All File Changes
v245_base to v246_preview (2011-01-04 to 2010-01-11) v246
- src/hg/encode/DAFs/2.0/haibCnv.daf
- lines changed 9, context: html, text, full: html, text
working with lab to specify what they are submitting
- lines changed 4, context: html, text, full: html, text
Updating the DAF's in the development process
- src/hg/encode/DAFs/2.0/haibRnaSeq.daf
- lines changed 14, context: html, text, full: html, text
working with lab to specify what they are submitting
- src/hg/encode/DAFs/2.0/sunyRipSeq.daf
- lines changed 3, context: html, text, full: html, text
Updating the DAF's in the development process
- src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
- lines changed 2, context: html, text, full: html, text
Added code in encodeDownlaodsPage to not show dccNotes and added description in cv.ra as type of term.
- lines changed 3, context: html, text, full: html, text
Hide mdb var 'dccInternalNotes' from '...', index.html and files.txt
- lines changed 2, context: html, text, full: html, text
files.txt file should only be made when making 'index.html'. Don't bother when making a test html.
- src/hg/encode/encodeValidate/doEncodeValidate.pl
- lines changed 16, context: html, text, full: html, text
First pieces of code to deal with new variable obtainedBy.
- lines changed 2, context: html, text, full: html, text
Added comments trying to figure out how subGroups is printed out.
- src/hg/encode/metaCheck/metaCheck.c
- lines changed 12, context: html, text, full: html, text
add release tag specification, don't assume tableName in object
- src/hg/hgGateway/hgGateway.c
- lines changed 11, context: html, text, full: html, text
Adding 'import tracks' button to hgGateway.
- lines changed 5, context: html, text, full: html, text
Updating import button to work with changes in main branch.
- lines changed 2, context: html, text, full: html, text
Commenting out import button in preparation for merging with main tree.
- lines changed 2, context: html, text, full: html, text
Adding back in import button
- src/hg/hgHubConnect/hgHubConnect.c
- lines changed 101, context: html, text, full: html, text
Checking in a skeletal hub connection page.
- lines changed 56, context: html, text, full: html, text
Adding genome and assembly to hgHubConnect, and a submit button. Adding dbList to hubConnect table.
- lines changed 13, context: html, text, full: html, text
Starting to make hgHubConnect talk with hgTracks and hgTrackUi. Right now the tracks appear on the track list, but are not displaying properly.
- lines changed 1, context: html, text, full: html, text
Fixing it's/its grammar mistake.
- src/hg/hgHubConnect/makefile
- lines changed 17, context: html, text, full: html, text
Checking in a skeletal hub connection page.
- src/hg/hgTables/filterFields.c
- lines changed 4, context: html, text, full: html, text
Handle default behavior outside of cgiMakeCheckboxGroup.
- src/hg/hgTrackUi/hgTrackUi.c
- lines changed 24, context: html, text, full: html, text
Starting to make hgHubConnect talk with hgTracks and hgTrackUi. Right now the tracks appear on the track list, but are not displaying properly.
- lines changed 1, context: html, text, full: html, text
Starting to get trackHub stuff to work with composite tracks. (Using UNC Faire as a test set on hg19.)
- lines changed 135, context: html, text, full: html, text
Track #1864 (SNPs 132 (dbSNP)):
1. Added new-in-snp132 columns (exceptions, submitters, alleles) to
hgc. Wrapped an html table around several parts of the details page
so that they could be made expandable/collapsible using utils.js's
setTableRowVisibility. Also wrapped some SNP attributes in an html
table for readability.
2. Changed attribute-filter cart variables in hg/lib/snp125Ui.c,
hgTrackUi.c and hgTracks/variation.c to use one checkbox group per
attribute, with the cart variable based on the track name, instead
of one checkbox per attribute value with hardcoded cart var name
that applies to all SNP tracks. Refactored to remove a lot of
redundant extern global variables. Still need to make other SNP
control cart vars based on track name.
- src/hg/hgTracks/bigBedTrack.c
- lines changed 6, context: html, text, full: html, text
Redoing dataHub using new trackHub library routines. Still pretty embryonic, but once again is displaying a couple of tracks for me, this time ones that are genuinely remote. Code is activated by having a 'tracksHub' variable in the cart, which currently is only possible by hacking with cartDump.
- lines changed 2, context: html, text, full: html, text
Fixing bug where bogus NULL would be returned for bbiFileName.
- lines changed 1, context: html, text, full: html, text
Removing some debugging statements.
- src/hg/hgTracks/bigWigTrack.c
- lines changed 3, context: html, text, full: html, text
Redoing dataHub using new trackHub library routines. Still pretty embryonic, but once again is displaying a couple of tracks for me, this time ones that are genuinely remote. Code is activated by having a 'tracksHub' variable in the cart, which currently is only possible by hacking with cartDump.
- src/hg/hgTracks/cds.h
- src/hg/hgTracks/hgTracks.c
- lines changed 23, context: html, text, full: html, text
Adding a bunch of debugging stuff.
- lines changed 12, context: html, text, full: html, text
Making dataHubs work with oneWig.ra and reducing the debugging.
- lines changed 32, context: html, text, full: html, text
Redoing dataHub using new trackHub library routines. Still pretty embryonic, but once again is displaying a couple of tracks for me, this time ones that are genuinely remote. Code is activated by having a 'tracksHub' variable in the cart, which currently is only possible by hacking with cartDump.
- lines changed 44, context: html, text, full: html, text
Making hubs appear in group list.
- lines changed 27, context: html, text, full: html, text
Starting to make hgHubConnect talk with hgTracks and hgTrackUi. Right now the tracks appear on the track list, but are not displaying properly.
- lines changed 4, context: html, text, full: html, text
Removing some debugging statements.
- lines changed 11, context: html, text, full: html, text
Removing debugging statements.
