All File Changes
v270_preview2 to v270_base (2012-07-10 to 2012-07-17) v270
- src/hg/encode/DAFs/3.0/mm9/wgEncodeCshlLongRnaSeq.daf
- lines changed 2, context: html, text, full: html, text
Increaseing to 10 mismatches
- src/hg/encode/encodeQaInit/encodeQaInit
- lines changed 2, context: html, text, full: html, text
made it so that the qa table tests aren't run on an empty table set
- src/hg/encode/validateFiles/validateFiles.c
- lines changed 5, context: html, text, full: html, text
fixing validateFiles bug to support non-tab default fieldCount with chopByWhite that somehow got lost
- src/hg/hgCustom/hgCustom.c
- lines changed 3, context: html, text, full: html, text
fixing simple html table tag errors caught with htmlCheck
- src/hg/hgFileSearch/hgFileSearch.c
- lines changed 2, context: html, text, full: html, text
fixing bug in html output found by htmlCheck
- src/hg/hgGene/hgGeneData/Mouse/mm10/links.ra
- lines changed 9, context: html, text, full: html, text
add some data files for mm10 UCSC genes (#7045)
- lines changed 8, context: html, text, full: html, text
comment out ExonPrimer for the moment (#7045)
- src/hg/hgGene/hgGeneData/Mouse/mm10/otherOrgs.ra
- lines changed 17, context: html, text, full: html, text
add some data files for mm10 UCSC genes (#7045)
- src/hg/hgHubConnect/hgHubConnect.c
- lines changed 17, context: html, text, full: html, text
fixed html error found by htmlCheck; added some newlines to make show source more legible
- src/hg/hgLiftOver/hgLiftOver.c
- lines changed 1, context: html, text, full: html, text
fix html error in hgLiftOver found by htmlCheck
- src/hg/hgTables/bedList.c
- lines changed 11, context: html, text, full: html, text
Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
- src/hg/hgTables/correlate.c
- lines changed 4, context: html, text, full: html, text
Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
- src/hg/hgTables/filterFields.c
- lines changed 6, context: html, text, full: html, text
Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
- src/hg/hgTables/hgTables.c
- lines changed 2, context: html, text, full: html, text
Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
- src/hg/hgTables/mainPage.c
- lines changed 40, context: html, text, full: html, text
Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
- src/hg/hgTables/schema.c
- lines changed 6, context: html, text, full: html, text
Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
- src/hg/hgTrackUi/encodePeakUi.c
- lines changed 0, context: html, text, full: html, text
Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
- src/hg/hgTrackUi/hgTrackUi.c
- lines changed 2, context: html, text, full: html, text
Just removed old ifdef SUBTRACK_CFG. That feature released for 6 months. Not going back.
- lines changed 66, context: html, text, full: html, text
Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
- src/hg/hgTracks/chromGraphTrack.c
- lines changed 2, context: html, text, full: html, text
Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
- src/hg/hgTracks/config.c
- lines changed 27, context: html, text, full: html, text
Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
- src/hg/hgTracks/encode.c
- lines changed 0, context: html, text, full: html, text
Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
- src/hg/hgTracks/expRatioTracks.c
- lines changed 10, context: html, text, full: html, text
Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
- src/hg/hgTracks/hgTracks.c
- lines changed 188, context: html, text, full: html, text
Maybe last batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes (mostly) limited to lines last touched by tdreszer (git blame) so as not to ruin history. Some things not mine were 'fixed' so that my changes were in context. None of these changes should affect executables in any way.
- src/hg/hgTracks/hgTracks.h
- lines changed 13, context: html, text, full: html, text
Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
- src/hg/hgTracks/imageV2.c
- lines changed 259, context: html, text, full: html, text
Maybe last batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes (mostly) limited to lines last touched by tdreszer (git blame) so as not to ruin history. Some things not mine were 'fixed' so that my changes were in context. None of these changes should affect executables in any way.
- src/hg/hgTracks/imageV2.h
- lines changed 190, context: html, text, full: html, text
Maybe last batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes (mostly) limited to lines last touched by tdreszer (git blame) so as not to ruin history. Some things not mine were 'fixed' so that my changes were in context. None of these changes should affect executables in any way.
