All File Changes

v250_preview to v250_preview2 (2011-04-05 to 2011-04-12) v250

• src/hg/dbTrash/dbTrash.c
  • lines changed 32, context: html, text, full: html, text
    indicate total tables even when not using tableStatus and indicate no tables when no tables
  • lines changed 27, context: html, text, full: html, text
    adding delLostTable option to avoid any show table status
• src/hg/encode/DAFs/2.0/broadChipSeq.daf
  • lines changed 2, context: html, text, full: html, text
    Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
• src/hg/encode/DAFs/2.0/haibChipSeq.daf
  • lines changed 3, context: html, text, full: html, text
    Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
• src/hg/encode/DAFs/2.0/licrMm9Histone.daf
  • lines changed 2, context: html, text, full: html, text
    Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
• src/hg/encode/DAFs/2.0/licrMm9Tfbs.daf
  • lines changed 2, context: html, text, full: html, text
    Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
• src/hg/encode/DAFs/2.0/psuMm9Histone.daf
  • lines changed 2, context: html, text, full: html, text
    Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
• src/hg/encode/DAFs/2.0/psuMm9Tfbs.daf
  • lines changed 2, context: html, text, full: html, text
    Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
• src/hg/encode/DAFs/2.0/stanfordChipSeq.daf
  • lines changed 1, context: html, text, full: html, text
    Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
• src/hg/encode/DAFs/2.0/stanfordHg19Hist.daf
  • lines changed 2, context: html, text, full: html, text
    Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
• src/hg/encode/DAFs/2.0/stanfordHg19HistInput.daf
  • lines changed 2, context: html, text, full: html, text
    Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
• src/hg/encode/DAFs/2.0/stanfordHg19Tfbs.daf
  • lines changed 2, context: html, text, full: html, text
    Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
• src/hg/encode/DAFs/2.0/stanfordHg19TfbsInput.daf
  • lines changed 2, context: html, text, full: html, text
    Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
• src/hg/encode/DAFs/2.0/stanfordMm9Hist.daf
  • lines changed 2, context: html, text, full: html, text
    Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
• src/hg/encode/DAFs/2.0/stanfordMm9Tfbs.daf
  • lines changed 2, context: html, text, full: html, text
    Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
• src/hg/encode/DAFs/2.0/stanfordMm9TfbsInput.daf
  • lines changed 2, context: html, text, full: html, text
    Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
• src/hg/encode/DAFs/2.0/stanfordNucleosome.daf
  • lines changed 2, context: html, text, full: html, text
    Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
• src/hg/encode/DAFs/2.0/uChicagoTfbs.daf
  • lines changed 1, context: html, text, full: html, text
    Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
• src/hg/encode/DAFs/2.0/uwChipSeq.daf
  • lines changed 3, context: html, text, full: html, text
    Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
• src/hg/encode/DAFs/2.0/uwTfbs.daf
  • lines changed 3, context: html, text, full: html, text
    Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
• src/hg/encode/DAFs/2.0/ydhrRnaSeq.daf
  • lines changed 2, context: html, text, full: html, text
    Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
• src/hg/encode/encodeExp/encodeExp.c
  • lines changed 16, context: html, text, full: html, text
    Fix handling of NULL fields. Add tests -- most functions now covered. Schema cleanup. Fix problem with automated timestamp
  • lines changed 18, context: html, text, full: html, text
    Add history table updated via triggers
• src/hg/encode/encodeExp/tests/expected/addTest.out.ra
  • lines changed 7, context: html, text, full: html, text
    Fix handling of NULL fields. Add tests -- most functions now covered. Schema cleanup. Fix problem with automated timestamp
• src/hg/encode/encodeExp/tests/expected/idTest.out.ra
  • lines changed 2, context: html, text, full: html, text
    Fix handling of NULL fields. Add tests -- most functions now covered. Schema cleanup. Fix problem with automated timestamp
• src/hg/encode/encodeExp/tests/expected/showTest.out.ra
  • lines changed 14, context: html, text, full: html, text
    Fix handling of NULL fields. Add tests -- most functions now covered. Schema cleanup. Fix problem with automated timestamp
• src/hg/encode/encodeExp/tests/input/addTest.in.ra
  • lines changed 7, context: html, text, full: html, text
    Fix handling of NULL fields. Add tests -- most functions now covered. Schema cleanup. Fix problem with automated timestamp
• src/hg/encode/encodeExp/tests/makefile
  • lines changed 39, context: html, text, full: html, text
    Fix handling of NULL fields. Add tests -- most functions now covered. Schema cleanup. Fix problem with automated timestamp
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • lines changed 74, context: html, text, full: html, text
    Changes to validator/loader to tar.gz sets of fastqs and docs, and to support docs that are already tgz's.
• src/hg/encode/encodeLoad/doEncodeUnload.pl
  • lines changed 16, context: html, text, full: html, text
    Changes to validator/loader to tar.gz sets of fastqs and docs, and to support docs that are already tgz's.
• src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes
  • lines changed 1, context: html, text, full: html, text
    Added txt files to encodeMkChangeNotes and reran the script to get correct release notes for HaibGenoType
• src/hg/encode/encodeValidate/config/expVars.ra
  • lines changed 2, context: html, text, full: html, text
    Removed replicate from wgEncodeSunyAlbanyTiling and wgEncodeSunySwitchgear
  • lines changed 5, context: html, text, full: html, text
    Added wgEncodeAffyRnaChip composite and variables
• src/hg/encode/encodeValidate/config/fields.ra
  • lines changed 15, context: html, text, full: html, text
    Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
  • lines changed 5, context: html, text, full: html, text
    Sunsetted use of order from use in pipeline. Commented out initilization and use in Encode.pm and doEncodevalidate.pm. Commented out and retired term in fields.ra/ Redmine #1090.
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 7, context: html, text, full: html, text
    Sunsetted use of order from use in pipeline. Commented out initilization and use in Encode.pm and doEncodevalidate.pm. Commented out and retired term in fields.ra/ Redmine #1090.
  • lines changed 77, context: html, text, full: html, text
    Changes to validator/loader to tar.gz sets of fastqs and docs, and to support docs that are already tgz's.
  • lines changed 7, context: html, text, full: html, text
    Extended functionality to get sex,strain,age into meta-data from cv, for mouse ENCODE project if type=Cell Line and category not Tissue so that labs don't have to enter information every time and all mouse meta-data will be consistent against all tracks.