- lines changed 3, context: html, text, full: html, text
Starting to get trackHub stuff to work with composite tracks. (Using UNC Faire as a test set on hg19.)
- lines changed 18, context: html, text, full: html, text
Fixing subtrack sorting problem in composite tracks in track hub.
- src/hg/hgTracks/hgTracks.h
- lines changed 2, context: html, text, full: html, text
Redoing dataHub using new trackHub library routines. Still pretty embryonic, but once again is displaying a couple of tracks for me, this time ones that are genuinely remote. Code is activated by having a 'tracksHub' variable in the cart, which currently is only possible by hacking with cartDump.
- lines changed 1, context: html, text, full: html, text
Starting to make hgHubConnect talk with hgTracks and hgTrackUi. Right now the tracks appear on the track list, but are not displaying properly.
- lines changed 1, context: html, text, full: html, text
Fixing redmine issue #2151 where multiWig tracks had to be visibility full in trackDb.ra to _ever_ be seen properly.
- src/hg/hgTracks/multiWig.c
- lines changed 10, context: html, text, full: html, text
Making it so system handles missing aggregate tag in multiWig trackDb stanzas.
- lines changed 1, context: html, text, full: html, text
Fixing redmine issue #2151 where multiWig tracks had to be visibility full in trackDb.ra to _ever_ be seen properly.
- lines changed 0, context: html, text, full: html, text
Removing debugging statements.
- src/hg/hgTracks/searchTracks.c
- lines changed 2, context: html, text, full: html, text
Fixed bug an multiple mdb term query where early round has no results, so later hits are mistakenly seen as valid.
- src/hg/hgTracks/simpleTracks.c
- lines changed 15, context: html, text, full: html, text
Fixing redmine issue #2151 where multiWig tracks had to be visibility full in trackDb.ra to _ever_ be seen properly.
- lines changed 2, context: html, text, full: html, text
Fixing subtrack sorting problem in composite tracks in track hub.
- src/hg/hgTracks/variation.c
- lines changed 131, context: html, text, full: html, text
Track #1864 (SNPs 132 (dbSNP)):
1. Added new-in-snp132 columns (exceptions, submitters, alleles) to
hgc. Wrapped an html table around several parts of the details page
so that they could be made expandable/collapsible using utils.js's
setTableRowVisibility. Also wrapped some SNP attributes in an html
table for readability.
2. Changed attribute-filter cart variables in hg/lib/snp125Ui.c,
hgTrackUi.c and hgTracks/variation.c to use one checkbox group per
attribute, with the cart variable based on the track name, instead
of one checkbox per attribute value with hardcoded cart var name
that applies to all SNP tracks. Refactored to remove a lot of
redundant extern global variables. Still need to make other SNP
control cart vars based on track name.
- src/hg/hgc/hgc.c
- lines changed 0, context: html, text, full: html, text
added innocuous space to get user.name changed in git blame from b0b back to kuhn
- lines changed 17, context: html, text, full: html, text
incorrect initialization of dateReference string in ensembl links
- lines changed 267, context: html, text, full: html, text
Track #1864 (SNPs 132 (dbSNP)):
1. Added new-in-snp132 columns (exceptions, submitters, alleles) to
hgc. Wrapped an html table around several parts of the details page
so that they could be made expandable/collapsible using utils.js's
setTableRowVisibility. Also wrapped some SNP attributes in an html
table for readability.
2. Changed attribute-filter cart variables in hg/lib/snp125Ui.c,
hgTrackUi.c and hgTracks/variation.c to use one checkbox group per
attribute, with the cart variable based on the track name, instead
of one checkbox per attribute value with hardcoded cart var name
that applies to all SNP tracks. Refactored to remove a lot of
redundant extern global variables. Still need to make other SNP
control cart vars based on track name.
- src/hg/htdocs/ENCODE/index.html
- lines changed 34, context: html, text, full: html, text
announcing most recent 3 track releases, collapsing last announcement, adding last announcement to archives, removing oldest item from news page
- src/hg/htdocs/ENCODE/newsarch.html
- lines changed 25, context: html, text, full: html, text
announcing most recent 3 track releases, collapsing last announcement, adding last announcement to archives, removing oldest item from news page
- src/hg/htdocs/goldenPath/help/hg18ToHg19LiftOver.html
- lines changed 10, context: html, text, full: html, text
expanded warning a bit. beware of large regions
- src/hg/htdocs/goldenPath/help/hgTracksHelp.html
- lines changed 22, context: html, text, full: html, text
Added section on right-click navigation.
- lines changed 21, context: html, text, full: html, text
More right-click nav mods -- added links to a few more sections, incorporated Brooke's comments.
- lines changed 2, context: html, text, full: html, text
Clarified statement about PDF/PS option.
- src/hg/htdocs/goldenPath/pubs.html
- lines changed 6, context: html, text, full: html, text
Added Rachel's GB tutorial.
- src/hg/htdocs/training.html
- lines changed 4, context: html, text, full: html, text
Replaced Fishing... tutorial with updated Nature Education GB tutorial.
- lines changed 2, context: html, text, full: html, text
Readded Rachel's Fishing... doc -- she and Mark decided that both need to be on this page for now until she can put the Nature Education doc into PDF format.
- src/hg/inc/cart.h
- lines changed 3, context: html, text, full: html, text
Keep the multShadow vars in the cart so that we can distinguish alist that has been set to empty from a list that has never been
set. cartListVarExists is the external interface.
- src/hg/inc/hdb.h
- lines changed 4, context: html, text, full: html, text
Adding trackDbPolishAfterLinkup routine that bundles together a number of other calls, and exposing it for use by data hub trackDb list makers.
- src/hg/inc/hubConnect.h
- lines changed 15, context: html, text, full: html, text
Adding hubConnect module to help manage list of hubs that are available.