- src/hg/hgTracks/mainMain.c
- lines changed 1, context: html, text, full: html, text
Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
- src/hg/hgTracks/oneTrack.c
- lines changed 0, context: html, text, full: html, text
Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
- src/hg/hgTracks/rnaFoldTrack.c
- lines changed 0, context: html, text, full: html, text
Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
- src/hg/hgTracks/searchTracks.c
- lines changed 130, context: html, text, full: html, text
Maybe last batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes (mostly) limited to lines last touched by tdreszer (git blame) so as not to ruin history. Some things not mine were 'fixed' so that my changes were in context. None of these changes should affect executables in any way.
- src/hg/hgTracks/simpleTracks.c
- lines changed 6, context: html, text, full: html, text
Just removed old ifdef SUBTRACK_CFG. That feature released for 6 months. Not going back.
- lines changed 93, context: html, text, full: html, text
Maybe last batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes (mostly) limited to lines last touched by tdreszer (git blame) so as not to ruin history. Some things not mine were 'fixed' so that my changes were in context. None of these changes should affect executables in any way.
- src/hg/hgTracks/variation.c
- lines changed 4, context: html, text, full: html, text
Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
- src/hg/hgTracks/wigMafTrack.c
- lines changed 8, context: html, text, full: html, text
Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
- src/hg/hgTracks/wigTrack.c
- lines changed 1, context: html, text, full: html, text
Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
- src/hg/hgVarAnnogrator/hgVarAnnogrator.c
- lines changed 3, context: html, text, full: html, text
Deal with cryptic (to say it politely) IE8 behavior (for #6152).
- src/hg/hgc/hgc.c
- lines changed 128, context: html, text, full: html, text
Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
- src/hg/hgc/lowelab.c
- lines changed 16, context: html, text, full: html, text
Format changes as dictated by Jim. Formatting lines to 100 chars. Only touching lines git blames on 'tdreszer'. Because most of file has formatting differences from kent style, changes here conform to the local style. These changes should affect executable in any way.
- src/hg/hgc/mafClick.c
- lines changed 6, context: html, text, full: html, text
Next batch of many checkins as dictated by Jim. Formatting if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. None of these changes should affect executables in any way.
- src/hg/htdocs/ENCODE/dataStandards.html
- lines changed 2, context: html, text, full: html, text
Add News and menu highlights for Quality Metrics page on portal
- src/hg/htdocs/ENCODE/downloads.html
- lines changed 1, context: html, text, full: html, text
Changed '7' to '9' in title of Regulation Transcription track (redmine #7990)
- src/hg/htdocs/ENCODE/downloadsMouse.html
- lines changed 4, context: html, text, full: html, text
Added line for UW RNA-seq (redmine #4469)
- src/hg/htdocs/ENCODE/index.html
- lines changed 19, context: html, text, full: html, text
Add News and menu highlights for Quality Metrics page on portal
- lines changed 3, context: html, text, full: html, text
Made some corrections to Kate's additions (redmine #7780)
- src/hg/htdocs/ENCODE/qualityMetrics.html
- lines changed 1, context: html, text, full: html, text
Made some corrections to Kate's additions (redmine #7780)
- src/hg/htdocs/FAQ/FAQreleases.html
- lines changed 1, context: html, text, full: html, text
added sarHar1 release info
- src/hg/htdocs/goldenPath/credits.html
- lines changed 58, context: html, text, full: html, text
added tasmanina devil credits
- src/hg/htdocs/goldenPath/newsarch.html
- lines changed 35, context: html, text, full: html, text
Added new sarHar1 announcement
- lines changed 1, context: html, text, full: html, text
fixed a typo and added a space
- lines changed 1, context: html, text, full: html, text
corrected name attribute for hgText announcement
- src/hg/htdocs/images/Trichechus_manatus_latirostris.jpg
- lines changed 0, context: html, text, full: html, text
Bob's photograph for Trichechus_manatus
- src/hg/htdocs/images/Vicugna_pacos.png
- lines changed 0, context: html, text, full: html, text
WUSTL says this photo is from USDA - can not find at USDA
- src/hg/htdocs/indexNews.html
- lines changed 140, context: html, text, full: html, text
Added sarHar1 announcement
- src/hg/inc/hui.h
- lines changed 109, context: html, text, full: html, text
Next batch of many checkins as dictated by Jim. Formatting space after if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. This checkin also includes removal of SUBTRACK_CFG ifdefs, and a bug fix for downloads link.