• src/hg/hgApi/hgApi.c
  • lines changed 4, context: html, text, full: html, text
    Tightened the screws on searching by mdb vars where the search is either for files or tables
  • lines changed 1, context: html, text, full: html, text
    Missed a few more references in changing searchTracks.h to search.h
• src/hg/hgFileSearch/hgFileSearch.c
  • lines changed 2, context: html, text, full: html, text
    Tightened the screws on searching by mdb vars where the search is either for files or tables
  • lines changed 1, context: html, text, full: html, text
    Renamed lib file searchTracks.c and .h to search.c and .h to avoid conflict with hgTracks file searchTracks.c and to emphasize that this is common code to both track and file seartch.
  • lines changed 84, context: html, text, full: html, text
    Cleaned out some ifdefs and made track search name and description fields work like file search
  • lines changed 53, context: html, text, full: html, text
    Moved common name and description matching code into search lib and removed it from hgFileSearch and hgTracks/searchTracks.c
• src/hg/hgFileUi/hgFileUi.c
  • lines changed 7, context: html, text, full: html, text
    Smoothing out the handling of the track->children pointer and track->subtracks pointer so that it works the same in hgTrackUi as elsewhere. The children pointers are set after pruning the track list for ones where the data table is not available.
  • lines changed 1, context: html, text, full: html, text
    Fixed a type
• src/hg/hgGateway/hgGateway.c
  • lines changed 1, context: html, text, full: html, text
    Missed a few more references in changing searchTracks.h to search.h
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 50, context: html, text, full: html, text
    Smoothing out the handling of the track->children pointer and track->subtracks pointer so that it works the same in hgTrackUi as elsewhere. The children pointers are set after pruning the track list for ones where the data table is not available.
  • lines changed 5, context: html, text, full: html, text
    Removing some debugging.
• src/hg/hgTracks/config.c
  • lines changed 1, context: html, text, full: html, text
    Missed a few more references in changing searchTracks.h to search.h
• src/hg/hgTracks/hgTracks.c
  • lines changed 5, context: html, text, full: html, text
    Missed a few more references in changing searchTracks.h to search.h
  • lines changed 4, context: html, text, full: html, text
    restore some code that got removed by previous checkin
• src/hg/hgTracks/mainMain.c
  • lines changed 2, context: html, text, full: html, text
    Missed a few more references in changing searchTracks.h to search.h
  • lines changed 1, context: html, text, full: html, text
    restore some code that got removed by previous checkin
• src/hg/hgTracks/searchTracks.c
  • lines changed 28, context: html, text, full: html, text
    Tightened the screws on searching by mdb vars where the search is either for files or tables
  • lines changed 1, context: html, text, full: html, text
    Renamed lib file searchTracks.c and .h to search.c and .h to avoid conflict with hgTracks file searchTracks.c and to emphasize that this is common code to both track and file seartch.
  • lines changed 103, context: html, text, full: html, text
    Cleaned out some ifdefs and made track search name and description fields work like file search
  • lines changed 65, context: html, text, full: html, text
    Moved common name and description matching code into search lib and removed it from hgFileSearch and hgTracks/searchTracks.c
• src/hg/hgTracks/simpleTracks.c
  • lines changed 2, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Renaming tables to match shortLabelsas suggested by Brooke, much better in the long run: snp132Patient -> snp132Flagged; snp132NonUnique -> snp132Mult
• src/hg/htdocs/goldenPath/help/fileSearch.html
  • lines changed 93, context: html, text, full: html, text
    edits to fileSearch doc and trying a different template. Having trouble getting topbar to display
  • lines changed 0, context: html, text, full: html, text
    making executable so that the server side include (for the topbar) will work
  • lines changed 4, context: html, text, full: html, text
    making changes suggested by Vanessa
  • lines changed 1, context: html, text, full: html, text
    fixed a repeated word
• src/hg/inc/encode/encodeExp.h
  • lines changed 16, context: html, text, full: html, text
    Fix handling of NULL fields. Add tests -- most functions now covered. Schema cleanup. Fix problem with automated timestamp
  • lines changed 4, context: html, text, full: html, text
    Add history table updated via triggers
• src/hg/inc/hdb.h
  • lines changed 3, context: html, text, full: html, text
    Smoothing out the handling of the track->children pointer and track->subtracks pointer so that it works the same in hgTrackUi as elsewhere. The children pointers are set after pruning the track list for ones where the data table is not available.
  • lines changed 9, context: html, text, full: html, text
    Fix case where databases are split between two servers with a trackDb specifcationpointing to both servers, e.g.: db.trackDb=localDb:trackDb_markd,db:trackDb If a given genome databases existed on only one of the servers, then it would cause an error when checking for a trackDb in that server. This change checks for the existance of the database as well as the table.
• src/hg/inc/hui.h
  • lines changed 4, context: html, text, full: html, text
    Smoothing out the handling of the track->children pointer and track->subtracks pointer so that it works the same in hgTrackUi as elsewhere. The children pointers are set after pruning the track list for ones where the data table is not available.
• src/hg/inc/jksql.h
  • lines changed 6, context: html, text, full: html, text
    Fix case where databases are split between two servers with a trackDb specifcationpointing to both servers, e.g.: db.trackDb=localDb:trackDb_markd,db:trackDb If a given genome databases existed on only one of the servers, then it would cause an error when checking for a trackDb in that server. This change checks for the existance of the database as well as the table.
• src/hg/inc/mdb.h
  • lines changed 9, context: html, text, full: html, text
    Tightened the screws on searching by mdb vars where the search is either for files or tables
  • lines changed 2, context: html, text, full: html, text
    Adjusted encodeExp funtionality to handle compositeless experiments without choking
• src/hg/inc/search.h
  • lines changed 47, context: html, text, full: html, text
    Renamed lib file searchTracks.c and .h to search.c and .h to avoid conflict with hgTracks file searchTracks.c and to emphasize that this is common code to both track and file seartch.
  • lines changed 10, context: html, text, full: html, text
    Moved common name and description matching code into search lib and removed it from hgFileSearch and hgTracks/searchTracks.c
• src/hg/inc/searchTracks.h
  • lines changed 5, context: html, text, full: html, text
    Tightened the screws on searching by mdb vars where the search is either for files or tables
  • lines changed 49, context: html, text, full: html, text
    Renamed lib file searchTracks.c and .h to search.c and .h to avoid conflict with hgTracks file searchTracks.c and to emphasize that this is common code to both track and file seartch.