- lines changed 2, context: html, text, full: html, text
Making hubConnect.as and hubConnect.sql. This is _not_ done by autoSql since we just want field-by-field access of this in the code.
- lines changed 3, context: html, text, full: html, text
Adding genome and assembly to hgHubConnect, and a submit button. Adding dbList to hubConnect table.
- lines changed 48, context: html, text, full: html, text
Starting to make hgHubConnect talk with hgTracks and hgTrackUi. Right now the tracks appear on the track list, but are not displaying properly.
- src/hg/inc/hui.h
- lines changed 4, context: html, text, full: html, text
Starting to make hgHubConnect talk with hgTracks and hgTrackUi. Right now the tracks appear on the track list, but are not displaying properly.
- src/hg/inc/peptideMapping.h
- lines changed 1, context: html, text, full: html, text
Updated the peptide mapping schema to change the data type of precursorMz froma float to a string. Why did I do such a bizarre and unexpected thing?
Because it turns out that when data is loaded into mysql, the precursorMz field
(and all other floats) are rounded to three digits after the decimal point. This is often not enough to distinguish between precursorMz values that we've seen in practice so far, where the first differences may be five digits after the decimal point. The precursorMz field is used to identify the spectra, not as a float on which any further computation is done. So, by making its data type a string, we've ensured that the significant distinctions between spectra will not be rounded away, and that all spectra continue to be identifiable via precursorMz.
- src/hg/inc/snp125Ui.h
- lines changed 80, context: html, text, full: html, text
Track #1864 (SNPs 132 (dbSNP)):
1. Added new-in-snp132 columns (exceptions, submitters, alleles) to
hgc. Wrapped an html table around several parts of the details page
so that they could be made expandable/collapsible using utils.js's
setTableRowVisibility. Also wrapped some SNP attributes in an html
table for readability.
2. Changed attribute-filter cart variables in hg/lib/snp125Ui.c,
hgTrackUi.c and hgTracks/variation.c to use one checkbox group per
attribute, with the cart variable based on the track name, instead
of one checkbox per attribute value with hardcoded cart var name
that applies to all SNP tracks. Refactored to remove a lot of
redundant extern global variables. Still need to make other SNP
control cart vars based on track name.
- src/hg/inc/trackDb.h
- lines changed 3, context: html, text, full: html, text
Adding trackDbFromOpenRa entry point.
- lines changed 10, context: html, text, full: html, text
Fixing conflicts from merging with master.
- lines changed 4, context: html, text, full: html, text
Fixing subtrack sorting problem in composite tracks in track hub.
- src/hg/inc/trackHub.h
- lines changed 76, context: html, text, full: html, text
Moving many routines from hubCheck to trackHub.c library file.
- lines changed 6, context: html, text, full: html, text
Adding trackHubAddNamePrefix to help give hubs their own name space within cart.
- lines changed 7, context: html, text, full: html, text
Making hubs appear in group list.
- lines changed 3, context: html, text, full: html, text
Starting to make hgHubConnect talk with hgTracks and hgTrackUi. Right now the tracks appear on the track list, but are not displaying properly.
- src/hg/js/hgTracks.js
- lines changed 12, context: html, text, full: html, text
make sure the link contains chrom info for cmd == followLink; fixes redmine 1333#note-56
- lines changed 4, context: html, text, full: html, text
Fixed redmine 1333.15. Subtrack specific vis should be eliminated when rightClicking to hide.
- lines changed 1, context: html, text, full: html, text
keep class of group selects accurate (see redmine 2186#note-1)
- lines changed 24, context: html, text, full: html, text
Moved almost all functionality of toggleTrackGroupVisibility fromhgTracks.js into utils.js's setTableRowVisibility so hgc can use it too.
- src/hg/js/utils.js
- lines changed 34, context: html, text, full: html, text
Moved almost all functionality of toggleTrackGroupVisibility fromhgTracks.js into utils.js's setTableRowVisibility so hgc can use it too.
- src/hg/lib/cart.c
- lines changed 20, context: html, text, full: html, text
Keep the multShadow vars in the cart so that we can distinguish alist that has been set to empty from a list that has never been
set. cartListVarExists is the external interface.
- src/hg/lib/encode/peptideMapping.as
- lines changed 1, context: html, text, full: html, text
Updated the peptide mapping schema to change the data type of precursorMz froma float to a string. Why did I do such a bizarre and unexpected thing?
Because it turns out that when data is loaded into mysql, the precursorMz field
(and all other floats) are rounded to three digits after the decimal point. This is often not enough to distinguish between precursorMz values that we've seen in practice so far, where the first differences may be five digits after the decimal point. The precursorMz field is used to identify the spectra, not as a float on which any further computation is done. So, by making its data type a string, we've ensured that the significant distinctions between spectra will not be rounded away, and that all spectra continue to be identifiable via precursorMz.
- src/hg/lib/encode/peptideMapping.c
- lines changed 7, context: html, text, full: html, text
Updated the peptide mapping schema to change the data type of precursorMz froma float to a string. Why did I do such a bizarre and unexpected thing?
Because it turns out that when data is loaded into mysql, the precursorMz field
(and all other floats) are rounded to three digits after the decimal point. This is often not enough to distinguish between precursorMz values that we've seen in practice so far, where the first differences may be five digits after the decimal point. The precursorMz field is used to identify the spectra, not as a float on which any further computation is done. So, by making its data type a string, we've ensured that the significant distinctions between spectra will not be rounded away, and that all spectra continue to be identifiable via precursorMz.
- src/hg/lib/encode/peptideMapping.sql
- lines changed 3, context: html, text, full: html, text
Updated the peptide mapping schema to change the data type of precursorMz froma float to a string. Why did I do such a bizarre and unexpected thing?