- src/hg/inc/mafGene.h
- lines changed 1, context: html, text, full: html, text
Added support for option to add UTR.
- src/hg/inc/versionInfo.h
- src/hg/js/hgVarAnnogrator.js
- lines changed 2, context: html, text, full: html, text
Deal with cryptic (to say it politely) IE8 behavior (for #6152).
- src/hg/lib/hui.c
- lines changed 1044, context: html, text, full: html, text
Next batch of many checkins as dictated by Jim. Formatting space after if and limiting lines to 100 chars. Changes limited to lines last touched by tdreszer (git blame) so as not to ruin history. This checkin also includes removal of SUBTRACK_CFG ifdefs, and a bug fix for downloads link.
- src/hg/lib/mafGene.c
- lines changed 18, context: html, text, full: html, text
Added code so that if the utr option is set, then alignments are retrieved for all exons not just the CDS region.
- src/hg/lib/pal.c
- lines changed 3, context: html, text, full: html, text
fix simple html error in pal.c found by htmlCheck
- src/hg/lib/web.c
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeUchicagoTfbs.release2.notes
- lines changed 420, context: html, text, full: html, text
Adding a notes files for UChicago
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeUncBsuProt.release2.notes
- lines changed 106, context: html, text, full: html, text
creating the notes file
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwAffyExonArray.release3.notes
- lines changed 429, context: html, text, full: html, text
Preparing for pushQ, adding expIds, notes file, fixing names in the downloads files
- src/hg/makeDb/doc/gorGor3.txt
- lines changed 19, context: html, text, full: html, text
Finished LASTZ rheMac3 vw hg19, gorGor3, ponAbe2.
- src/hg/makeDb/doc/hg19.txt
- lines changed 402, context: html, text, full: html, text
Track #8360 (snp137): after the usual slog through slightly changingformats and contents, snp137 and its auxiliary tables are here!
- lines changed 65, context: html, text, full: html, text
Finished LASTZ rheMac3 vw hg19, gorGor3, ponAbe2.
- src/hg/makeDb/doc/ponAbe2.txt
- lines changed 19, context: html, text, full: html, text
Finished LASTZ rheMac3 vw hg19, gorGor3, ponAbe2.
- src/hg/makeDb/doc/rheMac3.txt
- lines changed 125, context: html, text, full: html, text
Finished LASTZ rheMac3 vw hg19, gorGor3, ponAbe2.
- src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes13.csh
- lines changed 11, context: html, text, full: html, text
more work on mm10 UCSC genes
- src/hg/makeDb/genbank/etc/hgwbeta.dbs
- lines changed 1, context: html, text, full: html, text
Adding sacCer1 updates again. The assembly is not being archived, by popular demand.
- src/hg/makeDb/genbank/etc/rr.dbs
- lines changed 1, context: html, text, full: html, text
Adding sacCer1 updates again. The assembly is not being archived, by popular demand.
- src/hg/makeDb/schema/all.joiner
- lines changed 4, context: html, text, full: html, text
add ce10 and dm3 to Human Protein key checks
- lines changed 19, context: html, text, full: html, text
Track #8360 (snp137): added to trackDb, all.joiner.