• src/hg/js/utils.js
  • lines changed 7, context: html, text, full: html, text
    Tightened the screws on searching by mdb vars where the search is either for files or tables
• src/hg/lib/cv.c
  • lines changed 57, context: html, text, full: html, text
    Tightened the screws on searching by mdb vars where the search is either for files or tables
• src/hg/lib/encode/encodeExp.as
  • lines changed 6, context: html, text, full: html, text
    Fix handling of NULL fields. Add tests -- most functions now covered. Schema cleanup. Fix problem with automated timestamp
• src/hg/lib/encode/encodeExp.c
  • lines changed 185, context: html, text, full: html, text
    Fix handling of NULL fields. Add tests -- most functions now covered. Schema cleanup. Fix problem with automated timestamp
  • lines changed 105, context: html, text, full: html, text
    Add history table updated via triggers
  • lines changed 2, context: html, text, full: html, text
    Adjusted encodeExp funtionality to handle compositeless experiments without choking
• src/hg/lib/encode/encodeExp.sql
  • lines changed 6, context: html, text, full: html, text
    Fix handling of NULL fields. Add tests -- most functions now covered. Schema cleanup. Fix problem with automated timestamp
• src/hg/lib/fileUi.c
  • lines changed 1, context: html, text, full: html, text
    Tightened the screws on searching by mdb vars where the search is either for files or tables
  • lines changed 10, context: html, text, full: html, text
    Make fileIndex an implied mdb var as far as file search is concerned.
• src/hg/lib/hdb.c
  • lines changed 42, context: html, text, full: html, text
    Smoothing out the handling of the track->children pointer and track->subtracks pointer so that it works the same in hgTrackUi as elsewhere. The children pointers are set after pruning the track list for ones where the data table is not available.
  • lines changed 33, context: html, text, full: html, text
    Fix case where databases are split between two servers with a trackDb specifcationpointing to both servers, e.g.: db.trackDb=localDb:trackDb_markd,db:trackDb If a given genome databases existed on only one of the servers, then it would cause an error when checking for a trackDb in that server. This change checks for the existance of the database as well as the table.
• src/hg/lib/hui.c
  • lines changed 3, context: html, text, full: html, text
    Smoothing out the handling of the track->children pointer and track->subtracks pointer so that it works the same in hgTrackUi as elsewhere. The children pointers are set after pruning the track list for ones where the data table is not available.
• src/hg/lib/jksql.c
  • lines changed 9, context: html, text, full: html, text
    Fix case where databases are split between two servers with a trackDb specifcationpointing to both servers, e.g.: db.trackDb=localDb:trackDb_markd,db:trackDb If a given genome databases existed on only one of the servers, then it would cause an error when checking for a trackDb in that server. This change checks for the existance of the database as well as the table.
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Renamed lib file searchTracks.c and .h to search.c and .h to avoid conflict with hgTracks file searchTracks.c and to emphasize that this is common code to both track and file seartch.
• src/hg/lib/mdb.c
  • lines changed 129, context: html, text, full: html, text
    Tightened the screws on searching by mdb vars where the search is either for files or tables
  • lines changed 51, context: html, text, full: html, text
    Adjusted encodeExp funtionality to handle compositeless experiments without choking
• src/hg/lib/search.c
  • lines changed 253, context: html, text, full: html, text
    Renamed lib file searchTracks.c and .h to search.c and .h to avoid conflict with hgTracks file searchTracks.c and to emphasize that this is common code to both track and file seartch.
  • lines changed 56, context: html, text, full: html, text
    Moved common name and description matching code into search lib and removed it from hgFileSearch and hgTracks/searchTracks.c
  • lines changed 5, context: html, text, full: html, text
    Make fileIndex an implied mdb var as far as file search is concerned.
• src/hg/lib/searchTracks.c
  • lines changed 22, context: html, text, full: html, text
    Tightened the screws on searching by mdb vars where the search is either for files or tables
  • lines changed 253, context: html, text, full: html, text
    Renamed lib file searchTracks.c and .h to search.c and .h to avoid conflict with hgTracks file searchTracks.c and to emphasize that this is common code to both track and file seartch.
• src/hg/lib/trackDb.c
  • lines changed 1, context: html, text, full: html, text
    Smoothing out the handling of the track->children pointer and track->subtracks pointer so that it works the same in hgTrackUi as elsewhere. The children pointers are set after pruning the track list for ones where the data table is not available.
• src/hg/lib/trackDbCustom.c
  • lines changed 5, context: html, text, full: html, text
    Smoothing out the handling of the track->children pointer and track->subtracks pointer so that it works the same in hgTrackUi as elsewhere. The children pointers are set after pruning the track list for ones where the data table is not available.
• src/hg/lib/txCommon.c
  • lines changed 2, context: html, text, full: html, text
    Increased the maximum accession length to accommodate txWalk-Rfam accessions. Rfam accessions can be as long as 57 characters. The txWalk combo adds about a dozen more characters
• src/hg/lib/web.c
  • lines changed 3, context: html, text, full: html, text
    Missed this reference as part of the rename from searchTracks.c to search.h
• src/hg/makeDb/doc/encodeDccHg18/wgEncodeDukeAffyExonArray.release2.notes.txt
  • lines changed 28, context: html, text, full: html, text
    Reran the script with release 2 replacing release 1. Jeff had run it backwards.
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibGenotype.release1.notes
  • lines changed 16, context: html, text, full: html, text
    Added txt files to encodeMkChangeNotes and reran the script to get correct release notes for HaibGenoType
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUchicagoTfbs.release1.notes
  • lines changed 145, context: html, text, full: html, text
    Release 1 Notes for Uchicago track.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 12, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Renaming tables to match shortLabelsas suggested by Brooke, much better in the long run: snp132Patient -> snp132Flagged; snp132NonUnique -> snp132Mult
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    Fix oviAri1.xenoRefFlat table error from checkJoiner
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 20, context: html, text, full: html, text
    Added in expId and dccAccxession into typeOfTerms as they will soon be added to the mdb. Also labelled Stam grant by his fully unspellable and unpronounceable name
  • lines changed 1, context: html, text, full: html, text
    Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
  • lines changed 11, context: html, text, full: html, text
    expVars should now be official. It is an objType=composite only var.