Because it turns out that when data is loaded into mysql, the precursorMz field
(and all other floats) are rounded to three digits after the decimal point. This is often not enough to distinguish between precursorMz values that we've seen in practice so far, where the first differences may be five digits after the decimal point. The precursorMz field is used to identify the spectra, not as a float on which any further computation is done. So, by making its data type a string, we've ensured that the significant distinctions between spectra will not be rounded away, and that all spectra continue to be identifiable via precursorMz.
- src/hg/lib/fileUi.c
- lines changed 7, context: html, text, full: html, text
Support for supplemental materials directory in hgFileUi cgi.
- lines changed 4, context: html, text, full: html, text
Refinement of supplemental link. If supplemental is soft link as with Open Chrom, it was failing to appear.
- src/hg/lib/genomicSuperDups.as
- lines changed 1, context: html, text, full: html, text
Changed description for score field.
- src/hg/lib/hdb.c
- lines changed 2, context: html, text, full: html, text
Removing some ugly debugging statements.
- lines changed 16, context: html, text, full: html, text
Adding trackDbPolishAfterLinkup routine that bundles together a number of other calls, and exposing it for use by data hub trackDb list makers.
- lines changed 8, context: html, text, full: html, text
Fixing subtrack sorting problem in composite tracks in track hub.
- src/hg/lib/hubConnect.as
- lines changed 13, context: html, text, full: html, text
Making hubConnect.as and hubConnect.sql. This is _not_ done by autoSql since we just want field-by-field access of this in the code.
- lines changed 2, context: html, text, full: html, text
Adding genome and assembly to hgHubConnect, and a submit button. Adding dbList to hubConnect table.
- src/hg/lib/hubConnect.c
- lines changed 24, context: html, text, full: html, text
Adding hubConnect module to help manage list of hubs that are available.
- lines changed 2, context: html, text, full: html, text
Making hubConnect.as and hubConnect.sql. This is _not_ done by autoSql since we just want field-by-field access of this in the code.
- lines changed 125, context: html, text, full: html, text
Starting to make hgHubConnect talk with hgTracks and hgTrackUi. Right now the tracks appear on the track list, but are not displaying properly.
- lines changed 7, context: html, text, full: html, text
Making it so only hubs actually turned on are added.
- lines changed 1, context: html, text, full: html, text
Removing debugging statements.
- src/hg/lib/hubConnect.sql
- lines changed 20, context: html, text, full: html, text
Making hubConnect.as and hubConnect.sql. This is _not_ done by autoSql since we just want field-by-field access of this in the code.
- lines changed 2, context: html, text, full: html, text
Adding genome and assembly to hgHubConnect, and a submit button. Adding dbList to hubConnect table.
- src/hg/lib/hui.c
- lines changed 1, context: html, text, full: html, text
Hide mdb var 'dccInternalNotes' from '...', index.html and files.txt
- lines changed 1, context: html, text, full: html, text
Starting to make hgHubConnect talk with hgTracks and hgTrackUi. Right now the tracks appear on the track list, but are not displaying properly.
- src/hg/lib/makefile
- lines changed 1, context: html, text, full: html, text
Moving many routines from hubCheck to trackHub.c library file.
- lines changed 1, context: html, text, full: html, text
Adding hubConnect module to help manage list of hubs that are available.
- src/hg/lib/snp125Ui.c
- lines changed 258, context: html, text, full: html, text
Track #1864 (SNPs 132 (dbSNP)):
1. Added new-in-snp132 columns (exceptions, submitters, alleles) to
hgc. Wrapped an html table around several parts of the details page
so that they could be made expandable/collapsible using utils.js's
setTableRowVisibility. Also wrapped some SNP attributes in an html
table for readability.
2. Changed attribute-filter cart variables in hg/lib/snp125Ui.c,
hgTrackUi.c and hgTracks/variation.c to use one checkbox group per
attribute, with the cart variable based on the track name, instead
of one checkbox per attribute value with hardcoded cart var name
that applies to all SNP tracks. Refactored to remove a lot of
redundant extern global variables. Still need to make other SNP
control cart vars based on track name.
- src/hg/lib/trackDbCustom.c
- lines changed 1, context: html, text, full: html, text
Making trackDbFromRa() able to take a URL as well as a file name.
- lines changed 14, context: html, text, full: html, text
Adding trackDbFromOpenRa entry point.
- lines changed 62, context: html, text, full: html, text
Fixing subtrack sorting problem in composite tracks in track hub.
- src/hg/lib/trackHub.c
- lines changed 281, context: html, text, full: html, text
Moving many routines from hubCheck to trackHub.c library file.
- lines changed 57, context: html, text, full: html, text
Adding trackHubAddNamePrefix to help give hubs their own name space within cart.
- lines changed 10, context: html, text, full: html, text
Making hubs appear in group list.
- lines changed 17, context: html, text, full: html, text
Starting to make hgHubConnect talk with hgTracks and hgTrackUi. Right now the tracks appear on the track list, but are not displaying properly.
- lines changed 1, context: html, text, full: html, text
Fixing conflicts from merging with master.
- lines changed 4, context: html, text, full: html, text
Removing debugging statements.
- lines changed 4, context: html, text, full: html, text
Making trackHub tolerate 'on' and 'off' in a parent line in trackDb.ra file.
- src/hg/makeDb/doc/calJac3.txt
- lines changed 24, context: html, text, full: html, text
Create liftOver files to and from: calJac3 <-> hg18
- src/hg/makeDb/doc/danRer7.txt
- lines changed 58, context: html, text, full: html, text
adding downloads for 8-way business
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibMethylRrbs.release2.notes
- src/hg/makeDb/doc/hg18.txt
- lines changed 58, context: html, text, full: html, text
Create liftOver files to and from: calJac3 <-> hg18
- src/hg/makeDb/doc/hg19.txt
- lines changed 111, context: html, text, full: html, text
Lift consIndelsHgMmCanFam track to hg19
- lines changed 21, context: html, text, full: html, text
add polyA track with polyaDb subtrack
- lines changed 20, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): dbSNP re-dumped the allele frequency data;re-ran doDbSnp.pl to rebuild snp132, snp132ExceptionDesc, snp132Seq.
