All File Changes
v252_preview to v252_preview2 (2011-05-17 to 2011-05-31) v252
- python/ucscgenomics/rafile/RaFile.py
- lines changed 5, context: html, text, full: html, text
updated Cv suite with unittest
- python/ucscgenomics/rafile/cv/CvFile.py
- lines changed 505, context: html, text, full: html, text
Finished first version of validation script
- lines changed 8, context: html, text, full: html, text
moved error list to validate script, still only gets first error in each stanza
- lines changed 63, context: html, text, full: html, text
updated Cv suite with unittest
- lines changed 2, context: html, text, full: html, text
public build pushed to master
- python/ucscgenomics/rafile/cv/CvRaFile.py
- lines changed 93, context: html, text, full: html, text
moved error list to validate script, still only gets first error in each stanza
- python/ucscgenomics/rafile/cv/CvRaFile.pyc
- lines changed 0, context: html, text, full: html, text
moved error list to validate script, still only gets first error in each stanza
- python/ucscgenomics/rafile/cv/cvPseudo
- lines changed 18, context: html, text, full: html, text
Finished first version of validation script
- python/ucscgenomics/rafile/cv/cvValidate.py
- lines changed 81, context: html, text, full: html, text
moved error list to validate script, still only gets first error in each stanza
- python/ucscgenomics/rafile/cv/cvValidate.pyc
- lines changed 0, context: html, text, full: html, text
moved error list to validate script, still only gets first error in each stanza
- python/ucscgenomics/rafile/cv/test.py
- lines changed 5, context: html, text, full: html, text
Finished first version of validation script
- python/ucscgenomics/rafile/cv/unittest/input/Antibody/BlankKey.ra
- lines changed 25, context: html, text, full: html, text
updated Cv suite with unittest
- python/ucscgenomics/rafile/cv/unittest/input/Antibody/ExtraKey.ra
- lines changed 26, context: html, text, full: html, text
updated Cv suite with unittest
- python/ucscgenomics/rafile/cv/unittest/input/Antibody/MissingKey.ra
- lines changed 24, context: html, text, full: html, text
updated Cv suite with unittest
- python/ucscgenomics/rafile/cv/unittest/input/Antibody/NonmatchKey.ra
- lines changed 25, context: html, text, full: html, text
updated Cv suite with unittest
- python/ucscgenomics/rafile/cv/unittest/input/Antibody/ValidStanza.ra
- lines changed 25, context: html, text, full: html, text
updated Cv suite with unittest
- python/ucscgenomics/rafile/cv/unittest/input/CellLine/BlankKey.ra
- lines changed 34, context: html, text, full: html, text
updated Cv suite with unittest
- python/ucscgenomics/rafile/cv/unittest/input/CellLine/ExtraKey.ra
- lines changed 35, context: html, text, full: html, text
updated Cv suite with unittest
- python/ucscgenomics/rafile/cv/unittest/input/CellLine/MissingKey.ra
- lines changed 33, context: html, text, full: html, text
updated Cv suite with unittest
- python/ucscgenomics/rafile/cv/unittest/input/CellLine/NonmatchKey.ra
- lines changed 34, context: html, text, full: html, text
updated Cv suite with unittest
- python/ucscgenomics/rafile/cv/unittest/input/CellLine/ValidStanza.ra
- lines changed 33, context: html, text, full: html, text
updated Cv suite with unittest
- python/ucscgenomics/rafile/cv/unittest/input/Mouse/BlankKey.ra
- lines changed 37, context: html, text, full: html, text
updated Cv suite with unittest
- python/ucscgenomics/rafile/cv/unittest/input/Mouse/ExtraKey.ra
- lines changed 38, context: html, text, full: html, text
updated Cv suite with unittest
- python/ucscgenomics/rafile/cv/unittest/input/Mouse/MissingKey.ra
- lines changed 36, context: html, text, full: html, text
updated Cv suite with unittest
- python/ucscgenomics/rafile/cv/unittest/input/Mouse/NonmatchKey.ra
- lines changed 37, context: html, text, full: html, text
updated Cv suite with unittest
- python/ucscgenomics/rafile/cv/unittest/input/Mouse/ValidStanza.ra
- lines changed 37, context: html, text, full: html, text
updated Cv suite with unittest
- python/ucscgenomics/rafile/cv/unittest/testCvFile
- lines changed 95, context: html, text, full: html, text
updated Cv suite with unittest
- python/ucscgenomics/rafile/cv/validate
- lines changed 7, context: html, text, full: html, text
Finished first version of validation script
- lines changed 10, context: html, text, full: html, text
moved error list to validate script, still only gets first error in each stanza
- lines changed 23, context: html, text, full: html, text
updated Cv suite with unittest
- python/ucscgenomics/rafile/cv/validatescript.py
- lines changed 4, context: html, text, full: html, text
Finished first version of validation script
- src/hg/cartDump/cartDump.c
- lines changed 1, context: html, text, full: html, text
changing uses of cgiServerName to better cgiServerNamePort
- src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
- lines changed 23, context: html, text, full: html, text
Made -redirect an option not the default. Made -db=hg19 the default. Reorganized usage page to bring most used options to the top.