  • lines changed 1, context: html, text, full: html, text
    Adding in validate setting for expVars
• src/hg/makeDb/trackDb/human/hg18/ceuBcellComposite.html
  • lines changed 1, context: html, text, full: html, text
    Created ceuBcellComposite.html.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeAffyRnaChip.ra
  • lines changed 6, context: html, text, full: html, text
    Adding expVars to the metaDb for all composites
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeBroadChipSeq.ra
  • lines changed 6, context: html, text, full: html, text
    Added expVars to major DNA composites for hg18
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeBroadHmm.ra
  • lines changed 6, context: html, text, full: html, text
    Added in missing expVars into objType=composite
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeBuOrchid.ra
  • lines changed 6, context: html, text, full: html, text
    Adding expVars to the metaDb for all composites
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeChromatinMap.ra
  • lines changed 2, context: html, text, full: html, text
    Added expVars to major DNA composites for hg18
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 2, context: html, text, full: html, text
    Adding expVars to the metaDb for all composites
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 2, context: html, text, full: html, text
    Adding expVars to the metaDb for all composites
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeDukeAffyExonArray.ra
  • lines changed 6, context: html, text, full: html, text
    Added in missing expVars into objType=composite
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeGisDnaPet.ra
  • lines changed 6, context: html, text, full: html, text
    Adding expVars to the metaDb for all composites
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeGisPet.ra
  • lines changed 127, context: html, text, full: html, text
    Adding expVars to the metaDb for all composites
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeGisRnaSeq.ra
  • lines changed 6, context: html, text, full: html, text
    Adding expVars to the metaDb for all composites
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHelicosRnaSeq.ra
  • lines changed 6, context: html, text, full: html, text
    A few more expVars added to metaDb
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaChipSeq.ra
  • lines changed 6, context: html, text, full: html, text
    Added expVars to major DNA composites for hg18
  • lines changed 202, context: html, text, full: html, text
    Removed fileNames for RawSignal meta-data that were associated with tagAlign files as this was confusing to users. Redmine issue 792.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaCnv.ra
  • lines changed 6, context: html, text, full: html, text
    Added in missing expVars into objType=composite
  • lines changed 52, context: html, text, full: html, text
    Removed old metaData for release 1
  • lines changed 6, context: html, text, full: html, text
    I believe I missed this one earlier.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaMethyl27.ra
  • lines changed 6, context: html, text, full: html, text
    Added in missing expVars into objType=composite
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaMethylSeq.ra
  • lines changed 6, context: html, text, full: html, text
    Added in missing expVars into objType=composite
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaRnaSeq.ra
  • lines changed 6, context: html, text, full: html, text
    Added in missing expVars into objType=composite
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeMapability.ra
  • lines changed 6, context: html, text, full: html, text
    Added in missing expVars into objType=composite
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeNhgriBip.ra
  • lines changed 2, context: html, text, full: html, text
    Adding expVars to the objType=table on this one which does not belong to a composite.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeNhgriNRE.ra
  • lines changed 6, context: html, text, full: html, text
    Added in missing expVars into objType=composite
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 6, context: html, text, full: html, text
    Adding expVars to the metaDb for all composites
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeSunyalbanyRnaGeneChip.ra
  • lines changed 6, context: html, text, full: html, text
    Adding expVars to the metaDb for all composites
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUmasshaTfbsValid.ra
  • lines changed 6, context: html, text, full: html, text
    Added in missing expVars into objType=composite
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwAffyExonArray.ra
  • lines changed 6, context: html, text, full: html, text
    Added in missing expVars into objType=composite
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwChIPSeq.ra
  • lines changed 6, context: html, text, full: html, text
    Added expVars to major DNA composites for hg18
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwDGF.ra
  • lines changed 6, context: html, text, full: html, text
    Added expVars to major DNA composites for hg18
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwDnaseSeq.ra
  • lines changed 6, context: html, text, full: html, text
    Added expVars to major DNA composites for hg18
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleChIPseq.ra
  • lines changed 6, context: html, text, full: html, text
    Added expVars to major DNA composites for hg18
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleRNAseq.ra
  • lines changed 6, context: html, text, full: html, text
    Added in missing expVars into objType=composite
  • lines changed 7, context: html, text, full: html, text
    Changed the treatment IFN*30m to IFN*30 to match the CV
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/makefile
  • lines changed 2, context: html, text, full: html, text
    Changing Mapability (hg18) and NHGRI Bi-Pro (hg18) to using metaDb instead of metadata lines in trackDb
  • lines changed 1, context: html, text, full: html, text
    changing hg18 NHGRI NRE track to using the metaDb, redmine #1605
  • lines changed 1, context: html, text, full: html, text
    changing hg18 CSHL Sm RNA-seq track to using the metaDb, redmine #1605; also fixed an indent minor inconsistency in wgEncodeCshlShortRnaSeq.new.ra
  • lines changed 1, context: html, text, full: html, text
    changing hg18 GIS DNA Pet track to using the metaDb, redmine #1650
  • lines changed 1, context: html, text, full: html, text
    changing hg18 wgEncodeHudsonalphaMethylSeq.ra track to using the metaDb, redmine #1650
  • lines changed 1, context: html, text, full: html, text
