All File Changes

v250_preview2 to v250_base (2011-04-12 to 2011-04-19) v250

• src/hg/encode/DAFs/2.0/cshlLongSpikeIns.daf
  • lines changed 42, context: html, text, full: html, text
    First draft at a DAF for spike-ins
• src/hg/encode/DAFs/2.0/uwMm9DnaseDgf.daf
  • lines changed 82, context: html, text, full: html, text
    Added two new data type daf for Mouse UW (DGF and Chip-Seq, TFBS). Also upadted DAFs to keep track of the pooling of tissue samples using new term tissueSourceType.
• src/hg/encode/DAFs/2.0/uwMm9DnaseSeq.daf
  • lines changed 4, context: html, text, full: html, text
    Added two new data type daf for Mouse UW (DGF and Chip-Seq, TFBS). Also upadted DAFs to keep track of the pooling of tissue samples using new term tissueSourceType.
• src/hg/encode/DAFs/2.0/uwMm9Tfbs.daf
  • lines changed 69, context: html, text, full: html, text
    Added two new data type daf for Mouse UW (DGF and Chip-Seq, TFBS). Also upadted DAFs to keep track of the pooling of tissue samples using new term tissueSourceType.
• src/hg/encode/encodeExp/encodeExp.c
  • lines changed 40, context: html, text, full: html, text
    Fixes to history table. Tests not yet working. Interim checkin to integrate with Tim on experimentification code
  • lines changed 2, context: html, text, full: html, text
    Fix bug in 'show'. Remove primary key as timestamp lacks granularity to assure uniqueness (add an auto_inc or msec timestamp later if needed)
• src/hg/encode/encodeExp/tests/expected/addTest.out.ra
  • lines changed 1, context: html, text, full: html, text
    Fixes to history table. Tests not yet working. Interim checkin to integrate with Tim on experimentification code
• src/hg/encode/encodeExp/tests/makefile
  • lines changed 21, context: html, text, full: html, text
    Fixes to history table. Tests not yet working. Interim checkin to integrate with Tim on experimentification code
• src/hg/encode/encodeLoad/doEncodeUnload.pl
  • lines changed 1, context: html, text, full: html, text
    Fixed uploader bug that I caused and Angie caught in code review.
• src/hg/encode/encodeMkGeoPkg/encodeMkGeoPkg
  • lines changed 2, context: html, text, full: html, text
    No longer looks for metadata in cv when the expVar is antibody and it is labeled Control
• src/hg/encode/encodePatchTdb/tests/expected/add1.ra
  • lines changed 1, context: html, text, full: html, text
    Updated tests that should have been updated long ago.
• src/hg/encode/encodePatchTdb/tests/expected/add3.ra
  • lines changed 3, context: html, text, full: html, text
    Updated tests that should have been updated long ago.
• src/hg/encode/encodePatchTdb/tests/expected/composite.ra
  • lines changed 1, context: html, text, full: html, text
    Updated tests that should have been updated long ago.
• src/hg/encode/encodePatchTdb/tests/expected/replace1.ra
  • lines changed 1, context: html, text, full: html, text
    Updated tests that should have been updated long ago.
• src/hg/encode/encodePatchTdb/tests/expected/replace3.ra
  • lines changed 3, context: html, text, full: html, text
    Updated tests that should have been updated long ago.
• src/hg/encode/encodePatchTdb/tests/expected/replace3NoComment.ra
  • lines changed 3, context: html, text, full: html, text
    Updated tests that should have been updated long ago.
• src/hg/encode/encodeValidate/config/expVars.ra
  • lines changed 1, context: html, text, full: html, text
    Corrected expvars -> expVars
• src/hg/encode/encodeValidate/config/fields.ra
  • lines changed 6, context: html, text, full: html, text
    Added support for tissueSource to be tracked for pooled and individual animals in meta-data.
  • lines changed 2, context: html, text, full: html, text
    Added new DDF term tissueSourceType to capture the act of pooling mouse tisses or the use of an individual mouse for an experiment.
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 2, context: html, text, full: html, text
    Fixed file naming bug that Venkat found.
  • lines changed 1, context: html, text, full: html, text
    Another one found by Venkat
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 203, context: html, text, full: html, text
    add support for private hubs. Needs more work and doc, the biggest problem I know of is that you can't switch off the private hubs, but it should give folks an idea of how I'm thinking of supporting them.
  • lines changed 41, context: html, text, full: html, text
    fixed up the forms to act a little more rationally... added error catching so new hubs that can't be opened don't errAbort
  • lines changed 32, context: html, text, full: html, text
    rearrange some things to make more sense
• src/hg/hgHubConnect/makefile
  • lines changed 1, context: html, text, full: html, text
    add support for private hubs. Needs more work and doc, the biggest problem I know of is that you can't switch off the private hubs, but it should give folks an idea of how I'm thinking of supporting them.