- src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes
- lines changed 1, context: html, text, full: html, text
Added peptideMapping to the list of expected types
- src/hg/encode/validateCv/validateCv.c
- lines changed 295, context: html, text, full: html, text
A validator for cv.ra, but it turns out there is a python version already. Hopefully the two are not entire duplicates.
- lines changed 47, context: html, text, full: html, text
Made 'must haves' visible when validating a single type of term.
- src/hg/encode/validateFiles/validateFiles.c
- lines changed 1, context: html, text, full: html, text
allow the dash character in csqual strings.
- src/hg/hgGene/hgGene.c
- lines changed 1, context: html, text, full: html, text
remove pseudogene from hgGene details page
- src/hg/hgGene/hgGeneData/section.ra
- lines changed 6, context: html, text, full: html, text
retro track changes to add ucscRetroOrtho table and hgc, hgTrackUI changes.
- lines changed 1, context: html, text, full: html, text
restore accidental deletion of name pathways
- src/hg/hgGene/pseudoGene.c
- lines changed 33, context: html, text, full: html, text
retro track changes to add ucscRetroOrtho table and hgc, hgTrackUI changes.
- src/hg/hgHubConnect/hgHubConnect.c
- lines changed 220, context: html, text, full: html, text
move hub connection stuff into hg/lib so hgTracks can add hubs on its own
- lines changed 3, context: html, text, full: html, text
add some printf's for hub clear
- src/hg/hgSession/hgSession.c
- lines changed 4, context: html, text, full: html, text
changing uses of cgiServerName to better cgiServerNamePort
- src/hg/hgTables/galaxy.c
- lines changed 1, context: html, text, full: html, text
changing uses of cgiServerName to better cgiServerNamePort
- src/hg/hgTables/great.c
- lines changed 1, context: html, text, full: html, text
changing uses of cgiServerName to better cgiServerNamePort
- src/hg/hgTables/hgTables.c
- lines changed 1, context: html, text, full: html, text
changing uses of cgiServerName to better cgiServerNamePort
- src/hg/hgTrackUi/hgTrackUi.c
- lines changed 5, context: html, text, full: html, text
retro track changes to add ucscRetroOrtho table and hgc, hgTrackUI changes.
- lines changed 77, context: html, text, full: html, text
Stuff to do with microarray subsetting. It might need a little smoothing over
- lines changed 10, context: html, text, full: html, text
Updated class descriptions for OMIM tracks.
- lines changed 8, context: html, text, full: html, text
Minor edits of OMIM tracks configureation language.
- src/hg/hgTracks/config.c
- lines changed 9, context: html, text, full: html, text
Adjusted the blue toggleBars to look similar in 'config' and below the track image
- lines changed 2, context: html, text, full: html, text
backing out float:right until I figure out why FF wraps the TH to 2 lines
- lines changed 8, context: html, text, full: html, text
Forget about floating, Just use the same table that under the image toggleBars use.
