines changed 65, context: html, text, full: html, text
Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter,
annoRow, annoStreamer, annoGrator, and annoFormatter define the core
interfaces for passing data and configuration to and from components.
The annoGrator superclass can join annoRows on position and pass
forward all rows of secondary source. The annoGratorQuery module
orchestrates the passing of annoRows between the primary source,
annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and
annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join
columns of two database tables such as hg19's pgNA12878 and knownGene
into tab-separated output.
- src/inc/annoFormatTab.h
- lines changed 11, context: html, text, full: html, text
Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter,
annoRow, annoStreamer, annoGrator, and annoFormatter define the core
interfaces for passing data and configuration to and from components.
The annoGrator superclass can join annoRows on position and pass
forward all rows of secondary source. The annoGratorQuery module
orchestrates the passing of annoRows between the primary source,
annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and
annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join
columns of two database tables such as hg19's pgNA12878 and knownGene
into tab-separated output.
- src/inc/annoFormatter.h
- lines changed 60, context: html, text, full: html, text
Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter,
annoRow, annoStreamer, annoGrator, and annoFormatter define the core
interfaces for passing data and configuration to and from components.
The annoGrator superclass can join annoRows on position and pass
forward all rows of secondary source. The annoGratorQuery module
orchestrates the passing of annoRows between the primary source,
annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and
annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join
columns of two database tables such as hg19's pgNA12878 and knownGene
into tab-separated output.
- src/inc/annoGrator.h
- lines changed 52, context: html, text, full: html, text
Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter,
annoRow, annoStreamer, annoGrator, and annoFormatter define the core
interfaces for passing data and configuration to and from components.
The annoGrator superclass can join annoRows on position and pass
forward all rows of secondary source. The annoGratorQuery module
orchestrates the passing of annoRows between the primary source,
annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and
annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join
columns of two database tables such as hg19's pgNA12878 and knownGene
into tab-separated output.
- src/inc/annoGratorQuery.h
- lines changed 44, context: html, text, full: html, text
Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter,
annoRow, annoStreamer, annoGrator, and annoFormatter define the core
interfaces for passing data and configuration to and from components.
The annoGrator superclass can join annoRows on position and pass
forward all rows of secondary source. The annoGratorQuery module
orchestrates the passing of annoRows between the primary source,
annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and
annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join
columns of two database tables such as hg19's pgNA12878 and knownGene
into tab-separated output.
- src/inc/annoRow.h
- lines changed 36, context: html, text, full: html, text
Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter,
annoRow, annoStreamer, annoGrator, and annoFormatter define the core
interfaces for passing data and configuration to and from components.
The annoGrator superclass can join annoRows on position and pass
forward all rows of secondary source. The annoGratorQuery module
orchestrates the passing of annoRows between the primary source,
annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and
annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join
columns of two database tables such as hg19's pgNA12878 and knownGene
into tab-separated output.
- src/inc/annoStreamer.h
- lines changed 88, context: html, text, full: html, text
Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter,
annoRow, annoStreamer, annoGrator, and annoFormatter define the core
interfaces for passing data and configuration to and from components.
The annoGrator superclass can join annoRows on position and pass
forward all rows of secondary source. The annoGratorQuery module
orchestrates the passing of annoRows between the primary source,
annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and
annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join
columns of two database tables such as hg19's pgNA12878 and knownGene
into tab-separated output.
- src/inc/options.h
- lines changed 3, context: html, text, full: html, text
Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter,
annoRow, annoStreamer, annoGrator, and annoFormatter define the core
interfaces for passing data and configuration to and from components.
The annoGrator superclass can join annoRows on position and pass
forward all rows of secondary source. The annoGratorQuery module
orchestrates the passing of annoRows between the primary source,
annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and
annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join
columns of two database tables such as hg19's pgNA12878 and knownGene
into tab-separated output.
- src/lib/annoColumn.c
- lines changed 41, context: html, text, full: html, text
Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter,
annoRow, annoStreamer, annoGrator, and annoFormatter define the core
interfaces for passing data and configuration to and from components.
The annoGrator superclass can join annoRows on position and pass
forward all rows of secondary source. The annoGratorQuery module
orchestrates the passing of annoRows between the primary source,
annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and
annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join
columns of two database tables such as hg19's pgNA12878 and knownGene
into tab-separated output.
- src/lib/annoFilter.c
- lines changed 184, context: html, text, full: html, text
Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter,
annoRow, annoStreamer, annoGrator, and annoFormatter define the core
interfaces for passing data and configuration to and from components.
The annoGrator superclass can join annoRows on position and pass
forward all rows of secondary source. The annoGratorQuery module
orchestrates the passing of annoRows between the primary source,
annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and
annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join
columns of two database tables such as hg19's pgNA12878 and knownGene
into tab-separated output.
- src/lib/annoFormatTab.c
- lines changed 149, context: html, text, full: html, text
Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter,
annoRow, annoStreamer, annoGrator, and annoFormatter define the core
interfaces for passing data and configuration to and from components.
The annoGrator superclass can join annoRows on position and pass
forward all rows of secondary source. The annoGratorQuery module
orchestrates the passing of annoRows between the primary source,
annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and
annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join
columns of two database tables such as hg19's pgNA12878 and knownGene
into tab-separated output.
- src/lib/annoFormatter.c
- lines changed 119, context: html, text, full: html, text
Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter,
annoRow, annoStreamer, annoGrator, and annoFormatter define the core
interfaces for passing data and configuration to and from components.
The annoGrator superclass can join annoRows on position and pass
forward all rows of secondary source. The annoGratorQuery module
orchestrates the passing of annoRows between the primary source,
annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and
annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join
columns of two database tables such as hg19's pgNA12878 and knownGene
into tab-separated output.