• src/hg/hgTables/gffOut.c
  • lines changed 1, context: html, text, full: html, text
    Bug #3575 (GTF output in Table Browser contains start > end): Fixed byadding an end > start test I forgot to work into a42565e69, which was the fix for #2964.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 1, context: html, text, full: html, text
    add support for private hubs. Needs more work and doc, the biggest problem I know of is that you can't switch off the private hubs, but it should give folks an idea of how I'm thinking of supporting them.
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    add support for private hubs. Needs more work and doc, the biggest problem I know of is that you can't switch off the private hubs, but it should give folks an idea of how I'm thinking of supporting them.
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 1, context: html, text, full: html, text
    fixed typo: changed 'Bidning' to 'Binding'
  • lines changed 5, context: html, text, full: html, text
    adding Duke DNaseI HS, redmine #63
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 1, context: html, text, full: html, text
    Added sheep to release list
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 64, context: html, text, full: html, text
    added sheep to the credits
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 121, context: html, text, full: html, text
    Added latest two new news items
  • lines changed 12, context: html, text, full: html, text
    Made snp132 announcement match indexNews.html after edits.
  • lines changed 3, context: html, text, full: html, text
    Fixed the font on snp132 announcement.
• src/hg/htdocs/indexNews.html
  • lines changed 43, context: html, text, full: html, text
    Added news release for Sheep Browser
  • lines changed 4, context: html, text, full: html, text
    Fixed error where I accidentally added a new paragraph.
  • lines changed 13, context: html, text, full: html, text
    Fixed some more grammar and formatting errors.
  • lines changed 85, context: html, text, full: html, text
    Added snp132 announcement.
  • lines changed 2, context: html, text, full: html, text
    Changed header html back to old style, as I didn't realize this page was set to html3.2 :P
  • lines changed 2, context: html, text, full: html, text
    Corrected month in two places. It's April, not March. Duh.
  • lines changed 101, context: html, text, full: html, text
    Archived older news stories to goldenPath/newsarch.html; moved two stories down to the Read More list at the bottom, added an additional link at the bottom to the news archive for easier access.
  • lines changed 3, context: html, text, full: html, text
    Changed location of link to dbSNP.
  • lines changed 3, context: html, text, full: html, text
    On SNP 132 description, changed single -> multiple, and standardized punctuation on PAR.
  • lines changed 7, context: html, text, full: html, text
    On the snp132 announcement, tried to make the sentence about multiple mappings more readable and informative... thanks, Mark.
• src/hg/inc/cv.h
  • lines changed 6, context: html, text, full: html, text
    Normalize CV inconsistencies. Remove uninformative experimental vars
• src/hg/inc/encode/encodeExp.h
  • lines changed 6, context: html, text, full: html, text
    Fixes to history table. Tests not yet working. Interim checkin to integrate with Tim on experimentification code
  • lines changed 3, context: html, text, full: html, text
    Turned on expId and dccAccession updating in mdbUpdate. Removed old expTbl function from mdbPrint
  • lines changed 2, context: html, text, full: html, text
    Fixed mdbUpdate -encodeExp to not require two rounds when updating both tables.
• src/hg/inc/hubConnect.h
  • lines changed 11, context: html, text, full: html, text
    add support for private hubs. Needs more work and doc, the biggest problem I know of is that you can't switch off the private hubs, but it should give folks an idea of how I'm thinking of supporting them.
• src/hg/inc/mdb.h
  • lines changed 3, context: html, text, full: html, text
    Turned on expId and dccAccession updating in mdbUpdate. Removed old expTbl function from mdbPrint
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v250
• src/hg/js/hui.js
  • lines changed 1, context: html, text, full: html, text
    Fix for redmine 1411. Unchecking subtrack failed to grey matrix CB in 1D matrix.
  • lines changed 3, context: html, text, full: html, text
    One more adjustment to the third state matrix CB for redmine 1411
• src/hg/lib/cv.c
  • lines changed 25, context: html, text, full: html, text
    Normalize CV inconsistencies. Remove uninformative experimental vars
• src/hg/lib/encode/encodeExp.c
  • lines changed 57, context: html, text, full: html, text
    Fixes to history table. Tests not yet working. Interim checkin to integrate with Tim on experimentification code
  • lines changed 7, context: html, text, full: html, text
    Fix bug in 'show'. Remove primary key as timestamp lacks granularity to assure uniqueness (add an auto_inc or msec timestamp later if needed)
  • lines changed 10, context: html, text, full: html, text
    Normalize CV inconsistencies. Remove uninformative experimental vars
  • lines changed 4, context: html, text, full: html, text
    1. Reuse MDB defn. 2. Add an MDB test
  • lines changed 10, context: html, text, full: html, text
    Turned on expId and dccAccession updating in mdbUpdate. Removed old expTbl function from mdbPrint
  • lines changed 14, context: html, text, full: html, text
    Fixed mdbUpdate -encodeExp to not require two rounds when updating both tables.