- src/hg/makeDb/trackDb/alpaca/vicPac1/description.html
- lines changed 116, context: html, text, full: html, text
minimal page from makeGenomeDb.pl
- src/hg/makeDb/trackDb/baboon/papHam1/description.html
- lines changed 118, context: html, text, full: html, text
minimal page from makeGenomeDb.pl
- src/hg/makeDb/trackDb/cat/felCat5/gap.html
- lines changed 31, context: html, text, full: html, text
gold and gap pages from the new template procedure in makeGenomeDb.pl
- lines changed 4, context: html, text, full: html, text
add link to NCBI assembly specifics
- lines changed 9, context: html, text, full: html, text
clean up text due to review comments
- lines changed 2, context: html, text, full: html, text
calrify link to NCBI assembly information
- src/hg/makeDb/trackDb/cat/felCat5/gold.html
- lines changed 33, context: html, text, full: html, text
gold and gap pages from the new template procedure in makeGenomeDb.pl
- lines changed 4, context: html, text, full: html, text
add link to NCBI assembly specifics
- lines changed 5, context: html, text, full: html, text
clean up text due to review comments
- lines changed 2, context: html, text, full: html, text
calrify link to NCBI assembly information
- src/hg/makeDb/trackDb/cat/felCat5/trackDb.ra
- lines changed 8, context: html, text, full: html, text
gold and gap pages from the new template procedure in makeGenomeDb.pl
- src/hg/makeDb/trackDb/chimp/panTro4/gap.html
- lines changed 61, context: html, text, full: html, text
add link to NCBI assembly specifics
- lines changed 11, context: html, text, full: html, text
clean up text due to review comments
- lines changed 2, context: html, text, full: html, text
calrify link to NCBI assembly information
- src/hg/makeDb/trackDb/chimp/panTro4/gold.html
- lines changed 21, context: html, text, full: html, text
add link to NCBI assembly specifics
- lines changed 4, context: html, text, full: html, text
clean up text due to review comments
- lines changed 2, context: html, text, full: html, text
calrify link to NCBI assembly information
- src/hg/makeDb/trackDb/chimp/trackDb.chainNet.ra
- lines changed 5, context: html, text, full: html, text
Finish build chaniNet track for rheMac3.
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 17, context: html, text, full: html, text
Adding endometrium cell type to CV
- lines changed 48, context: html, text, full: html, text
Adding bone marrow cell types to CV
- lines changed 2, context: html, text, full: html, text
Fixed description of C57BL/6J and spelling of donor, found by Kate.
- lines changed 30, context: html, text, full: html, text
Adding open chromatin cell type termId and termUrl to CV
- src/hg/makeDb/trackDb/cv/beta/cv.ra
- lines changed 809, context: html, text, full: html, text
Copying alpha CV to beta
- src/hg/makeDb/trackDb/dog/trackDb.chainNet.ra
- lines changed 1, context: html, text, full: html, text
Cow bosTau7 vs canFam2, hg19, mm10, mo,Dom5 and ornAna1 chain/Net.
- src/hg/makeDb/trackDb/dolphin/turTru2/description.html
- lines changed 117, context: html, text, full: html, text
minimal page from makeGenomeDb.pl
- src/hg/makeDb/trackDb/drosophila/dm3/trackDb.ra
- lines changed 3, context: html, text, full: html, text
Changed Human Proteins tracks default visbility to hide for dm3 and ce10.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUchicagoTfbs.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra
- lines changed 57, context: html, text, full: html, text
remove datasets using the new database search scheme, they have been unloaded and loaded for displaying in a new track
- lines changed 15, context: html, text, full: html, text
change SDS-Page to In-gel
- lines changed 3, context: html, text, full: html, text
update after expId change, see note 93, 97, 98
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwAffyExonArray.ra
- lines changed 321, context: html, text, full: html, text
Adding new data in, changing the matrix around a little bit
- lines changed 53, context: html, text, full: html, text
Preparing for pushQ, adding expIds, notes file, fixing names in the downloads files
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
- lines changed 1735, context: html, text, full: html, text
added in enw data tracks
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