- src/hg/hgTracks/expRatioTracks.c
- lines changed 9, context: html, text, full: html, text
Stuff to do with microarray subsetting. It might need a little smoothing over
- src/hg/hgTracks/hgTracks.c
- lines changed 3, context: html, text, full: html, text
Adjusted the blue toggleBars to look similar in 'config' and below the track image
- lines changed 22, context: html, text, full: html, text
move hub connection stuff into hg/lib so hgTracks can add hubs on its own
- lines changed 5, context: html, text, full: html, text
provide WormBase link for cb4
- lines changed 1, context: html, text, full: html, text
no need to strip chr from cb4 chrom names for WormBase
- src/hg/hgTracks/retroGene.c
- lines changed 49, context: html, text, full: html, text
retro track changes to add ucscRetroOrtho table and hgc, hgTrackUI changes.
- src/hg/hgTracks/retroGene.h
- lines changed 3, context: html, text, full: html, text
retro track changes to add ucscRetroOrtho table and hgc, hgTrackUI changes.
- src/hg/hgTracks/simpleTracks.c
- lines changed 4, context: html, text, full: html, text
Updated new OMIM related track processing, using the omimPhenotype tale instead of omimDisoroderPhenotype.
- lines changed 87, context: html, text, full: html, text
Implemented new color scheme for OMIM tracks.
- lines changed 1, context: html, text, full: html, text
Added itemNameColor method for omimGeneLocation track.
- src/hg/hgTracks/snakeTrack.c
- lines changed 380, context: html, text, full: html, text
now have pack and full modes. Coloring by strand is default. Needs a more useful way of drawing the lines that connect the blocks in pack mode. Maybe snake mode should be option in detail page? That way we can overload the track controls.
- lines changed 45, context: html, text, full: html, text
still under development.....
- src/hg/hgTracks/vcfTrack.c
- lines changed 17, context: html, text, full: html, text
Feature #3711 (VCF haplotype sorting): David didn't like the altered colorfor center variant, asked for thicker black outline instead.
- lines changed 47, context: html, text, full: html, text
Feature #3711 (VCF haplotype clustering): User can select which variantis used as the center (for center-weighted clustering) by clicking on a
link in its details page.
- lines changed 50, context: html, text, full: html, text
Feature #3711 (VCF haplotype clustering): David's suggestion:add mouseover text for the variant used as the center.
- src/hg/hgc/expClick.c
- lines changed 5, context: html, text, full: html, text
some lines I needed to NOT break the build. hgTrackUi and hgTracks were updated but not hgc
- src/hg/hgc/hgc.c
- lines changed 13, context: html, text, full: html, text
Updated new OMIM tracks processing to use the new omimPhenotype table.
- lines changed 92, context: html, text, full: html, text
Revamped omimGene2 processing logic and minor edits of links to OMIM page at omim.org.
- lines changed 4, context: html, text, full: html, text
Show phenotype class for omimGene2.
- lines changed 2, context: html, text, full: html, text
Removed target=_blank from refGene and KG links in omimGene2.
- src/hg/hgc/retroClick.c
- lines changed 51, context: html, text, full: html, text
retro track changes to add ucscRetroOrtho table and hgc, hgTrackUI changes.
- lines changed 8, context: html, text, full: html, text
use version number in retro click score calc
- src/hg/hgc/vcfClick.c
- lines changed 11, context: html, text, full: html, text
Feature #3711 (VCF haplotype clustering): User can select which variantis used as the center (for center-weighted clustering) by clicking on a
link in its details page.