    switching wgEncodeDukeAffyExonArray to use metaDb for its metadata, redmine #1650
  • lines changed 1, context: html, text, full: html, text
    switching wgEncodeHelicosRnaSeq to use metaDb for its metadata, redmine #1650
  • lines changed 1, context: html, text, full: html, text
    switching wgEncodeAffyRnaChip to use metaDb for its metadata, redmine #1650
  • lines changed 1, context: html, text, full: html, text
    switching wgEncodeGisRnaSeq to use metaDb for its metadata, redmine #1650
  • lines changed 1, context: html, text, full: html, text
    staging Common Cell CNV (Release 2) on beta
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeHudsonalphaCnv.ra
  • lines changed 10, context: html, text, full: html, text
    staging Common Cell CNV (Release 2) on beta
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeHudsonalphaMethylSeq.ra
  • lines changed 1612, context: html, text, full: html, text
    changing hg18 wgEncodeHudsonalphaMethylSeq.ra track to using the metaDb, redmine #1650
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeMapability.ra
  • lines changed 162, context: html, text, full: html, text
    Changing Mapability (hg18) and NHGRI Bi-Pro (hg18) to using metaDb instead of metadata lines in trackDb
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeNhgriBip.ra
  • lines changed 16, context: html, text, full: html, text
    Changing Mapability (hg18) and NHGRI Bi-Pro (hg18) to using metaDb instead of metadata lines in trackDb
• src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeNhgriNRE.ra
  • lines changed 69, context: html, text, full: html, text
    changing hg18 NHGRI NRE track to using the metaDb, redmine #1605
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/makefile
  • lines changed 2, context: html, text, full: html, text
    Changing Mapability (hg18) and NHGRI Bi-Pro (hg18) to using metaDb instead of metadata lines in trackDb
  • lines changed 1, context: html, text, full: html, text
    changing hg18 NHGRI NRE track to using the metaDb, redmine #1605
  • lines changed 1, context: html, text, full: html, text
    changing hg18 CSHL Sm RNA-seq track to using the metaDb, redmine #1605; also fixed an indent minor inconsistency in wgEncodeCshlShortRnaSeq.new.ra
  • lines changed 1, context: html, text, full: html, text
    changing hg18 GIS DNA Pet track to using the metaDb, redmine #1650
  • lines changed 1, context: html, text, full: html, text
    changing hg18 wgEncodeHudsonalphaMethylSeq.ra track to using the metaDb, redmine #1650
  • lines changed 1, context: html, text, full: html, text
    switching wgEncodeDukeAffyExonArray to use metaDb for its metadata, redmine #1650
  • lines changed 1, context: html, text, full: html, text
    switching wgEncodeHelicosRnaSeq to use metaDb for its metadata, redmine #1650
  • lines changed 1, context: html, text, full: html, text
    switching wgEncodeAffyRnaChip to use metaDb for its metadata, redmine #1650
  • lines changed 1, context: html, text, full: html, text
    switching wgEncodeGisRnaSeq to use metaDb for its metadata, redmine #1650
  • lines changed 1, context: html, text, full: html, text
    releasing Common Cell CNV (Release 2) to the RR, redmine #3499
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeAffyRnaChip.ra
  • lines changed 1873, context: html, text, full: html, text
    switching wgEncodeAffyRnaChip to use metaDb for its metadata, redmine #1650
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeCshlShortRnaSeq.ra
  • lines changed 1018, context: html, text, full: html, text
    changing hg18 CSHL Sm RNA-seq track to using the metaDb, redmine #1605; also fixed an indent minor inconsistency in wgEncodeCshlShortRnaSeq.new.ra
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeDukeAffyExonArray.ra
  • lines changed 1045, context: html, text, full: html, text
    switching wgEncodeDukeAffyExonArray to use metaDb for its metadata, redmine #1650
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeGisDnaPet.ra
  • lines changed 551, context: html, text, full: html, text
    changing hg18 GIS DNA Pet track to using the metaDb, redmine #1650
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeGisRnaSeq.ra
  • lines changed 439, context: html, text, full: html, text
    switching wgEncodeGisRnaSeq to use metaDb for its metadata, redmine #1650
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeHelicosRnaSeq.ra
  • lines changed 54, context: html, text, full: html, text
    switching wgEncodeHelicosRnaSeq to use metaDb for its metadata, redmine #1650
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeHudsonalphaCnv.ra
  • lines changed 103, context: html, text, full: html, text
    releasing Common Cell CNV (Release 2) to the RR, redmine #3499
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeHudsonalphaMethylSeq.ra
  • lines changed 1612, context: html, text, full: html, text
    changing hg18 wgEncodeHudsonalphaMethylSeq.ra track to using the metaDb, redmine #1650
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeMapability.ra
  • lines changed 162, context: html, text, full: html, text
    Changing Mapability (hg18) and NHGRI Bi-Pro (hg18) to using metaDb instead of metadata lines in trackDb
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeNhgriBip.ra
  • lines changed 16, context: html, text, full: html, text
    Changing Mapability (hg18) and NHGRI Bi-Pro (hg18) to using metaDb instead of metadata lines in trackDb
• src/hg/makeDb/trackDb/human/hg18/metaDb/public/wgEncodeNhgriNRE.ra
  • lines changed 69, context: html, text, full: html, text
    changing hg18 NHGRI NRE track to using the metaDb, redmine #1605
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 13, context: html, text, full: html, text
    Changed B-Cell RNA-Seq from super to composite track.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 18, context: html, text, full: html, text
    Changing Mapability (hg18) and NHGRI Bi-Pro (hg18) to using metaDb instead of metadata lines in trackDb
  • lines changed 44, context: html, text, full: html, text
    changing hg18 NHGRI NRE track to using the metaDb, redmine #1605
  • lines changed 2, context: html, text, full: html, text
    changing hg18 CSHL Sm RNA-seq track to using the metaDb, redmine #1605; also fixed an indent minor inconsistency in wgEncodeCshlShortRnaSeq.new.ra
  • lines changed 2, context: html, text, full: html, text
    changing hg18 GIS DNA Pet track to using the metaDb, redmine #1650
  • lines changed 736, context: html, text, full: html, text
    putting wgEncodeHudsonalphaMethylSeq in its own .ra and .new.ra file instead of having them in the trackDb.wgEncode.ra file; note there was already a .ra file, but it wasn't being used, so I just wrote over it.