- lines changed 3, context: html, text, full: html, text
Cricket reorganized the structure of wgEncodeReg.ra by breaking it up into three separate files as it should be. Also updated the makefiles. (redmine #7990)
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeReg.ra
- lines changed 295, context: html, text, full: html, text
Cricket reorganized the structure of wgEncodeReg.ra by breaking it up into three separate files as it should be. Also updated the makefiles. (redmine #7990)
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeRegDnaseClustered.ra
- lines changed 37, context: html, text, full: html, text
Cricket reorganized the structure of wgEncodeReg.ra by breaking it up into three separate files as it should be. Also updated the makefiles. (redmine #7990)
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeRegTfbsClustered.ra
- lines changed 53, context: html, text, full: html, text
Cricket reorganized the structure of wgEncodeReg.ra by breaking it up into three separate files as it should be. Also updated the makefiles. (redmine #7990)
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeRegTxn.ra
- lines changed 211, context: html, text, full: html, text
Cricket reorganized the structure of wgEncodeReg.ra by breaking it up into three separate files as it should be. Also updated the makefiles. (redmine #7990)
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUchicagoTfbs.ra
- lines changed 2856, context: html, text, full: html, text
Staging UChicago TFBS (Release 2) on beta (redmine #5697)
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwAffyExonArray.ra
- lines changed 369, context: html, text, full: html, text
Staging on beta Univ Wash Affymetrix Exon Array (Release 3) RM#6777
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
- lines changed 3, context: html, text, full: html, text
Cricket reorganized the structure of wgEncodeReg.ra by breaking it up into three separate files as it should be. Also updated the makefiles. (redmine #7990)
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeReg.ra
- lines changed 295, context: html, text, full: html, text
Cricket reorganized the structure of wgEncodeReg.ra by breaking it up into three separate files as it should be. Also updated the makefiles. (redmine #7990)
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeRegDnaseClustered.ra
- lines changed 37, context: html, text, full: html, text
Cricket reorganized the structure of wgEncodeReg.ra by breaking it up into three separate files as it should be. Also updated the makefiles. (redmine #7990)
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeRegTfbsClustered.ra
- lines changed 53, context: html, text, full: html, text
Cricket reorganized the structure of wgEncodeReg.ra by breaking it up into three separate files as it should be. Also updated the makefiles. (redmine #7990)
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeRegTxn.ra
- lines changed 211, context: html, text, full: html, text
Cricket reorganized the structure of wgEncodeReg.ra by breaking it up into three separate files as it should be. Also updated the makefiles. (redmine #7990)
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeUwAffyExonArray.ra
- lines changed 369, context: html, text, full: html, text
Staging on public Univ Wash Affy Exon Array (Release 3) RM# 6777
- src/hg/makeDb/trackDb/human/hg19/snp137.html
- lines changed 36, context: html, text, full: html, text
Track #8360 (snp137): added to trackDb, all.joiner.
- src/hg/makeDb/trackDb/human/hg19/snp137.shared.html
- lines changed 366, context: html, text, full: html, text
Track #8360 (snp137): added to trackDb, all.joiner.
- src/hg/makeDb/trackDb/human/hg19/snp137Common.html
- lines changed 28, context: html, text, full: html, text
Track #8360 (snp137): added to trackDb, all.joiner.
- src/hg/makeDb/trackDb/human/hg19/snp137Flagged.html
- lines changed 29, context: html, text, full: html, text
Track #8360 (snp137): added to trackDb, all.joiner.
- src/hg/makeDb/trackDb/human/hg19/snp137Mult.html
- lines changed 25, context: html, text, full: html, text
Track #8360 (snp137): added to trackDb, all.joiner.
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 90, context: html, text, full: html, text
Track #8360 (snp137): added to trackDb, all.joiner.