- src/hg/hgc/wikiTrack.c
- lines changed 1, context: html, text, full: html, text
changing uses of cgiServerName to better cgiServerNamePort
- src/hg/htdocs/ENCODE/downloads.html
- lines changed 5, context: html, text, full: html, text
adding BU Orchid to downloads list, redmine# 1440
- lines changed 7, context: html, text, full: html, text
added SYDH Histone, redmine #68
- lines changed 34, context: html, text, full: html, text
adding Regulation Super-track to downloads page since I released it yesterday, redmine 3454
- src/hg/htdocs/ENCODE/search.html
- lines changed 3, context: html, text, full: html, text
adding a link to the genome-preview search page
- src/hg/htdocs/FAQ/FAQtracks.html
- lines changed 10, context: html, text, full: html, text
Added text for more clarification, redmine #1308
- lines changed 3, context: html, text, full: html, text
Added commas and fixed spacing
- src/hg/htdocs/evoFold/hg18
- lines changed 1, context: html, text, full: html, text
symlinks suck, especially ones with absolute paths
- src/hg/htdocs/evoFold/hg19
- lines changed 1, context: html, text, full: html, text
symlinks suck, especially ones with absolute paths
- src/hg/htdocs/goldenPath/help/hgIndelDisplay.html
- lines changed 3, context: html, text, full: html, text
Added a '#' to hex colors to keep them from displaying as black in FF. (Redmine 2864, note 51).
- src/hg/htdocs/goldenPath/help/hgUserPsl.html
- lines changed 1, context: html, text, full: html, text
FireFox needs a '#' at the beginning of a hex color code, otherwise it displays as black.
- src/hg/htdocs/images/phylo/anoCar2_7way.png
- lines changed 0, context: html, text, full: html, text
phylo image for anoCar2 7-way
- src/hg/htdocs/indexNews.html
- lines changed 30, context: html, text, full: html, text
dropping Webinar announcement. it is full
- lines changed 129, context: html, text, full: html, text
Added news item about mm9 UCSC Genes.
- src/hg/htdocs/style/HGStyle.css
- lines changed 1, context: html, text, full: html, text
Increased the toggleButton size a bit.
- src/hg/inc/cdsEvidence.h
- lines changed 2, context: html, text, full: html, text
I previously modified txCdsToGene so that it would issue a warning and not errAbort when it came across a CDS with a premature stop codon. That change was at the urging of Markd, who pointed out that the CDS transcripts in question had not been provisionally accepted or rejected yet, and that it's now accepted that we don't understand NMD as well as we'd thought. But when I changed the premature stop codon condition from an errAbort to warning condition, I'd neglected to do the second part: addressing what sort of thick start and end to have in the output bed. I decided that if a PTC is detected when trying to generate a protein sequence (which yields no protein sequence), then the thickStart and thickEnd should be the same
- src/hg/inc/cv.h
- lines changed 16, context: html, text, full: html, text
Added some defines to help with the new validateCv tool.
- lines changed 7, context: html, text, full: html, text
Fixed mistake of not using tags on hgFileUi filterBy boxes. This resulted in UChicago downloads page not showing control terms properly.
- src/hg/inc/hubConnect.h
- lines changed 13, context: html, text, full: html, text
move hub connection stuff into hg/lib so hgTracks can add hubs on its own
- src/hg/inc/mdb.h
- lines changed 3, context: html, text, full: html, text
Fixed mistake of not using tags on hgFileUi filterBy boxes. This resulted in UChicago downloads page not showing control terms properly.
- src/hg/inc/microarray.h
- lines changed 19, context: html, text, full: html, text
Stuff to do with microarray subsetting. It might need a little smoothing over
- src/hg/inc/ucscRetroInfo.h
- lines changed 138, context: html, text, full: html, text
changes to hgTracks, hgc, hgTrackUi, ucscRetroOrtho, ucscRetroInfo to change data structure and cart handling
- src/hg/inc/ucscRetroOrtho.h
- lines changed 89, context: html, text, full: html, text
add ucscRetroOrtho table and code for ucscRetro child table
- src/hg/js/utils.js
- lines changed 5, context: html, text, full: html, text
fix an encoding related bug (see redmine 4051)
- src/hg/lib/cdsEvidence.c
- lines changed 3, context: html, text, full: html, text
I previously modified txCdsToGene so that it would issue a warning and not errAbort when it came across a CDS with a premature stop codon. That change was at the urging of Markd, who pointed out that the CDS transcripts in question had not been provisionally accepted or rejected yet, and that it's now accepted that we don't understand NMD as well as we'd thought. But when I changed the premature stop codon condition from an errAbort to warning condition, I'd neglected to do the second part: addressing what sort of thick start and end to have in the output bed. I decided that if a PTC is detected when trying to generate a protein sequence (which yields no protein sequence), then the thickStart and thickEnd should be the same
- src/hg/lib/cv.c
- lines changed 3, context: html, text, full: html, text
Added some defines to help with the new validateCv tool.