- lines changed 22, context: html, text, full: html, text
Lift polyaPredict track to hg19
- src/hg/makeDb/doc/mm9.txt
- lines changed 11, context: html, text, full: html, text
fix mm9.knownToVisiGene for RR without new ucsc genes update
- src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
- lines changed 10, context: html, text, full: html, text
Using the netFilter command to separate the syntenic from non-syntenic regions
- lines changed 11, context: html, text, full: html, text
FINALLY worked out how to make a syntenic chain with the desired behavior, andgenerated a set of Rfam hits that overlap the new syntenic blocks.
- lines changed 6, context: html, text, full: html, text
After learning the trick to netToBed usage at last - yay! - replaced use of netChainSubset, chainToPsl, etc. with one use of netToBed. The other way didn't yield a correct-looking bed file, anyway. The trick with netToBed is that unless you specify either the maxGap or minFill option, you end up with a bed file that contains entries for both fill and gap regions - which isn't what I want here.
- src/hg/makeDb/hgTrackDb/hgTrackDb.c
- lines changed 3, context: html, text, full: html, text
Making system work even when there are tabs rather than spaces in the type, shortLabel, or longLabel fields.
- lines changed 66, context: html, text, full: html, text
Fixing subtrack sorting problem in composite tracks in track hub.
- src/hg/makeDb/schema/all.joiner
- lines changed 2, context: html, text, full: html, text
Lift consIndelsHgMmCanFam track to hg19
- lines changed 13, context: html, text, full: html, text
joiner updates for new Agilent tracks
- src/hg/makeDb/trackDb/checkMetaDb
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 10, context: html, text, full: html, text
Added 2 strains B6D2F1/J and RIII, which are associated to 416B and 3134 Mouse cell lines, respectivley. Fixed the meta-data to accomadate with updated information.
- lines changed 32, context: html, text, full: html, text
Added two new antibodies for the Myers lab
- lines changed 2, context: html, text, full: html, text
Fixed the name of the validation documents for the new Myers lab antibodies
- lines changed 2, context: html, text, full: html, text
Once again, fixed the names of the validation documents for the new Myers lab antibodies. Hopefully this time, they're really fixed
- lines changed 22, context: html, text, full: html, text
White lab is actually an ARRA, not Mouse
- lines changed 8, context: html, text, full: html, text
Added typeofTerm for obtainedBy in CV.ra
- lines changed 8, context: html, text, full: html, text
Added code in encodeDownlaodsPage to not show dccNotes and added description in cv.ra as type of term.
- lines changed 2, context: html, text, full: html, text
Added Provional tag for 2 new strains.
- lines changed 7, context: html, text, full: html, text
Accepted two provisional changes: new typeOfTerm stanzas for dccInternalUse and obtainedBy
- lines changed 145, context: html, text, full: html, text
BTO URLs are displayed on the web browser with the suffix 'termId=BTO:<term>', but those URLs generally come off the wiki with the suffix 'termId=BTO%3A<term>'. For all this time, I've been replacing the %3A with a : for consistency. But I've just learned that the %3A is actually what's correct, according to the Uniform Resource Locator specification. So, I'm going to stop translating the new ones, and modified the old ones for consistency
- src/hg/makeDb/trackDb/cv/beta/cv.ra
- lines changed 82, context: html, text, full: html, text
Moving another stable bunch of changes from alpha to beta
- src/hg/makeDb/trackDb/human/altSeqComposite.html
- lines changed 7, context: html, text, full: html, text
adding specific references to the fetch alternate sequence link as well as fixing up the wording a bit
- src/hg/makeDb/trackDb/human/bamSLDenisova.html
- src/hg/makeDb/trackDb/human/eioJcviNAS.html
- lines changed 113, context: html, text, full: html, text
Moved HTML files matching the trackDb entries that were only in hg18 up a level... just like the trackDb entries were
- src/hg/makeDb/trackDb/human/hg18/eioJcviNAS.html
- lines changed 113, context: html, text, full: html, text
Moved HTML files matching the trackDb entries that were only in hg18 up a level... just like the trackDb entries were
- src/hg/makeDb/trackDb/human/hg18/laminB1.html
- lines changed 5, context: html, text, full: html, text
Moved HTML files matching the trackDb entries that were only in hg18 up a level... just like the trackDb entries were
- src/hg/makeDb/trackDb/human/hg18/laminB1Lads.html
- lines changed 5, context: html, text, full: html, text
Moved HTML files matching the trackDb entries that were only in hg18 up a level... just like the trackDb entries were
- src/hg/makeDb/trackDb/human/hg18/laminB1Super.html
- lines changed 144, context: html, text, full: html, text
Moved HTML files matching the trackDb entries that were only in hg18 up a level... just like the trackDb entries were
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwAffyExonArray.ra
- lines changed 2, context: html, text, full: html, text
Replaced dccNotes with dccInternalNotes.
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleChIPseq.ra
- lines changed 14, context: html, text, full: html, text
Replaced dccNotes with dccInternalNotes.
- src/hg/makeDb/trackDb/human/hg18/snpArray.html
- lines changed 190, context: html, text, full: html, text
Moved HTML files matching the trackDb entries that were only in hg18 up a level... just like the trackDb entries were
- src/hg/makeDb/trackDb/human/hg18/ucsfBrainMethyl.html
- lines changed 166, context: html, text, full: html, text
Moved HTML files matching the trackDb entries that were only in hg18 up a level... just like the trackDb entries were
- src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.new.html
- lines changed 108, context: html, text, full: html, text
made Release 4 html and added line in .new.ra to make the new html file.