• src/hg/lib/encode/tests/makefile
  • lines changed 25, context: html, text, full: html, text
    Fixes to history table. Tests not yet working. Interim checkin to integrate with Tim on experimentification code
• src/hg/lib/hdb.c
  • lines changed 3, context: html, text, full: html, text
    add support for private hubs. Needs more work and doc, the biggest problem I know of is that you can't switch off the private hubs, but it should give folks an idea of how I'm thinking of supporting them.
• src/hg/lib/hubConnect.c
  • lines changed 113, context: html, text, full: html, text
    add support for private hubs. Needs more work and doc, the biggest problem I know of is that you can't switch off the private hubs, but it should give folks an idea of how I'm thinking of supporting them.
  • lines changed 2, context: html, text, full: html, text
    take out no longer valid assertion
• src/hg/lib/mdb.c
  • lines changed 2, context: html, text, full: html, text
    Fixed bug that tripped up Kate's encodeExp.
  • lines changed 3, context: html, text, full: html, text
    Remove duplicate definition of default experiment table name
  • lines changed 32, context: html, text, full: html, text
    Turned on expId and dccAccession updating in mdbUpdate. Removed old expTbl function from mdbPrint
  • lines changed 7, context: html, text, full: html, text
    Fixed mdbUpdate -encodeExp to not require two rounds when updating both tables.
• src/hg/lib/trackDbCustom.c
  • lines changed 3, context: html, text, full: html, text
    Initial checkin of continuation char support in RA files
  • lines changed 4, context: html, text, full: html, text
    Streamlined and optimized continuation line code as Jim's suggests this is critical path.
• src/hg/lib/web.c
  • lines changed 2, context: html, text, full: html, text
    Ouch. I stepped on Galt's last change. Luckily Angie caught it in code review.
• src/hg/makeDb/doc/anoCar2.txt
  • lines changed 231, context: html, text, full: html, text
    initial browser build now running windowMasker
  • lines changed 160, context: html, text, full: html, text
    genbank tracks loaded
• src/hg/makeDb/doc/hg19.txt
  • lines changed 7, context: html, text, full: html, text
    running net step on self chain
  • lines changed 8, context: html, text, full: html, text
    adding hg19.hg19.net.gz to hgdownloads goldenPath
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    Added anoCar2.
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 17, context: html, text, full: html, text
    adding anoCar2 lizard
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added anoCar2.
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 1, context: html, text, full: html, text
    Added oviAri1
• src/hg/makeDb/mdbUpdate/mdbPrint.c
  • lines changed 2, context: html, text, full: html, text
    Removed reference to obsolete countObjs option which Kate tripped on
  • lines changed 89, context: html, text, full: html, text
    Turned on expId and dccAccession updating in mdbUpdate. Removed old expTbl function from mdbPrint
• src/hg/makeDb/mdbUpdate/mdbUpdate.c
  • lines changed 11, context: html, text, full: html, text
    Turned on expId and dccAccession updating in mdbUpdate. Removed old expTbl function from mdbPrint
• src/hg/makeDb/mdbUpdate/tests/expected/expTest1.ra
  • lines changed 7, context: html, text, full: html, text
    1. Reuse MDB defn. 2. Add an MDB test
• src/hg/makeDb/mdbUpdate/tests/input/smallTest.ra
  • lines changed 29, context: html, text, full: html, text
    1. Reuse MDB defn. 2. Add an MDB test
• src/hg/makeDb/mdbUpdate/tests/makefile
  • lines changed 22, context: html, text, full: html, text
    1. Reuse MDB defn. 2. Add an MDB test
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 4, context: html, text, full: html, text
    Accepted provisional stanzas from this week's alpha cv review
  • lines changed 22, context: html, text, full: html, text
    Added support for tissueSource to be tracked for pooled and individual animals in meta-data.
  • lines changed 6, context: html, text, full: html, text
    Added new DDF term tissueSourceType to capture the act of pooling mouse tisses or the use of an individual mouse for an experiment.