- lines changed 47, context: html, text, full: html, text
Fixed mistake of not using tags on hgFileUi filterBy boxes. This resulted in UChicago downloads page not showing control terms properly.
- src/hg/lib/fileUi.c
- lines changed 35, context: html, text, full: html, text
Fixed mistake of not using tags on hgFileUi filterBy boxes. This resulted in UChicago downloads page not showing control terms properly.
- src/hg/lib/hubConnect.c
- lines changed 208, context: html, text, full: html, text
move hub connection stuff into hg/lib so hgTracks can add hubs on its own
- lines changed 1, context: html, text, full: html, text
Fix compile warning for Ubuntu: warn's first argument must be a format string.
- src/hg/lib/jksql.c
- lines changed 18, context: html, text, full: html, text
errAbort if showTableCache config is set but table does not exist
- src/hg/lib/makefile
- lines changed 2, context: html, text, full: html, text
retro track changes to add ucscRetroOrtho table and hgc, hgTrackUI changes.
- src/hg/lib/mdb.c
- lines changed 4, context: html, text, full: html, text
Putting some verboseTimes in to try and find bottlenecks in mdbUpdate. Looks like bottleneck is the database load though....
- lines changed 5, context: html, text, full: html, text
Refreshing from Angie's tree.
- lines changed 1, context: html, text, full: html, text
Fixing too-many-args-for-format warning/error.
- lines changed 3, context: html, text, full: html, text
Fixed segfault in mdbUpdate -accession when part of the selection has no expId in encodeExp yet.
- lines changed 14, context: html, text, full: html, text
Fixed mistake of not using tags on hgFileUi filterBy boxes. This resulted in UChicago downloads page not showing control terms properly.
- src/hg/lib/microarray.c
- lines changed 6, context: html, text, full: html, text
something was a bit off with this maCombineGroupingFromCart function to say the least
- lines changed 202, context: html, text, full: html, text
Stuff to do with microarray subsetting. It might need a little smoothing over
- src/hg/lib/mim2gene.as
- src/hg/lib/omimAv.as
- lines changed 1, context: html, text, full: html, text
Added comment for description.
- src/hg/lib/omimAvRepl.as
- lines changed 2, context: html, text, full: html, text
Added comment for the last two fields.
- src/hg/lib/omimGeneMap.sql
- lines changed 16, context: html, text, full: html, text
Updated omimGeneMap.sql.
- src/hg/lib/omimPhenotype.as
- src/hg/lib/omimPhenotype.sql
- lines changed 9, context: html, text, full: html, text
Created omimPhenotype.sql.
- src/hg/lib/trackHub.c
- lines changed 3, context: html, text, full: html, text
fix problem with having "show" after "superTrack on" in the trackDb.txt file (reported by Ting's group)
- src/hg/lib/ucscRetroInfo.as
- lines changed 57, context: html, text, full: html, text
changes to hgTracks, hgc, hgTrackUi, ucscRetroOrtho, ucscRetroInfo to change data structure and cart handling
- src/hg/lib/ucscRetroInfo.c
- lines changed 488, context: html, text, full: html, text
changes to hgTracks, hgc, hgTrackUi, ucscRetroOrtho, ucscRetroInfo to change data structure and cart handling
- src/hg/lib/ucscRetroInfo.sql
- lines changed 30, context: html, text, full: html, text
retro track changes to add ucscRetroOrtho table and hgc, hgTrackUI changes.