- src/lib/annoGrator.c
- lines changed 194, context: html, text, full: html, text
Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter,
annoRow, annoStreamer, annoGrator, and annoFormatter define the core
interfaces for passing data and configuration to and from components.
The annoGrator superclass can join annoRows on position and pass
forward all rows of secondary source. The annoGratorQuery module
orchestrates the passing of annoRows between the primary source,
annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and
annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join
columns of two database tables such as hg19's pgNA12878 and knownGene
into tab-separated output.
- src/lib/annoGratorQuery.c
- lines changed 161, context: html, text, full: html, text
Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter,
annoRow, annoStreamer, annoGrator, and annoFormatter define the core
interfaces for passing data and configuration to and from components.
The annoGrator superclass can join annoRows on position and pass
forward all rows of secondary source. The annoGratorQuery module
orchestrates the passing of annoRows between the primary source,
annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and
annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join
columns of two database tables such as hg19's pgNA12878 and knownGene
into tab-separated output.
- src/lib/annoRow.c
- lines changed 57, context: html, text, full: html, text
Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter,
annoRow, annoStreamer, annoGrator, and annoFormatter define the core
interfaces for passing data and configuration to and from components.
The annoGrator superclass can join annoRows on position and pass
forward all rows of secondary source. The annoGratorQuery module
orchestrates the passing of annoRows between the primary source,
annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and
annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join
columns of two database tables such as hg19's pgNA12878 and knownGene
into tab-separated output.
- src/lib/annoStreamer.c
- lines changed 96, context: html, text, full: html, text
Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter,
annoRow, annoStreamer, annoGrator, and annoFormatter define the core
interfaces for passing data and configuration to and from components.
The annoGrator superclass can join annoRows on position and pass
forward all rows of secondary source. The annoGratorQuery module
orchestrates the passing of annoRows between the primary source,
annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and
annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join
columns of two database tables such as hg19's pgNA12878 and knownGene
into tab-separated output.
- src/lib/cheapcgi.c
- lines changed 3, context: html, text, full: html, text
cleanup message in cgiBadVar (from code review with Jim)
- src/lib/makefile
- lines changed 3, context: html, text, full: html, text
Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter,
annoRow, annoStreamer, annoGrator, and annoFormatter define the core
interfaces for passing data and configuration to and from components.
The annoGrator superclass can join annoRows on position and pass
forward all rows of secondary source. The annoGratorQuery module
orchestrates the passing of annoRows between the primary source,
annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and
annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join
columns of two database tables such as hg19's pgNA12878 and knownGene
into tab-separated output.
- src/lib/options.c
- lines changed 3, context: html, text, full: html, text
Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch. Superclasses annoColumn, annoFilter,
annoRow, annoStreamer, annoGrator, and annoFormatter define the core
interfaces for passing data and configuration to and from components.
The annoGrator superclass can join annoRows on position and pass
forward all rows of secondary source. The annoGratorQuery module
orchestrates the passing of annoRows between the primary source,
annoGrator(s) and annoFormatter(s). The subclasses annoStreamDb and
annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join
columns of two database tables such as hg19's pgNA12878 and knownGene
into tab-separated output.
- src/lib/pipeline.c
- lines changed 227, context: html, text, full: html, text
fixed timing problem that caused intermitent errors setting up process group by create a group leader process
- lines changed 230, context: html, text, full: html, text
Revert "fixed timing problem that caused intermitent errors setting up process group by create a group leader process"
This reverts commit c7424a546c4a83220fde16217b502bea2e4daff7.
braney says, "we decided to do this commit after the v264 build"
- src/lib/tests/expected/pipelineExecError.err
- lines changed 2, context: html, text, full: html, text
fixed timing problem that caused intermitent errors setting up process group by create a group leader process
- lines changed 2, context: html, text, full: html, text
Revert "fixed timing problem that caused intermitent errors setting up process group by create a group leader process"
This reverts commit c7424a546c4a83220fde16217b502bea2e4daff7.
braney says, "we decided to do this commit after the v264 build"
- src/lib/tests/expected/pipelineExecError.parent.err
- lines changed 2, context: html, text, full: html, text
fixed timing problem that caused intermitent errors setting up process group by create a group leader process
- lines changed 2, context: html, text, full: html, text
Revert "fixed timing problem that caused intermitent errors setting up process group by create a group leader process"
This reverts commit c7424a546c4a83220fde16217b502bea2e4daff7.
braney says, "we decided to do this commit after the v264 build"
- src/lib/tests/makefile
- lines changed 9, context: html, text, full: html, text
fixed timing problem that caused intermitent errors setting up process group by create a group leader process
- lines changed 9, context: html, text, full: html, text
Revert "fixed timing problem that caused intermitent errors setting up process group by create a group leader process"
This reverts commit c7424a546c4a83220fde16217b502bea2e4daff7.
braney says, "we decided to do this commit after the v264 build"
- src/utils/newProg/newProg.c
- lines changed 2, context: html, text, full: html, text
Adding a couple of comments, one of them to the generated code.
- src/utils/qa/bigPush.csh
- lines changed 20, context: html, text, full: html, text
Added sudo -v to the main loop, which will keep the sudo permission from timing out as long as no single table exceeds that time. Changed the usage message slightly. Changed hgwbeta to the mysqlbeta variable found in qaConfig.csh. Got rid of the removal of files at the end, since the files contain the mypush output. Redmine #4010.
- src/utils/qa/makeUniProtFile.csh
- lines changed 1, context: html, text, full: html, text
Fixed a typo I should have caught in code review redmine 7287
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed: 47128
- files changed: 311