  • lines changed 2, context: html, text, full: html, text
    changing hg18 wgEncodeHudsonalphaMethylSeq.ra track to using the metaDb, redmine #1650
  • lines changed 2, context: html, text, full: html, text
    switching wgEncodeDukeAffyExonArray to use metaDb for its metadata, redmine #1650
  • lines changed 2, context: html, text, full: html, text
    switching wgEncodeHelicosRnaSeq to use metaDb for its metadata, redmine #1650
  • lines changed 2, context: html, text, full: html, text
    switching wgEncodeAffyRnaChip to use metaDb for its metadata, redmine #1650
  • lines changed 2, context: html, text, full: html, text
    switching wgEncodeGisRnaSeq to use metaDb for its metadata, redmine #1650
  • lines changed 2, context: html, text, full: html, text
    staging Common Cell CNV (Release 2) on beta
  • lines changed 2, context: html, text, full: html, text
    releasing Common Cell CNV (Release 2) to the RR, redmine #3499
• src/hg/makeDb/trackDb/human/hg18/wgEncodeAffyRnaChip.ra
  • lines changed 104, context: html, text, full: html, text
    switching wgEncodeAffyRnaChip to use metaDb for its metadata, redmine #1650
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlShortRnaSeq.new.ra
  • lines changed 0, context: html, text, full: html, text
    changing hg18 CSHL Sm RNA-seq track to using the metaDb, redmine #1605; also fixed an indent minor inconsistency in wgEncodeCshlShortRnaSeq.new.ra
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCshlShortRnaSeq.ra
  • lines changed 44, context: html, text, full: html, text
    changing hg18 CSHL Sm RNA-seq track to using the metaDb, redmine #1605; also fixed an indent minor inconsistency in wgEncodeCshlShortRnaSeq.new.ra
• src/hg/makeDb/trackDb/human/hg18/wgEncodeDukeAffyExon.ra
  • lines changed 59, context: html, text, full: html, text
    switching wgEncodeDukeAffyExonArray to use metaDb for its metadata, redmine #1650
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisDnaPet.ra
  • lines changed 7, context: html, text, full: html, text
    changing hg18 GIS DNA Pet track to using the metaDb, redmine #1650
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisRnaSeq.ra
  • lines changed 18, context: html, text, full: html, text
    switching wgEncodeGisRnaSeq to use metaDb for its metadata, redmine #1650
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHelicosRnaSeq.ra
  • lines changed 4, context: html, text, full: html, text
    switching wgEncodeHelicosRnaSeq to use metaDb for its metadata, redmine #1650
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaCnv.html
  • lines changed 11, context: html, text, full: html, text
    releasing Common Cell CNV (Release 2) to the RR, redmine #3499
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaCnv.new.html
  • lines changed 2, context: html, text, full: html, text
    Changed the colors to swap oragne and red and choose a better orange
  • lines changed 2, context: html, text, full: html, text
    changed order of 'normal' items in list of colors
  • lines changed 6, context: html, text, full: html, text
    adding release notes section to the description of the hg18 Common cell cnv, redmine 3499
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaCnv.ra
  • lines changed 9, context: html, text, full: html, text
    releasing Common Cell CNV (Release 2) to the RR, redmine #3499
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethylSeq.new.ra
  • lines changed 324, context: html, text, full: html, text
    putting wgEncodeHudsonalphaMethylSeq in its own .ra and .new.ra file instead of having them in the trackDb.wgEncode.ra file; note there was already a .ra file, but it wasn't being used, so I just wrote over it.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaMethylSeq.ra
  • lines changed 33, context: html, text, full: html, text
    putting wgEncodeHudsonalphaMethylSeq in its own .ra and .new.ra file instead of having them in the trackDb.wgEncode.ra file; note there was already a .ra file, but it wasn't being used, so I just wrote over it.
  • lines changed 29, context: html, text, full: html, text
    forgot to copy the wgEncodeHudsonalphaMehthylSeq.new.ra over the wgEncodeHudsonalphaMethylSeq.ra; doing that now which finalizes switch to use of metaDb be removing trackDb metadata lines, redmine #1650
• src/hg/makeDb/trackDb/human/hg18/wgEncodeMapability.ra
  • lines changed 12, context: html, text, full: html, text
    Changing Mapability (hg18) and NHGRI Bi-Pro (hg18) to using metaDb instead of metadata lines in trackDb
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
  • lines changed 1, context: html, text, full: html, text
    Get HaibMethyl27 properly renamed to HaibMethylArray
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeAffyRnaChip.ra
  • lines changed 6, context: html, text, full: html, text
    Adding expVars to those that were forgotten in the first round
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHmm.ra
  • lines changed 6, context: html, text, full: html, text
    Added missing expVars to objType=composite
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBuOrchid.ra
  • lines changed 7, context: html, text, full: html, text
    Adding expVars to those that were forgotten in the first round
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 2, context: html, text, full: html, text
    Adding expVars to those that were forgotten in the first round
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 933, context: html, text, full: html, text
    Changing labels, adding dccRep, changing the fileSortOrder, adding Generation 0 to protocolID for early data
  • lines changed 596, context: html, text, full: html, text
    Revoking HepG2 experiments, wet lab issues
  • lines changed 259, context: html, text, full: html, text
    Changing according to Issue 1634
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethyl27.ra
  • lines changed 6, context: html, text, full: html, text
    Added missing expVars to objType=composite
  • lines changed 1466, context: html, text, full: html, text
    Must remove this old file
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibRnaSeq.ra
  • lines changed 36, context: html, text, full: html, text
    Removed R1x36 from file and tableNames
  • lines changed 1117, context: html, text, full: html, text
    Added new submissions 3838 and 3868
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 3, context: html, text, full: html, text
    Forgot to add meta-data that fixed code review.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeMapability.ra
  • lines changed 6, context: html, text, full: html, text
    Added missing expVars to objType=composite
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 290, context: html, text, full: html, text
    Adding md5sums to the metaData, showing with fileSortOrder
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 19, context: html, text, full: html, text
    Replaced submission 3258 with 3875.
  • lines changed 641, context: html, text, full: html, text
    Added 6 submission. One of them is a replacement submission 3875 for 3258.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra
  • lines changed 6, context: html, text, full: html, text
    A few more expVars added to metaDb
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 758, context: html, text, full: html, text
    Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
  • lines changed 484, context: html, text, full: html, text
    Sunsetted use of medianFragmentLength,fragmentLength,fragmentlengthRange from use in pipeline. Removed references from metaDb on hg19, and DAFs. Commented out and retired terms in fields.ra/ Redmine #1055.
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    preparing to release UW DNase, removed duplicate reference in beta metaDb makefile, redmine# 2398
  • lines changed 1, context: html, text, full: html, text
    staging Duke DNAseI HS on hgwbeta, redmine #63
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeOpenChromDnase.ra
  • lines changed 6676, context: html, text, full: html, text
    staging Duke DNAseI HS on hgwbeta, redmine #63
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
  • lines changed 2, context: html, text, full: html, text
    drop ExonArray which isn't here
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwDgf.ra
  • lines changed 972, context: html, text, full: html, text
    preparing to release UW DNase, removed duplicate reference in beta metaDb makefile, redmine# 2398
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 14, context: html, text, full: html, text
    add snakePanTro3
  • lines changed 2, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Renaming tables to match shortLabelsas suggested by Brooke, much better in the long run: snp132Patient -> snp132Flagged; snp132NonUnique -> snp132Mult
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    Smoothing out the handling of the track->children pointer and track->subtracks pointer so that it works the same in hgTrackUi as elsewhere. The children pointers are set after pruning the track list for ones where the data table is not available.
  • lines changed 1, context: html, text, full: html, text
    Commented out 'include wgEncodeRegNorm.ra alpha' upon Jim's recommendation. The include prevents make of hg19, since file doesn't exist.