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- lines changed 2, context: html, text, full: html, text
Releasing UCSC Regulation Transcription Track (Release 3) to the RR (redmine #7990)
- lines changed 2, context: html, text, full: html, text
Adding release 2 of FSU RepliChip
- lines changed 2, context: html, text, full: html, text
Removing patch file, not sure what the goal was with this pathch
- lines changed 2, context: html, text, full: html, text
Staging on beta Univ Wash Affymetrix Exon Array (Release 3) RM#6777
- lines changed 2, context: html, text, full: html, text
Staging on public Univ Wash Affy Exon Array (Release 3) RM# 6777
- lines changed 2, context: html, text, full: html, text
Staging UChicago TFBS (Release 2) on beta (redmine #5697)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.release3.ra
- lines changed 473, context: html, text, full: html, text
Changing the cell tags to promot tiers and to fix numeric tags
- src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHmm.ra
- lines changed 10, context: html, text, full: html, text
Tag changes only, no visible changes
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.release3.ra
- lines changed 1, context: html, text, full: html, text
removing from the super track
- src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliChip.release2.html
- lines changed 150, context: html, text, full: html, text
Adding release 2 of FSU RepliChip
- src/hg/makeDb/trackDb/human/hg19/wgEncodeFsuRepliChip.release2.ra
- lines changed 105, context: html, text, full: html, text
Adding release 2 of FSU RepliChip
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.ra
- lines changed 31, context: html, text, full: html, text
Promoting Tier 2 and cell line tag changes
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisDnaPet.ra
- lines changed 8, context: html, text, full: html, text
Fixing the numeric tags and adding Tier 1 label
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaSeq.ra
- lines changed 17, context: html, text, full: html, text
Changing cell labels and view labels, should be no visible change
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.patch.ra
- lines changed 870, context: html, text, full: html, text
Removing patch file, not sure what the goal was with this pathch
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.ra
- lines changed 25, context: html, text, full: html, text
Tag change, no visible change
- lines changed 3, context: html, text, full: html, text
Adding the hyphens for H1-hesc
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyTiling.ra
- lines changed 9, context: html, text, full: html, text
Fixing the numeric tags and adding Tier 1 label
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyRipSeq.ra
- lines changed 39, context: html, text, full: html, text
Fixing the numeric tags and adding Tier 1 label
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.release2.html
- lines changed 155, context: html, text, full: html, text
Made various corrections to the description page. Added links for Bowtie, SPP and MACS. Added the reference paper for SPP to the References section. (redmine #5697)
- lines changed 5, context: html, text, full: html, text
Made some additional changes (redmine #5697)
- lines changed 4, context: html, text, full: html, text
Made yet more corrections (redmine #5697)
- lines changed 4, context: html, text, full: html, text
Changing the long and short labels, the defaults and adding the release notes
- lines changed 6, context: html, text, full: html, text
Edited the Release Notes section (redmine #5697)
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.release2.ra
- lines changed 141, context: html, text, full: html, text
Answering ticket #5697Specifially, the long and short labels and
1. In the track controls, Peaks are set to dense, but they should be set to pack.
2. There is a cell line listed as "NCOR1", but the Input for it lists "COR1" in the matrix and in the Factor column below the matrix.
3. In hgTrackUi, when sorting by the Replicated column, "Pooled" shows up before 1 and 2. It seems like "Pooled" should show up after 1 and 2.
- lines changed 147, context: html, text, full: html, text
Changing the long and short labels, the defaults and adding the release notes
- lines changed 13, context: html, text, full: html, text
Changed the way Inputs appeared in the matrix
- lines changed 54, context: html, text, full: html, text
Changed the short labels to add Sg and Pk
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.html
- lines changed 18, context: html, text, full: html, text
added release note, reformatted the references, updated data release policy
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.release2.ra
- lines changed 33, context: html, text, full: html, text
remove datasets using the new database search scheme, they have been unloaded and loaded for displaying in a new track
- lines changed 9, context: html, text, full: html, text
add Hg19 to title and long labels
- lines changed 2, context: html, text, full: html, text
remove protocol column from sorting list
- lines changed 1, context: html, text, full: html, text
add protocol back to file sortlist
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProtGenc.release1.ra
- lines changed 1, context: html, text, full: html, text
specify database search of hg19 and GENCODE V11 in the title
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.release3.html
- lines changed 98, context: html, text, full: html, text
Trying to work on the html changes for Brian in ticket #6777
- lines changed 3, context: html, text, full: html, text
Changing Methods line for Univ Wash Affy Exon Array (Release 3) RM# 6777
- lines changed 2, context: html, text, full: html, text
Add protocol information under Description and Methods for Univ Wash Affy Exon Array (Release 3) RM#6777
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.release3.ra
- lines changed 267, context: html, text, full: html, text
Adding new data in, changing the matrix around a little bit
- lines changed 1, context: html, text, full: html, text
Trying to work on the html changes for Brian in ticket #6777
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.release6.ra
- lines changed 461, context: html, text, full: html, text
added in enw data tracks
- src/hg/makeDb/trackDb/human/trackDb.chainNet.ra
- lines changed 6, context: html, text, full: html, text
Finish build chaniNet track for rheMac3.