- lines changed 4, context: html, text, full: html, text
trackDb and sql changes for retrotracks
- src/hg/lib/ucscRetroOrtho.as
- lines changed 7, context: html, text, full: html, text
add ucscRetroOrtho table and code for ucscRetro child table
- src/hg/lib/ucscRetroOrtho.c
- lines changed 189, context: html, text, full: html, text
add ucscRetroOrtho table and code for ucscRetro child table
- src/hg/lib/ucscRetroOrtho.sql
- lines changed 13, context: html, text, full: html, text
add ucscRetroOrtho table and code for ucscRetro child table
- lines changed 1, context: html, text, full: html, text
trackDb and sql changes for retrotracks
- src/hg/lib/wikiLink.c
- lines changed 8, context: html, text, full: html, text
changing uses of cgiServerName to better cgiServerNamePort
- src/hg/makeDb/doc/anoCar2.txt
- lines changed 12, context: html, text, full: html, text
multiz run complete for 7-way
- lines changed 90, context: html, text, full: html, text
adding annotation rows to 7-way maf file
- lines changed 77, context: html, text, full: html, text
done with gene annotations on the 7-way maf
- lines changed 369, context: html, text, full: html, text
phylo tree estimate and phastCons done
- lines changed 64, context: html, text, full: html, text
construct download files for 7-way
- lines changed 56, context: html, text, full: html, text
hgPal downloads for 7way
- lines changed 1, context: html, text, full: html, text
5000 and loose for gasAcu1 summary
- src/hg/makeDb/doc/bosTau6.txt
- lines changed 251, context: html, text, full: html, text
Lastz Chain/Net bosTau6 vs mm9 and hg19
- src/hg/makeDb/doc/caeJap4.txt
- lines changed 231, context: html, text, full: html, text
initial sequence is ready for genbank run
- src/hg/makeDb/doc/caePb3.txt
- lines changed 230, context: html, text, full: html, text
ready for genbank run as soon as kluster node rsync is done
- src/hg/makeDb/doc/caeRem4.txt
- lines changed 61, context: html, text, full: html, text
initial makeGenomeDb.pl run
- lines changed 76, context: html, text, full: html, text
running genbank alignments
- src/hg/makeDb/doc/caeSp111.txt
- lines changed 299, context: html, text, full: html, text
ready for window masker cleaning
- src/hg/makeDb/doc/caeSp71.txt
- lines changed 3, context: html, text, full: html, text
ready for window masker cleaning
- src/hg/makeDb/doc/caeSp91.txt
- lines changed 300, context: html, text, full: html, text
ready for window masker cleaning
- src/hg/makeDb/doc/calJac3.txt
- lines changed 144, context: html, text, full: html, text
added hgPal downloads for 13way
- src/hg/makeDb/doc/canFam2.txt
- src/hg/makeDb/doc/cb3.txt
- lines changed 17, context: html, text, full: html, text
liftover cb3 to cb4 and genbank done for ce10
- src/hg/makeDb/doc/cb4.txt
- src/hg/makeDb/doc/ce10.txt
- lines changed 79, context: html, text, full: html, text
ready for kluster activity
- lines changed 73, context: html, text, full: html, text
running genbank and set default position
- lines changed 5, context: html, text, full: html, text
set this as defaultDb in gateway page
- lines changed 13, context: html, text, full: html, text
liftover cb3 to cb4 and genbank done for ce10
- src/hg/makeDb/doc/ce4.txt
- src/hg/makeDb/doc/ce6.txt
- src/hg/makeDb/doc/ce9.txt
- src/hg/makeDb/doc/encodeDccHg19/openChromCrawford.hg19.txt
- lines changed 27, context: html, text, full: html, text
Old doc stuff. Helped get tgz submission working.