  • lines changed 3, context: html, text, full: html, text
    Removed (Wold) from Caltech(Wold) at request of Kate
  • lines changed 1, context: html, text, full: html, text
    Changed Harvard(Weissman) -> Yale(Weissman) to be more accurate.
  • lines changed 1, context: html, text, full: html, text
    Changed Nre to NRE as it is alredy released to public that way
  • lines changed 2, context: html, text, full: html, text
    Trying to fix validation for bioRep and md5sum to get the correct terms
  • lines changed 1, context: html, text, full: html, text
    Forgot to add cv changes: Changed Yale(Weissman) -> Yale-Weissman to follow naming convention.
  • lines changed 1, context: html, text, full: html, text
    Removed the verification for bioRep
  • lines changed 189, context: html, text, full: html, text
    Making the changes requested by NHGRI. Everything should be commented out for Melissa's review. Issue 1363
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 35, context: html, text, full: html, text
    Updating beta with the changes from alpha
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 77, context: html, text, full: html, text
    Removed the false fastq and fasta entries from issue 3046
  • lines changed 284, context: html, text, full: html, text
    Changed the expVars for each of these and got rid of Wold in lab name
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeGisDnaPet.ra
  • lines changed 2, context: html, text, full: html, text
    Changed the expVars for each of these and got rid of Wold in lab name
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeGisPet.ra
  • lines changed 143, context: html, text, full: html, text
    Removed the false fastq and fasta entries from issue 3046
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaChipSeq.ra
  • lines changed 17, context: html, text, full: html, text
    Updated tracks on hg19 and hg18 to have correct meta-data for IRF4, EBF and HA-F2F1 antibodies. IRF4 and EBF were acceptiable previously, however they were duplicated and subsequently retired as EBF1_(SC-137065) and IRF4_(SC-6059) were used in hg19. As a result needed to rename the wgEncodeSydhTfbsGm12878EbfStd experiment tables and files to match the correct EBF1 tag. Updated all meta-data on hg18 and hg19. The HA-F2F1 antibody was incorrectly named and should be HA-E2F1, which was corrected. Re-ran mdbPrint -validate to verify that all antibodies are correct. Lastly, updated the lab UCD(Farnham) -> UCD which is in the cv.ra .
  • lines changed 6, context: html, text, full: html, text
    Changed the expVars for each of these and got rid of Wold in lab name
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaMethylSeq.ra
  • lines changed 2, context: html, text, full: html, text
    Changed the expVars for each of these and got rid of Wold in lab name
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleChIPseq.ra
  • lines changed 5, context: html, text, full: html, text
    Updated tracks on hg19 and hg18 to have correct meta-data for IRF4, EBF and HA-F2F1 antibodies. IRF4 and EBF were acceptiable previously, however they were duplicated and subsequently retired as EBF1_(SC-137065) and IRF4_(SC-6059) were used in hg19. As a result needed to rename the wgEncodeSydhTfbsGm12878EbfStd experiment tables and files to match the correct EBF1 tag. Updated all meta-data on hg18 and hg19. The HA-F2F1 antibody was incorrectly named and should be HA-E2F1, which was corrected. Re-ran mdbPrint -validate to verify that all antibodies are correct. Lastly, updated the lab UCD(Farnham) -> UCD which is in the cv.ra .
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleRNAseq.ra
  • lines changed 2, context: html, text, full: html, text
    Updated expVars to not say treatment,treatment
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    Added html def for B Cell RNA Seq sub tracks.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRegDnaseClustered.html
  • lines changed 1, context: html, text, full: html, text
    tiny edit to sentence for better readability
  • lines changed 0, context: html, text, full: html, text
    changing 'data set' to 'dataset' for consistency within the page; 'dataset' is the term used in the data release policy on every ENCODE description page
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRegTfbsClustered.html
  • lines changed 0, context: html, text, full: html, text
    changing 'data set' to 'dataset' for consistency within the page; 'dataset' is the term used in the data release policy on every ENCODE description page
• src/hg/makeDb/trackDb/human/hg18/wgEncodeRegTxn.html
  • lines changed 1, context: html, text, full: html, text
    fixing incorrect sentence
  • lines changed 0, context: html, text, full: html, text
    changing 'data set' to 'dataset' for consistency within the page; 'dataset' is the term used in the data release policy on every ENCODE description page
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 501, context: html, text, full: html, text
    Removing (Wold) at Kate's request
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibGenotype.ra
  • lines changed 2, context: html, text, full: html, text
    removed obtainedBy from the expVars
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylArray.ra
  • lines changed 2, context: html, text, full: html, text
    Removed obtainedBy from the expVars
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
  • lines changed 325, context: html, text, full: html, text
    Ran the renamer to rename all of the files listed in issue 2254. This should be scrutinized.