- lines changed 5, context: html, text, full: html, text
Cow bosTau7 vs canFam2, hg19, mm10, mo,Dom5 and ornAna1 chain/Net.
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 95, context: html, text, full: html, text
Cleanup: remove trackDb def's for long-gone experiment.
- src/hg/makeDb/trackDb/manatee/triMan1/description.html
- lines changed 118, context: html, text, full: html, text
minimal page from makeGenomeDb.pl
- src/hg/makeDb/trackDb/moleRat/hetGla1/description.html
- lines changed 127, context: html, text, full: html, text
minimal page from makeGenomeDb.pl
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/makefile
- lines changed 1, context: html, text, full: html, text
Releasing UW RNA-Seq (Release 1) to the RR (redmine #4469)
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeUwRnaSeq.ra
- lines changed 6123, context: html, text, full: html, text
Releasing UW RNA-Seq (Release 1) to the RR (redmine #4469)
- src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
- lines changed 1, context: html, text, full: html, text
Releasing UW RNA-Seq (Release 1) to the RR (redmine #4469)
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwRnaSeq.ra
- lines changed 9, context: html, text, full: html, text
remove 1 from ACel416B in subGroups and all the stanzas
- src/hg/makeDb/trackDb/mouse/trackDb.chainNet.ra
- lines changed 6, context: html, text, full: html, text
Cow bosTau7 vs canFam2, hg19, mm10, mo,Dom5 and ornAna1 chain/Net.
- src/hg/makeDb/trackDb/mouseLemur/micMur1/gap.html
- lines changed 60, context: html, text, full: html, text
new style automatic generated page from makeGenomeDb.pl
- lines changed 4, context: html, text, full: html, text
add link to NCBI assembly specifics
- lines changed 6, context: html, text, full: html, text
clean up text due to review comments
- lines changed 2, context: html, text, full: html, text
calrify link to NCBI assembly information
- src/hg/makeDb/trackDb/mouseLemur/micMur1/gold.html
- lines changed 19, context: html, text, full: html, text
new style automatic generated page from makeGenomeDb.pl
- lines changed 4, context: html, text, full: html, text
add link to NCBI assembly specifics
- lines changed 5, context: html, text, full: html, text
clean up text due to review comments
- lines changed 2, context: html, text, full: html, text
calrify link to NCBI assembly information
- src/hg/makeDb/trackDb/opossum/monDom5/trackDb.chainNet.ra
- lines changed 1, context: html, text, full: html, text
Cow bosTau7 vs canFam2, hg19, mm10, mo,Dom5 and ornAna1 chain/Net.
- src/hg/makeDb/trackDb/orangutan/trackDb.chainNet.ra
- lines changed 3, context: html, text, full: html, text
Finish build chaniNet track for rheMac3.
- src/hg/makeDb/trackDb/pig/susScr3/description.html
- lines changed 119, context: html, text, full: html, text
minimal page from makeGenomeDb.pl
- src/hg/makeDb/trackDb/platypus/trackDb.chainNet.ra
- lines changed 1, context: html, text, full: html, text
Cow bosTau7 vs canFam2, hg19, mm10, mo,Dom5 and ornAna1 chain/Net.
- src/hg/makeDb/trackDb/squirrel/speTri2/description.html
- lines changed 120, context: html, text, full: html, text
minimal page from makeGenomeDb.pl
- src/hg/makeDb/trackDb/trackDb.chainNet.ra
- lines changed 51, context: html, text, full: html, text
Add rheMac3 to trackDb.chainNet.ra.