- src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.new.ra
- lines changed 1, context: html, text, full: html, text
made Release 4 html and added line in .new.ra to make the new html file.
- src/hg/makeDb/trackDb/human/hg19/consIndelsHgMmCanFam.html
- lines changed 78, context: html, text, full: html, text
Lift consIndelsHgMmCanFam track to hg19
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
- lines changed 1, context: html, text, full: html, text
Added the two experiments, created metaData file, added to makefile
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBuOrchid.ra
- lines changed 35, context: html, text, full: html, text
Added the two experiments, created metaData file, added to makefile
- lines changed 2, context: html, text, full: html, text
changed dataResubmitted to dateResubmitted
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
- lines changed 1464, context: html, text, full: html, text
See redmine issue#35 note#17, mostly label changes and a few on/off settings
- lines changed 59, context: html, text, full: html, text
Adding new subtracks, changing labels, putting some data in the attic
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylSeq.ra
- lines changed 929, context: html, text, full: html, text
Used new DDF to update hg19 Methyl Seq data. Update meta-data to match when the submission was first accepted into our pipeline.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
- lines changed 1259, context: html, text, full: html, text
Added 7 Chip-seq submissions for the Jan freeze.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
- lines changed 20, context: html, text, full: html, text
Updated some fastqs and standardized labs.
- lines changed 104, context: html, text, full: html, text
Straighened out some V@s that should not have been
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
- lines changed 1, context: html, text, full: html, text
Updated some fastqs and standardized labs.
- lines changed 70, context: html, text, full: html, text
Straighened out some V@s that should not have been
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
- lines changed 379, context: html, text, full: html, text
Updated some fastqs and standardized labs.
- lines changed 193, context: html, text, full: html, text
Straighened out some V@s that should not have been
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 20, context: html, text, full: html, text
Lift consIndelsHgMmCanFam track to hg19
- lines changed 26, context: html, text, full: html, text
add polyA track with polyaDb subtrack
- lines changed 9, context: html, text, full: html, text
Lift polyaPredict track to hg19
- lines changed 3, context: html, text, full: html, text
making chain, net and psl off by default for GRC Patch Release track
- lines changed 4, context: html, text, full: html, text
ntSeqReads is NOT a lifted track
- lines changed 1, context: html, text, full: html, text
Sneaking in a commented out include for testing stuff vs. data hub tracks that do the same thing.
- lines changed 1, context: html, text, full: html, text
Changes shortLabel of the EIO/JCVI NAS track (pretty hard to remember that, isnt it?
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- lines changed 1, context: html, text, full: html, text
added the wgEncodeBuOrchid include
- lines changed 2, context: html, text, full: html, text
Adding new subtracks, changing labels, putting some data in the attic
- src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.html
- lines changed 2, context: html, text, full: html, text
Fixed a bunch of stuff in Open Chromatin docs and limited those 3 and Broad to max 900 pixels
- src/hg/makeDb/trackDb/human/hg19/wgEncodeBuOrchid.html
- lines changed 136, context: html, text, full: html, text
Created a new track for the incoming Orchid data
- lines changed 68, context: html, text, full: html, text
Changing defualt settings to lab request
- src/hg/makeDb/trackDb/human/hg19/wgEncodeBuOrchid.ra
- lines changed 49, context: html, text, full: html, text
Added the two experiments, created metaData file, added to makefile
- lines changed 9, context: html, text, full: html, text
Created a new track for the incoming Orchid data
- lines changed 9, context: html, text, full: html, text
Changing defualt settings to lab request
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.html
- lines changed 5, context: html, text, full: html, text
See redmine issue#35 note#17, mostly label changes and a few on/off settings
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.ra
- lines changed 4, context: html, text, full: html, text
See redmine issue#35 note#17, mostly label changes and a few on/off settings
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.ra
- lines changed 1851, context: html, text, full: html, text
See redmine issue#35 note#17, mostly label changes and a few on/off settings
- lines changed 42, context: html, text, full: html, text
Adding new subtracks, changing labels, putting some data in the attic
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylSeq.html
- lines changed 2, context: html, text, full: html, text
Updated track description. Removing reference to hg18 and replaced with hg19 reference.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylSeq.ra
- lines changed 189, context: html, text, full: html, text
Used new DDF to update hg19 Methyl Seq data. Update meta-data to match when the submission was first accepted into our pipeline.
- lines changed 1, context: html, text, full: html, text
Added release alpha to View.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
- lines changed 247, context: html, text, full: html, text
Added 7 Chip-seq submissions for the Jan freeze.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.html
- lines changed 8, context: html, text, full: html, text
Added link to supplemental materials.
- lines changed 115, context: html, text, full: html, text
Fixed a bunch of stuff in Open Chromatin docs and limited those 3 and Broad to max 900 pixels
- lines changed 1, context: html, text, full: html, text
Not important but these should link to their own subdirs. Not important because the contents should be identical and are soft-linked in genome-test.
- lines changed 8, context: html, text, full: html, text
Getting more clever in with CSS
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.ra
- lines changed 3, context: html, text, full: html, text
Reordered UTA TFBS cell lines and added fileSortOrder to use new hgFileUi cgi.
- lines changed 16, context: html, text, full: html, text
Updated notes with what should be done with track configuration, labels, display conventions. Need confirmation of long labels.
- lines changed 1, context: html, text, full: html, text
Added track name that was accidently deleted.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.html
- lines changed 9, context: html, text, full: html, text
Added link to supplemental materials.
- lines changed 98, context: html, text, full: html, text
Fixed a bunch of stuff in Open Chromatin docs and limited those 3 and Broad to max 900 pixels
- lines changed 8, context: html, text, full: html, text
Getting more clever in with CSS
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.ra
- lines changed 2, context: html, text, full: html, text
Reordered UTA TFBS cell lines and added fileSortOrder to use new hgFileUi cgi.