  • lines changed 2, context: html, text, full: html, text
    Two replicate numbers were swapped. They have been corrected
  • lines changed 89, context: html, text, full: html, text
    More filename changing with the renamer, I also uncommented the attic files to do a test for Galt. They should be recommented soon.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 469, context: html, text, full: html, text
    Added missing files, submission 3877.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 7, context: html, text, full: html, text
    Changed UT-A(Iyer) to UT-A to match the CV
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 21, context: html, text, full: html, text
    Removed parentTable
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
  • lines changed 3, context: html, text, full: html, text
    Changed UNC(Lieb) to UNC to match the CV
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyAlbanyGeneSt.ra
  • lines changed 25, context: html, text, full: html, text
    Changed the origAssembly and greyscale and ripTgtProtien according to issue 37
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 30, context: html, text, full: html, text
    Updated tracks on hg19 and hg18 to have correct meta-data for IRF4, EBF and HA-F2F1 antibodies. IRF4 and EBF were acceptiable previously, however they were duplicated and subsequently retired as EBF1_(SC-137065) and IRF4_(SC-6059) were used in hg19. As a result needed to rename the wgEncodeSydhTfbsGm12878EbfStd experiment tables and files to match the correct EBF1 tag. Updated all meta-data on hg18 and hg19. The HA-F2F1 antibody was incorrectly named and should be HA-E2F1, which was corrected. Re-ran mdbPrint -validate to verify that all antibodies are correct. Lastly, updated the lab UCD(Farnham) -> UCD which is in the cv.ra .
  • lines changed 22, context: html, text, full: html, text
    Removed metaobject wgEncodeSydhTfbsHuvecInputUcdAlnRep1 since bam were trying to be concatenated in submission 1207 and the bam never seemed to have loaded.
  • lines changed 49, context: html, text, full: html, text
    Changed Harvard(Weissman) -> Yale(Weissman) to be more accurate.
  • lines changed 49, context: html, text, full: html, text
    Changed Yale(Weissman) -> Yale-Weissman to follow naming convention.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 2, context: html, text, full: html, text
    adding treatment as an experimental variable
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeOpenChromDnase.ra
  • lines changed 21, context: html, text, full: html, text
    releasing Duke DNaseI HS, updated metaDb from alpha, changed link on UNC Faire to not point to preview, redmine #63
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSunyAlbanyGeneSt.ra
  • lines changed 25, context: html, text, full: html, text
    staging revised metadata for SUNY RIP GeneST on beta
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    releasing Duke DNaseI HS, updated metaDb from alpha, changed link on UNC Faire to not point to preview, redmine #63
  • lines changed 1, context: html, text, full: html, text
    added missing separator
  • lines changed 1, context: html, text, full: html, text
    removed extra separator
  • lines changed 1, context: html, text, full: html, text
    added line separator back in
  • lines changed 0, context: html, text, full: html, text
    removing trailing white space
  • lines changed 1, context: html, text, full: html, text
    adding wgEncodeUwAffyExonArray.ra back to the makefile so metadata shows on the RR
  • lines changed 1, context: html, text, full: html, text
    oops! Forgot the '.ra' at the end
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeOpenChromDnase.ra
  • lines changed 6656, context: html, text, full: html, text
    releasing Duke DNaseI HS, updated metaDb from alpha, changed link on UNC Faire to not point to preview, redmine #63
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwAffyExonArray.ra
  • lines changed 2650, context: html, text, full: html, text
    removed extra period, http://redmine.soe.ucsc.edu/issues/59#note-38
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    adding netSelf
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    staging Encode Regulation on beta, redmine #3454
  • lines changed 1, context: html, text, full: html, text
    releasing Duke DNaseI HS, updated metaDb from alpha, changed link on UNC Faire to not point to preview, redmine #63
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.new.ra
  • lines changed 426, context: html, text, full: html, text
    Changing long lables to say whole cell instead of cell, to conform to our new sort order, to say sm in the shortLabel
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.html
  • lines changed 109, context: html, text, full: html, text
    Updated Track Description
  • lines changed 109, context: html, text, full: html, text
    Replacing the clobbered old description
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.html
  • lines changed 6, context: html, text, full: html, text
    New description
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.ra
  • lines changed 148, context: html, text, full: html, text
    Ran the renamer to rename all of the files listed in issue 2254. This should be scrutinized.
  • lines changed 36, context: html, text, full: html, text
    More filename changing with the renamer, I also uncommented the attic files to do a test for Galt. They should be recommented soon.