  • lines changed 2, context: html, text, full: html, text
    preparing to release UW DNase, removed duplicate reference in beta metaDb makefile, redmine# 2398
  • lines changed 1, context: html, text, full: html, text
    staging Duke DNAseI HS on hgwbeta, redmine #63
  • lines changed 1, context: html, text, full: html, text
    Changed release tags to be in the include statement
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.new.ra
  • lines changed 107, context: html, text, full: html, text
    Changing labels, adding dccRep, changing the fileSortOrder, adding Generation 0 to protocolID for early data
  • lines changed 179, context: html, text, full: html, text
    Sort the Tier 1 and Tier 2 to the top
  • lines changed 60, context: html, text, full: html, text
    Revoking HepG2 experiments, wet lab issues
  • lines changed 507, context: html, text, full: html, text
    Changing according to Issue 1634
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.html
  • lines changed 2, context: html, text, full: html, text
    Changed Release 2 to Release Notes
  • lines changed 2, context: html, text, full: html, text
    Changed orange and red, redmine ticket 3499
  • lines changed 2, context: html, text, full: html, text
    Changed the order of the color listing Issue 3499 #6
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.ra
  • lines changed 144, context: html, text, full: html, text
    Patched in a couple of Aln files from sub 3868
  • lines changed 9, context: html, text, full: html, text
    Reformatted longLabels
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
  • lines changed 50, context: html, text, full: html, text
    fixed some discrepencies in files missing raised on code review, redmine #3519.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.ra
  • lines changed 141, context: html, text, full: html, text
    staging Duke DNAseI HS on hgwbeta, redmine #63
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 7, context: html, text, full: html, text
    Smoothing out the handling of the track->children pointer and track->subtracks pointer so that it works the same in hgTrackUi as elsewhere. The children pointers are set after pruning the track list for ones where the data table is not available.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.ra
  • lines changed 1, context: html, text, full: html, text
    Adding md5sums to the metaData, showing with fileSortOrder
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.ra
  • lines changed 1, context: html, text, full: html, text
    Long label had two RIP-Chips in it
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
  • lines changed 5, context: html, text, full: html, text
    Replaced submission 3258 with 3875.
  • lines changed 2, context: html, text, full: html, text
    2 tracks were missing release alpha tags.
  • lines changed 428, context: html, text, full: html, text
    Changed release tags to be in the include statement
  • lines changed 91, context: html, text, full: html, text
    Added 6 submission. One of them is a replacement submission 3875 for 3258.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.html
  • lines changed 3, context: html, text, full: html, text
    Removed Data sets section as this doesn't match the Track Description Standards.
  • lines changed 27, context: html, text, full: html, text
    Added track configuration section and added sentence about Peaks and Signals being from pooled data and replicate raw data is available for downlaod.
  • lines changed 4, context: html, text, full: html, text
    Added two sentences describing use of IgG controls by lab.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.ra
  • lines changed 9, context: html, text, full: html, text
    Updated settings for track view settings and controlled vocabullary links. Set minimal p value to be 5 -log(10^-5). Set signal range to be 0:50 and use vertical view range setting option. Updated windowing function to be mean=whiskers.
  • lines changed 1, context: html, text, full: html, text
    Updated track with fileSortOrder option.
  • lines changed 38, context: html, text, full: html, text
    Updated short and long lables in subtacks and Long label of track to follow standard. Will be checking with Kate before finallizing labels.
  • lines changed 34, context: html, text, full: html, text
    Fixed long and short labels to match standards proposed by Kate. Also removed eGFP- that was infront of factor name and used pure factor target.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.html
  • lines changed 18, context: html, text, full: html, text
    preparing to release UW DNase, removed duplicate reference in beta metaDb makefile, redmine# 2398
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.new.html
  • lines changed 1, context: html, text, full: html, text
    Fixed ftp link to link to Uw Dgf on hg19 and not hg18 YaleChipSeq.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.new.ra
  • lines changed 1, context: html, text, full: html, text
    Removed <BR> lines for 'Assembly originally mapped to' and used shorter verbiage to 'Original Assembly'. Also removed one <BR> line for 'GEO Sample Assession' to put 'GEO Sample' on the same line.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDgf.ra
  • lines changed 310, context: html, text, full: html, text
    preparing to release UW DNase, removed duplicate reference in beta metaDb makefile, redmine# 2398
  • lines changed 1, context: html, text, full: html, text
    The following edit was done on .new.ra file but was failed to be copied over to this file, adding the change back :Removed <BR> lines for 'Assembly originally mapped to' and used shorter verbiage to 'Original Assembly'. Also removed one <BR> line for 'GEO Sample Assession' to put 'GEO Sample' on the same line.
• src/hg/makeDb/trackDb/human/snpArray.html
  • lines changed 3, context: html, text, full: html, text
    Fixed broken Affy product links
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
  • lines changed 6, context: html, text, full: html, text
    Added experimental vars so that all mouse data can be given experiment Ids
  • lines changed 7, context: html, text, full: html, text
    Fixed incorrect data-types in LICR tracks. Removed extra variable in expVars for UwDnase track.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
  • lines changed 6, context: html, text, full: html, text
    Added experimental vars so that all mouse data can be given experiment Ids
  • lines changed 5, context: html, text, full: html, text
    Fixed incorrect data-types in LICR tracks. Removed extra variable in expVars for UwDnase track.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuHistone.ra
  • lines changed 6, context: html, text, full: html, text
    Added experimental vars so that all mouse data can be given experiment Ids
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
  • lines changed 6, context: html, text, full: html, text
    Added experimental vars so that all mouse data can be given experiment Ids
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 6, context: html, text, full: html, text
    Added experimental vars so that all mouse data can be given experiment Ids
  • lines changed 2, context: html, text, full: html, text
    Added treatment as expVar for two Sydh tracks. Also removed an extranous meta-data obj in wgEncodeSydhTfbs.ra
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 6, context: html, text, full: html, text
    Added experimental vars so that all mouse data can be given experiment Ids
  • lines changed 26, context: html, text, full: html, text
    Added treatment as expVar for two Sydh tracks. Also removed an extranous meta-data obj in wgEncodeSydhTfbs.ra
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 6, context: html, text, full: html, text
    Added experimental vars so that all mouse data can be given experiment Ids
  • lines changed 2, context: html, text, full: html, text
    Fixed incorrect data-types in LICR tracks. Removed extra variable in expVars for UwDnase track.