- lines changed 24, context: html, text, full: html, text
Updated notes with what should be done with track configuration, labels, display conventions.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.html
- lines changed 8, context: html, text, full: html, text
Added link to supplemental materials.
- lines changed 105, context: html, text, full: html, text
Fixed a bunch of stuff in Open Chromatin docs and limited those 3 and Broad to max 900 pixels
- lines changed 1, context: html, text, full: html, text
Not important but these should link to their own subdirs. Not important because the contents should be identical and are soft-linked in genome-test.
- lines changed 8, context: html, text, full: html, text
Getting more clever in with CSS
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.ra
- lines changed 2, context: html, text, full: html, text
Reordered UTA TFBS cell lines and added fileSortOrder to use new hgFileUi cgi.
- lines changed 20, context: html, text, full: html, text
Updated notes with what should be done with track configuration, labels, display conventions. Need confirmation of long labels.
- src/hg/makeDb/trackDb/human/laminB1.html
- lines changed 5, context: html, text, full: html, text
Moved HTML files matching the trackDb entries that were only in hg18 up a level... just like the trackDb entries were
- src/hg/makeDb/trackDb/human/laminB1Lads.html
- lines changed 5, context: html, text, full: html, text
Moved HTML files matching the trackDb entries that were only in hg18 up a level... just like the trackDb entries were
- src/hg/makeDb/trackDb/human/laminB1Super.html
- lines changed 144, context: html, text, full: html, text
Moved HTML files matching the trackDb entries that were only in hg18 up a level... just like the trackDb entries were
- src/hg/makeDb/trackDb/human/snpArray.html
- lines changed 190, context: html, text, full: html, text
Moved HTML files matching the trackDb entries that were only in hg18 up a level... just like the trackDb entries were
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 1, context: html, text, full: html, text
suppressing links on hg17,hg18 to vista since they are no longer supported
- lines changed 80, context: html, text, full: html, text
Added search stuff for new Agilent tracks
- src/hg/makeDb/trackDb/human/ucsfBrainMethyl.html
- lines changed 166, context: html, text, full: html, text
Moved HTML files matching the trackDb entries that were only in hg18 up a level... just like the trackDb entries were
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
- lines changed 16, context: html, text, full: html, text
Updated track short labels for views. Also update age for cell lines to immortalized.
- lines changed 16, context: html, text, full: html, text
Added 2 strains B6D2F1/J and RIII, which are associated to 416B and 3134 Mouse cell lines, respectivley. Fixed the meta-data to accomadate with updated information.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/makefile
- lines changed 4, context: html, text, full: html, text
staging metaDb for SydhTfbs on beta
- lines changed 2, context: html, text, full: html, text
remove spurious backslash
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeSydhTfbs.ra
- lines changed 4442, context: html, text, full: html, text
staging metaDb for SydhTfbs on beta
- src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
- lines changed 14, context: html, text, full: html, text
Updated Encode specific trackDb to clearly layout tracks with comments about tracks. Also improve orginization of track specific includes to make easy readability.
- lines changed 2, context: html, text, full: html, text
Implemented new release tags at compsosite level rather than subTrack level.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.html
- lines changed 8, context: html, text, full: html, text
making minor edits to the description page
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.newR2.ra
- lines changed 63, context: html, text, full: html, text
Implemented new release tags at compsosite level rather than subTrack level.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.ra
- lines changed 20, context: html, text, full: html, text
Implemented new release tags at compsosite level rather than subTrack level.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.ra
- lines changed 63, context: html, text, full: html, text
Updated track short labels for views. Also update age for cell lines to immortalized.
- lines changed 10, context: html, text, full: html, text
Added 2 strains B6D2F1/J and RIII, which are associated to 416B and 3134 Mouse cell lines, respectivley. Fixed the meta-data to accomadate with updated information.
- lines changed 2, context: html, text, full: html, text
Updated notes of possible shortlabels.
- src/hg/makeDb/trackDb/mouse/trackDb.ra
- lines changed 32, context: html, text, full: html, text
Added search stuff for new Agilent tracks
- src/hg/makeDb/trackDb/rat/trackDb.ra
- lines changed 32, context: html, text, full: html, text
Added search stuff for new Agilent tracks
- src/hg/makeDb/trackDb/rmsk.html
- lines changed 1, context: html, text, full: html, text
corrected reference formating
- src/hg/makeDb/trackDb/tagTypes.tab
- lines changed 1, context: html, text, full: html, text
added bigWig to smoothingWindow
- src/hg/makeDb/trackDb/zebrafish/danRer7/ctgPos2.html
- lines changed 8, context: html, text, full: html, text
contents for Contigs track description
- lines changed 4, context: html, text, full: html, text
add note about chromosomes ctg2acc
- lines changed 4, context: html, text, full: html, text
Changed wording slightly and added a period.
- src/hg/near/hgMapToGene/hgMapToGene.c
- lines changed 14, context: html, text, full: html, text
When looking for the bed that best represents a gene prediction, added one more check: to ensure that the gene prediction is a 'compatible extension' of the bed. This means that all the introns in the bed must also be present in the gene prediction, and the portion of the gene prediction within the bed start/stop range cannot have any introns that are not found in the bed
- src/hg/oneShot/freen/freen.c
- lines changed 30, context: html, text, full: html, text
Making freen test netLineFileOpen.
- lines changed 17, context: html, text, full: html, text
Changing freen to test stripRegEx
- src/hg/pythonLib/styleGuide.txt
- lines changed 2, context: html, text, full: html, text
Added PythonLib directory and started styleGuide.
- src/hg/snp/snpLoad/snpNcbiToUcsc.c
- lines changed 8, context: html, text, full: html, text
Oops, bitfields needs to be comma-separated list not overwritten by each val.