  • lines changed 27, context: html, text, full: html, text
    Recommented out the attic files
  • lines changed 1, context: html, text, full: html, text
    Fixed estradiol
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.ra
  • lines changed 1, context: html, text, full: html, text
    New track description
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.html
  • lines changed 118, context: html, text, full: html, text
    New track description
  • lines changed 10, context: html, text, full: html, text
    Reorder References
  • lines changed 112, context: html, text, full: html, text
    Replacing the clobbered old description
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.new.html
  • lines changed 92, context: html, text, full: html, text
    New description page
  • lines changed 10, context: html, text, full: html, text
    New description
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.ra
  • lines changed 1, context: html, text, full: html, text
    Added new html
  • lines changed 1, context: html, text, full: html, text
    Fixed misspelling of ESTRADIOL
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
  • lines changed 68, context: html, text, full: html, text
    Added missing files, submission 3877.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.html
  • lines changed 2, context: html, text, full: html, text
    fixing release date and added a space, redmine #63
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.html
  • lines changed 2, context: html, text, full: html, text
    releasing Duke DNaseI HS, updated metaDb from alpha, changed link on UNC Faire to not point to preview, redmine #63
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegDnaseClustered.html
  • lines changed 1, context: html, text, full: html, text
    tiny edit to sentence for better readability
  • lines changed 0, context: html, text, full: html, text
    changing 'data set' to 'dataset' for consistency within the page; 'dataset' is the term used in the data release policy on every ENCODE description page
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTfbsClustered.html
  • lines changed 1, context: html, text, full: html, text
    fixing typo: date to data
  • lines changed 0, context: html, text, full: html, text
    changing 'data set' to 'dataset' for consistency within the page; 'dataset' is the term used in the data release policy on every ENCODE description page
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTxn.html
  • lines changed 1, context: html, text, full: html, text
    fixing incorrect sentence
  • lines changed 0, context: html, text, full: html, text
    changing 'data set' to 'dataset' for consistency within the page; 'dataset' is the term used in the data release policy on every ENCODE description page
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.html
  • lines changed 25, context: html, text, full: html, text
    alphabetizing refs and putting period after titles on outside of hyperlink
  • lines changed 6, context: html, text, full: html, text
    grammar and punctuation edits
  • lines changed 6, context: html, text, full: html, text
    changing breaks that weren't working to paragraphs
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.ra
  • lines changed 27, context: html, text, full: html, text
    Changed the origAssembly and greyscale and ripTgtProtien according to issue 37
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyRipSeq.new.html
  • lines changed 136, context: html, text, full: html, text
    Fixed estradiol
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyRipSeq.ra
  • lines changed 1, context: html, text, full: html, text
    Fixed estradiol
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhNsome.html
  • lines changed 79, context: html, text, full: html, text
    New track description
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
  • lines changed 9, context: html, text, full: html, text
    When changing the metaData, file and table names for EBF -> EBF1_(SC-137065), I forgot to add the changes to trackDb file.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.html
  • lines changed 1, context: html, text, full: html, text
    removed a period that Katrina noticed, thought this was checked in already and pushed
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.html
  • lines changed 16, context: html, text, full: html, text
    Added release 2 notes. Also updated windowingFunction from maximum -> mean+whiskers.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.ra
  • lines changed 1, context: html, text, full: html, text
    Added release 2 notes. Also updated windowingFunction from maximum -> mean+whiskers.
• src/hg/makeDb/trackDb/human/iscaRetrospective.html
  • lines changed 123, context: html, text, full: html, text
    checking in tracks description and changing longLabel to match actual (new) name of the consortium
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    checking in tracks description and changing longLabel to match actual (new) name of the consortium
• src/hg/makeDb/trackDb/lizard/anoCar2/description.html
  • lines changed 129, context: html, text, full: html, text
    initial trackDb files for anoCar2
  • lines changed 44, context: html, text, full: html, text
    coming close to final versions of documentation
• src/hg/makeDb/trackDb/lizard/anoCar2/gap.html
  • lines changed 64, context: html, text, full: html, text
    initial trackDb files for anoCar2
  • lines changed 38, context: html, text, full: html, text
    coming close to final versions of documentation
• src/hg/makeDb/trackDb/lizard/anoCar2/gold.html
  • lines changed 23, context: html, text, full: html, text
    initial trackDb files for anoCar2
  • lines changed 12, context: html, text, full: html, text
    coming close to final versions of documentation
• src/hg/makeDb/trackDb/lizard/anoCar2/trackDb.ra
  • lines changed 40, context: html, text, full: html, text
    initial trackDb files for anoCar2
  • lines changed 33, context: html, text, full: html, text
    coming close to final versions of documentation
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding anoCar2
• src/hg/makeDb/trackDb/marmoset/calJac3/cons13way.html
  • lines changed 12, context: html, text, full: html, text
    removing paragraph from calJac3 conservation page that was for human only
  • lines changed 1, context: html, text, full: html, text
    fixing broken link
• src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    adding dog and subtracking chimp from marmoset conservation track default species
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/makefile
  • lines changed 2, context: html, text, full: html, text
    Added meta-data for Sydh RNA-seq in make file so that meta-data would be visible when alpha was made.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
  • lines changed 765, context: html, text, full: html, text
    Added 9 submissions to 2 tracks. Included 5 resubmissions of tracks with updated data(Signals, peaks).