- src/hg/makeDb/trackDb/worm/ce10/trackDb.ra
- lines changed 3, context: html, text, full: html, text
Changed Human Proteins tracks default visbility to hide for dm3 and ce10.
- src/hg/ratStuff/mafGene/mafGene.c
- lines changed 21, context: html, text, full: html, text
Added option and support for using a genePred file as input instead of a genePred table.
- lines changed 9, context: html, text, full: html, text
Added -utr option so that alignments can be retrieved for all exons not just the CDS region. Abort if the noTrans option is not used with the utr option.
- src/hg/snp/snpLoad/snpNcbiToUcsc.c
- lines changed 67, context: html, text, full: html, text
Track #8360 (snp137): after the usual slog through slightly changingformats and contents, snp137 and its auxiliary tables are here!
- src/hg/utils/automation/EnsGeneAutomate.pm
- lines changed 188, context: html, text, full: html, text
Set parameters for ensGene 67 update.
- src/hg/utils/automation/HgAutomate.pm
- lines changed 2, context: html, text, full: html, text
restore memk to potential cluster list
- src/hg/utils/automation/configFiles/hetGla2.config.ra
- lines changed 24, context: html, text, full: html, text
up to date with required parameters
- src/hg/utils/automation/configFiles/speTri2.config.ra
- lines changed 22, context: html, text, full: html, text
up to date with required parameters
- src/hg/utils/automation/configFiles/susScr3.config.ra
- lines changed 29, context: html, text, full: html, text
up to date with required parameters
- src/hg/utils/automation/configFiles/triMan1.config.ra
- lines changed 23, context: html, text, full: html, text
up to date with required parameters
- src/hg/utils/automation/configFiles/turTru2.config.ra
- lines changed 24, context: html, text, full: html, text
up to date with required parameters
- src/hg/utils/automation/configFiles/vicPac1.config.ra
- lines changed 23, context: html, text, full: html, text
up to date with required parameters
- src/hg/utils/automation/doDbSnp.pl
- lines changed 12, context: html, text, full: html, text
Track #8360 (snp137): after the usual slog through slightly changingformats and contents, snp137 and its auxiliary tables are here!
- src/hg/utils/automation/makeGenomeDb.pl
- lines changed 57, context: html, text, full: html, text
update the gold.html to a generic page with external references
- lines changed 103, context: html, text, full: html, text
now constructing the gap description page
- lines changed 3, context: html, text, full: html, text
update gap page count size format
- lines changed 6, context: html, text, full: html, text
add link to NCBI assembly information
- lines changed 14, context: html, text, full: html, text
cleaning up the text for gold and gap pages
- lines changed 4, context: html, text, full: html, text
clarify link to NCBI assembly information for gold and gap pages
- src/hg/utils/automation/snpAddTGPAlleleFreq.pl
- lines changed 14, context: html, text, full: html, text
Track #8360 (snp137): after the usual slog through slightly changingformats and contents, snp137 and its auxiliary tables are here!
- src/hg/utils/automation/synBlastp.csh
- lines changed 12, context: html, text, full: html, text
allow synBlastp.csh to use something other than knownGene for gene table (part of UCSC gene pipeline)
- src/hg/visiGene/hgVisiGene/hgVisiGene.c
- lines changed 1, context: html, text, full: html, text
removing simple html error in hgVisiGene found by htmlCheck
- src/lib/common.c
- lines changed 7, context: html, text, full: html, text
fixing subtle problem with tabs and empty strings in b2bb input parsing
- src/lib/htmlPage.c
- lines changed 3, context: html, text, full: html, text
adding an exception for hidden db value outside form - argument has been made that such use is legal, and we cannot use htmlPage very well without it
- lines changed 7, context: html, text, full: html, text
adding some more chars to the list of those legal in urls
- src/utils/bedToBigBed/bedToBigBed.c
- lines changed 2, context: html, text, full: html, text
fixing subtle problem with tabs and empty strings in b2bb input parsing
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed: 24466
- files changed: 239