- src/hg/utils/automation/doDbSnp.pl
- lines changed 6, context: html, text, full: html, text
Track #1684 (SNPs 132 (dbSNP)): Oops, there is no snp*Exceptions.bed.gzanymore. Don't try to load the table, and extract exception summary from
the new exceptions column in the main snp table.
- lines changed 1, context: html, text, full: html, text
Fixed a spot that assumed that snp* would match ${snpBase} (it generally does, so there has been no symptom).
- src/hg/utils/automation/makePushQSql.pl
- lines changed 9, context: html, text, full: html, text
better detection of axtNet vs net.axt.gz files
- src/hg/utils/hubCheck/hubCheck.c
- lines changed 200, context: html, text, full: html, text
Start version of hub checker.
- lines changed 23, context: html, text, full: html, text
Reading tdb list for a given genome for a hub.
- lines changed 135, context: html, text, full: html, text
Checking trackDb.ra file to make sure items are containers or have bigDataUrl. Some other checks.
- lines changed 246, context: html, text, full: html, text
Moving many routines from hubCheck to trackHub.c library file.
- lines changed 1, context: html, text, full: html, text
Adding name parameter to hubOpen call.
- src/hg/utils/hubCheck/makefile
- lines changed 18, context: html, text, full: html, text
Start version of hub checker.
- lines changed 2, context: html, text, full: html, text
Reading tdb list for a given genome for a hub.
- src/hg/utils/refSeqGet/tests/expected/basicListTest.gp
- lines changed 1, context: html, text, full: html, text
fixed updated test results due to database update. Modified test to us proper rules
- src/hg/utils/refSeqGet/tests/expected/basicListTest.meta
- lines changed 1, context: html, text, full: html, text
fixed updated test results due to database update. Modified test to us proper rules
- src/hg/utils/refSeqGet/tests/expected/basicListTest.psl
- lines changed 2, context: html, text, full: html, text
fixed updated test results due to database update. Modified test to us proper rules
- src/hg/utils/refSeqGet/tests/expected/basicListTest.rna.fa
- lines changed 2, context: html, text, full: html, text
fixed updated test results due to database update. Modified test to us proper rules
- src/hg/utils/refSeqGet/tests/expected/versionedListTest.gp
- lines changed 1, context: html, text, full: html, text
fixed updated test results due to database update. Modified test to us proper rules
- src/hg/utils/refSeqGet/tests/expected/versionedListTest.meta
- lines changed 1, context: html, text, full: html, text
fixed updated test results due to database update. Modified test to us proper rules
- src/hg/utils/refSeqGet/tests/expected/versionedListTest.psl
- lines changed 2, context: html, text, full: html, text
fixed updated test results due to database update. Modified test to us proper rules
- src/hg/utils/refSeqGet/tests/expected/versionedListTest.rna.fa
- lines changed 2, context: html, text, full: html, text
fixed updated test results due to database update. Modified test to us proper rules
- src/hg/utils/refSeqGet/tests/input/versioned.acc
- lines changed 1, context: html, text, full: html, text
fixed updated test results due to database update. Modified test to us proper rules
- src/hg/utils/refSeqGet/tests/makefile
- lines changed 9, context: html, text, full: html, text
fixed updated test results due to database update. Modified test to us proper rules
- src/inc/common.h
- lines changed 5, context: html, text, full: html, text
Adding catTwoStrings to common library.
- src/inc/filePath.h
- lines changed 10, context: html, text, full: html, text
Adding new function pathRelativeToFile
- src/inc/udc.h
- lines changed 13, context: html, text, full: html, text
Adding new functions udcFileReadAll and udcWrapShortLineFile
- src/lib/basicBed.c
- lines changed 12, context: html, text, full: html, text
Added one more condition to bedCompatibleExtension. After checking that all the introns in the old bed also exist in the new bed, check to make sure that the new bed does not have any additional introns within the old bed's start-stop range. In other words, check that the new bed doesn't have some intron that overlaps with a terminal exon in the old bed
- src/lib/cheapcgi.c
- lines changed 1, context: html, text, full: html, text
In cgiMakeCheckboxGroupWithVals, don't force the first item to bechecked when no checked items are specified -- let the caller control
the behavior.
- src/lib/common.c
- lines changed 13, context: html, text, full: html, text
Adding catTwoStrings to common library.
- src/lib/filePath.c
- lines changed 21, context: html, text, full: html, text
Adding new function pathRelativeToFile
- src/lib/net.c
- lines changed 8, context: html, text, full: html, text
Made it so that netUrlOpenSockets (and hence netUrlOpen and netLineFileOpen) can handle a plain unix file name as well as a URL.
- src/lib/pipeline.c
- lines changed 4, context: html, text, full: html, text
made an error message more informative Bug #1201
- src/lib/udc.c
- lines changed 31, context: html, text, full: html, text
Adding new functions udcFileReadAll and udcWrapShortLineFile
- src/utils/bedClip/makefile
- lines changed 1, context: html, text, full: html, text
these apps need networking libs
- src/utils/bigWigInfo/makefile
- lines changed 1, context: html, text, full: html, text
these apps need networking libs
- src/utils/bigWigSummary/makefile
- lines changed 1, context: html, text, full: html, text
these apps need networking libs
- src/utils/bigWigToBedGraph/makefile
- lines changed 1, context: html, text, full: html, text
these apps need networking libs
- src/utils/bigWigToWig/makefile
- lines changed 1, context: html, text, full: html, text
these apps need networking libs
- src/utils/git-reports/git-reports.c
- src/utils/paraFetch/makefile
- lines changed 3, context: html, text, full: html, text
because there may SOMEDAY be an official install target
- src/utils/paraSync/makefile
- lines changed 3, context: html, text, full: html, text
because there may SOMEDAY be an official install target
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed: 18893
- files changed: 286