  • lines changed 51, context: html, text, full: html, text
    Removed replicate 3's as adivsed by lab. And updated metaData for Input for TFBS data for resubmitted data.
  • lines changed 313, context: html, text, full: html, text
    Added 3 submissions of lung Tissue data.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
  • lines changed 199, context: html, text, full: html, text
    Added 9 submissions to 2 tracks. Included 5 resubmissions of tracks with updated data(Signals, peaks).
  • lines changed 60, context: html, text, full: html, text
    Removed replicate 3's as adivsed by lab. And updated metaData for Input for TFBS data for resubmitted data.
  • lines changed 313, context: html, text, full: html, text
    Added 2 submissions for the TFBS track.
  • lines changed 157, context: html, text, full: html, text
    Added 3 submissions of lung Tissue data.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhRnaSeq.ra
  • lines changed 125, context: html, text, full: html, text
    Forgot to add the meta-data for the new Sydh RNA-seq track.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 43, context: html, text, full: html, text
    Fixed incorrect lab name for mouse track as Stanford -> Stanford-m
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 101, context: html, text, full: html, text
    Added tissueSourceType meta-data for the UW lab for 20 experiments.
  • lines changed 19, context: html, text, full: html, text
    Updated replicate for T-Naive to be replicate 2. redime #2985
  • lines changed 7, context: html, text, full: html, text
    Updated tissueSourceType for the wgEncodeUwDnaseTnaiveC57bl6MAdult8wks Rep2 experiments.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 4, context: html, text, full: html, text
    Added the first 2 submissions of RNA-seq for Mouse from Stanford/Yale.
  • lines changed 6, context: html, text, full: html, text
    removed release tag alphas in tracks. Also updated spacing of trackDb.ra files to be sperated by tabs and not white spaces.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.ra
  • lines changed 109, context: html, text, full: html, text
    Added 9 submissions to 2 tracks. Included 5 resubmissions of tracks with updated data(Signals, peaks).
  • lines changed 14, context: html, text, full: html, text
    removed release tag alphas in tracks. Also updated spacing of trackDb.ra files to be sperated by tabs and not white spaces.
  • lines changed 37, context: html, text, full: html, text
    Added 3 submissions of lung Tissue data.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.ra
  • lines changed 55, context: html, text, full: html, text
    Added 9 submissions to 2 tracks. Included 5 resubmissions of tracks with updated data(Signals, peaks).
  • lines changed 37, context: html, text, full: html, text
    Added 2 submissions for the TFBS track.
  • lines changed 16, context: html, text, full: html, text
    removed release tag alphas in tracks. Also updated spacing of trackDb.ra files to be sperated by tabs and not white spaces.
  • lines changed 19, context: html, text, full: html, text
    Added 3 submissions of lung Tissue data.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.ra
  • lines changed 12, context: html, text, full: html, text
    removed release tag alphas in tracks. Also updated spacing of trackDb.ra files to be sperated by tabs and not white spaces.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.ra
  • lines changed 16, context: html, text, full: html, text
    removed release tag alphas in tracks. Also updated spacing of trackDb.ra files to be sperated by tabs and not white spaces.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHistone.ra
  • lines changed 9, context: html, text, full: html, text
    removed release tag alphas in tracks. Also updated spacing of trackDb.ra files to be sperated by tabs and not white spaces.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhRnaSeq.ra
  • lines changed 92, context: html, text, full: html, text
    Added the first 2 submissions of RNA-seq for Mouse from Stanford/Yale.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.ra
  • lines changed 100, context: html, text, full: html, text
    removed release tag alphas in tracks. Also updated spacing of trackDb.ra files to be sperated by tabs and not white spaces.
  • lines changed 12, context: html, text, full: html, text
    Updated replicate for T-Naive to be replicate 2. redime #2985
• src/hg/makeDb/trackDb/sheep/oviAri1/description.html
  • lines changed 1, context: html, text, full: html, text
    Fixed two errors in grammar/typing.