• src/hg/makeDb/trackDb/snp132.html
  • lines changed 1, context: html, text, full: html, text
    Changed Patient SNPs to Flagged SNPs.
• src/hg/makeDb/trackDb/snp132.shared.html
  • lines changed 1, context: html, text, full: html, text
    Changed Patient SNPs to Flagged SNPs.
• src/hg/makeDb/trackDb/snp132Flagged.html
  • lines changed 29, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Renaming tables to match shortLabelsas suggested by Brooke, much better in the long run: snp132Patient -> snp132Flagged; snp132NonUnique -> snp132Mult
• src/hg/makeDb/trackDb/snp132Mult.html
  • lines changed 25, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Renaming tables to match shortLabelsas suggested by Brooke, much better in the long run: snp132Patient -> snp132Flagged; snp132NonUnique -> snp132Mult
• src/hg/makeDb/trackDb/snp132NonUnique.html
  • lines changed 25, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Renaming tables to match shortLabelsas suggested by Brooke, much better in the long run: snp132Patient -> snp132Flagged; snp132NonUnique -> snp132Mult
• src/hg/makeDb/trackDb/snp132Patient.html
  • lines changed 29, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Renaming tables to match shortLabelsas suggested by Brooke, much better in the long run: snp132Patient -> snp132Flagged; snp132NonUnique -> snp132Mult
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
  • lines changed 1, context: html, text, full: html, text
    changed call for the short label so that it would display Sheep, rather than oviAri1
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Renaming tables to match shortLabelsas suggested by Brooke, much better in the long run: snp132Patient -> snp132Flagged; snp132NonUnique -> snp132Mult
• src/hg/oneShot/freen/freen.c
  • lines changed 258, context: html, text, full: html, text
    Smoothing out the handling of the track->children pointer and track->subtracks pointer so that it works the same in hgTrackUi as elsewhere. The children pointers are set after pruning the track list for ones where the data table is not available.
  • lines changed 44, context: html, text, full: html, text
    Testing some correlation ideas with freen.
• src/hg/regulate/companion/regCompanionChia/makefile
  • lines changed 18, context: html, text, full: html, text
    Some analysis code for chia-pet. Makes a big table other things can crawl through at their leisure.
• src/hg/regulate/companion/regCompanionChia/regCompanionChia.c
  • lines changed 331, context: html, text, full: html, text
    Some analysis code for chia-pet. Makes a big table other things can crawl through at their leisure.
  • lines changed 26, context: html, text, full: html, text
    Describing output better mostly.
• src/hg/regulate/companion/regCompanionCorrelateEnhancerAndExpression/regCompanionCorrelateEnhancerAndExpression.c
  • lines changed 15, context: html, text, full: html, text
    Adding several command line options to control tunable variables.
  • lines changed 68, context: html, text, full: html, text
    Adding permuteTest option.
• src/hg/regulate/companion/regCompanionCorrelateEnhancerAndExpression/test.csh
  • lines changed 1, context: html, text, full: html, text
    Moving routine to find next on list with a different chromosome to library since it keeps coming up.
• src/hg/regulate/companion/regCompanionGraphVsFixedPoints/regCompanionGraphVsFixedPoints.c
  • lines changed 12, context: html, text, full: html, text
    Moving routine to find next on list with a different chromosome to library since it keeps coming up.
• src/hg/regulate/companion/regCompanionHistoneBox/makefile
  • lines changed 18, context: html, text, full: html, text
    Adding simple box filter around peaks method.
• src/hg/regulate/companion/regCompanionHistoneBox/regCompanionHistoneBox.c
  • lines changed 168, context: html, text, full: html, text
    Adding simple box filter around peaks method.
• src/hg/regulate/companion/regCompanionPickEnhancers/regCompanionPickEnhancers.c
  • lines changed 47, context: html, text, full: html, text
    Adding several command line options to control tunable variables.
• src/hg/regulate/companion/regCompanionPickEnhancers/test.csh
  • lines changed 0, context: html, text, full: html, text
    Adding several command line options to control tunable variables.
• src/hg/regulate/companion/regCompanionPickGeneSet/makefile
  • lines changed 18, context: html, text, full: html, text
    Adding simple box filter around peaks method.
• src/hg/regulate/companion/regCompanionPickGeneSet/regCompanionPickGeneSet.c
  • lines changed 189, context: html, text, full: html, text
    Adding simple box filter around peaks method.
• src/hg/regulate/regCluster/regCluster.c
  • lines changed 9, context: html, text, full: html, text
    Adding -aveScore optoin.
• src/hg/txGraph/txWalk/txWalk.c
  • lines changed 5, context: html, text, full: html, text
    Added rfam and trna to the list of accession types to be tracked
• src/hg/utils/automation/Encode.pm
  • lines changed 2, context: html, text, full: html, text
    Sunsetted use of order from use in pipeline. Commented out initilization and use in Encode.pm and doEncodevalidate.pm. Commented out and retired term in fields.ra/ Redmine #1090.
• src/inc/basicBed.h
  • lines changed 3, context: html, text, full: html, text
    Moving routine to find next on list with a different chromosome to library since it keeps coming up.
• src/lib/basicBed.c
  • lines changed 11, context: html, text, full: html, text
    Moving routine to find next on list with a different chromosome to library since it keeps coming up.
• src/utils/bedGeneParts/bedGeneParts.c
  • lines changed 47, context: html, text, full: html, text
    Adding firstCodingSplice as a region you can get with bedGeneParts.
  • lines changed 66, context: html, text, full: html, text
    Adding exons as a type of bedGenePart output.
• src/utils/bedGeneParts/firstCodingSplice.expected
  • lines changed 6, context: html, text, full: html, text
    Adding firstCodingSplice as a region you can get with bedGeneParts.
• src/utils/bedGeneParts/makefile
  • lines changed 2, context: html, text, full: html, text
    Adding firstCodingSplice as a region you can get with bedGeneParts.
• src/utils/bigWigAverageOverBed/makefile
  • lines changed 1, context: html, text, full: html, text
    Added -lz to a couple makefiles that need it when no special USE_ vars are set.
• src/utils/bigWigMerge/makefile
  • lines changed 1, context: html, text, full: html, text
    Added -lz to a couple makefiles that need it when no special USE_ vars are set.
• src/utils/qa/weeklybld/buildEnv.csh
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    v250 preview

• lines changed: 31521
• files changed: 318