  • lines changed 19, context: html, text, full: html, text
    Made a few small edits for grammar/clarity.
• src/hg/makeDb/trackDb/sheep/oviAri1/gap.html
  • lines changed 1, context: html, text, full: html, text
    added a period at the end of one bullet point to be consistent with the others
• src/hg/makeDb/trackDb/worm/ce4/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    add autoTranslate 0 to sangerRnaGene
• src/hg/makeDb/trackDb/worm/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    add search for sangerRnaGene table
• src/hg/makeDb/trackDb/zebrafish/danRer5/trackDb.ra
  • lines changed 26, context: html, text, full: html, text
    Updated U Mass subTracks parameters.
• src/hg/makeDb/trackDbPatch/trackDbPatch.c
  • lines changed 37, context: html, text, full: html, text
    Initial checkin of continuation char support in RA files
• src/hg/utils/automation/makePushQSql.pl
  • lines changed 3, context: html, text, full: html, text
    new column in the pushQ
• src/inc/common.h
  • lines changed 3, context: html, text, full: html, text
    Added routine to find the last non-whitespace char in a string
  • lines changed 1, context: html, text, full: html, text
    Checked in minor changes from Jim's review. Only think of consequence here is the dyStringLen macro had been using strlen, when the stringSize is part of the structure
• src/inc/dystring.h
  • lines changed 1, context: html, text, full: html, text
    Fixed an inefficient macro from long ago. Jim caought this in code review
• src/inc/linefile.h
  • lines changed 16, context: html, text, full: html, text
    Add simple support for reading lines with continuation characters as single lines.
  • lines changed 1, context: html, text, full: html, text
    Checked in minor changes from Jim's review. Only think of consequence here is the dyStringLen macro had been using strlen, when the stringSize is part of the structure
  • lines changed 4, context: html, text, full: html, text
    Streamlined and optimized continuation line code as Jim's suggests this is critical path.
• src/inc/ra.h
  • lines changed 30, context: html, text, full: html, text
    Initial checkin of continuation char support in RA files
  • lines changed 2, context: html, text, full: html, text
    The param should have been TRE=joined
  • lines changed 2, context: html, text, full: html, text
    Checked in minor changes from Jim's review. Only think of consequence here is the dyStringLen macro had been using strlen, when the stringSize is part of the structure
• src/lib/common.c
  • lines changed 15, context: html, text, full: html, text
    Added routine to find the last non-whitespace char in a string
  • lines changed 1, context: html, text, full: html, text
    Checked in minor changes from Jim's review. Only think of consequence here is the dyStringLen macro had been using strlen, when the stringSize is part of the structure
• src/lib/linefile.c
  • lines changed 80, context: html, text, full: html, text
    Add simple support for reading lines with continuation characters as single lines.
  • lines changed 6, context: html, text, full: html, text
    Checked in minor changes from Jim's review. Only think of consequence here is the dyStringLen macro had been using strlen, when the stringSize is part of the structure
  • lines changed 87, context: html, text, full: html, text
    Streamlined and optimized continuation line code as Jim's suggests this is critical path.
• src/lib/net.c
  • lines changed 13, context: html, text, full: html, text
    fixing complaint from Italy mirror that socket is already connected.
• src/lib/ra.c
  • lines changed 174, context: html, text, full: html, text
    Initial checkin of continuation char support in RA files
  • lines changed 7, context: html, text, full: html, text
    Checked in minor changes from Jim's review. Only think of consequence here is the dyStringLen macro had been using strlen, when the stringSize is part of the structure
  • lines changed 90, context: html, text, full: html, text
    Streamlined and optimized continuation line code as Jim's suggests this is critical path.
  • lines changed 2, context: html, text, full: html, text
    Insignificant edit
• src/utils/qa/alertBqueue.csh
  • lines changed 8, context: html, text, full: html, text
    moved an exit statement into bebug. may have fixed donna's email
  • lines changed 1, context: html, text, full: html, text
    dropped donna from routine notification
• src/utils/qa/getChainLines.csh
  • lines changed 1, context: html, text, full: html, text
    Changed usage statement to be slightly more specific.
• src/utils/qa/getMatrixLines.csh
  • lines changed 1, context: html, text, full: html, text
    Changed usage statement to be slightly more specific.
• src/utils/qa/sessionStats.csh
  • lines changed 25, context: html, text, full: html, text
    added support for short version of report
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v250 final build
• src/utils/qa/weeklybld/makeUserApps.csh
  • lines changed 11, context: html, text, full: html, text
    put blat, gfServer, and gfClient in subdirectory with special information about licensing

• lines changed: 19242
• files changed: 254