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeCshlShort.release2.notes
- lines changed 19, context: html, text, full: html, text
Final packaging for QA, moved the Contigs to only be in release3, some short and long label edits, some clean up of inconsitant metadata
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhRnaSeq.release1.notes
- lines changed 79, context: html, text, full: html, text
Generating new notes file for YaleRnaSeq that is renamed to SydhRnaSeq
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeUncBsuProt.release1.notes
- lines changed 48, context: html, text, full: html, text
Adding the release notes for the UNC/BSU Prot track, which was just added to the pushQ
- src/hg/makeDb/doc/felCat4.txt
- lines changed 150, context: html, text, full: html, text
Finished redmine Track #3880 redo felCat4 conservation track
- src/hg/makeDb/doc/hg18.txt
- src/hg/makeDb/doc/hg19.txt
- lines changed 57, context: html, text, full: html, text
LASTZ Cow BosTau6 vs hg19
- lines changed 193, context: html, text, full: html, text
Rebuilt new OMIM tracks using new data, new omimPhenotype table, and updated programs.
- lines changed 1, context: html, text, full: html, text
Added mimAV.txt to the list of files we get from OMIM.
- lines changed 2, context: html, text, full: html, text
Lastz Chain/Net bosTau6 vs mm9 and hg19
- src/hg/makeDb/doc/mm9.txt
- lines changed 57, context: html, text, full: html, text
LASTZ Cow BosTau6 vs mm9
- lines changed 2, context: html, text, full: html, text
Lastz Chain/Net bosTau6 vs mm9 and hg19
- lines changed 12, context: html, text, full: html, text
Polishing doc for laminB1 tracks.
- src/hg/makeDb/doc/ornAna1.txt
- lines changed 1, context: html, text, full: html, text
small correction to an old command
- src/hg/makeDb/doc/panTro3.txt
- lines changed 101, context: html, text, full: html, text
hgPal downloads for 12way
- src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
- lines changed 39, context: html, text, full: html, text
Replaced a mkdir command for creating a temporary directory with mkdir -p, so that the code won't blow up if it has to be rerun before it reaches the point where that temporary directory is removed
- lines changed 9, context: html, text, full: html, text
Added a -p switch to some mkdir commands for making temporary directories, so that the script doesn't fail if it has to be restarted after the temp directories are created but before they're removed
- lines changed 11, context: html, text, full: html, text
Changed the (previously incorrect) order of some arguments for a testing script.
- src/hg/makeDb/genbank/etc/align.dbs
- lines changed 1, context: html, text, full: html, text
Added ce10 - C. elegans WS220
- lines changed 1, context: html, text, full: html, text
Added cb4 - C. briggsae WS220
- lines changed 1, context: html, text, full: html, text
Added caeRem4 C. remanei WS220
- lines changed 1, context: html, text, full: html, text
adding caePb3 C. brenneri WS220
- src/hg/makeDb/genbank/etc/genbank.conf
- lines changed 2, context: html, text, full: html, text
adding ensGene for upstream table on anoCar2
- lines changed 17, context: html, text, full: html, text
Added ce10 C. elegans WS220
- lines changed 22, context: html, text, full: html, text
adding cb4 C. briggsae WS225
- lines changed 19, context: html, text, full: html, text
Added caeRem4 C. remanei WS220
- lines changed 19, context: html, text, full: html, text
Added caePb3 C. brenneri WS220
- src/hg/makeDb/genbank/etc/hgwdev.dbs
- lines changed 1, context: html, text, full: html, text
Added ce10 - C. elegans WS220
- lines changed 1, context: html, text, full: html, text
Added cb4 - C. briggsae WS220
- lines changed 1, context: html, text, full: html, text
Added caeRem4 C. remanei WS220
- lines changed 1, context: html, text, full: html, text
adding caePb3 C. brenneri WS220
- src/hg/makeDb/hgCgiData/makefile
- lines changed 1, context: html, text, full: html, text
remove install hgCgiData directory for user builds
- lines changed 2, context: html, text, full: html, text
oops... didn't do this right the first time. #4039
- src/hg/makeDb/mdbUpdate/mdbUpdate.c
- lines changed 4, context: html, text, full: html, text
Putting some verboseTimes in to try and find bottlenecks in mdbUpdate. Looks like bottleneck is the database load though....
- src/hg/makeDb/schema/all.joiner
- lines changed 6, context: html, text, full: html, text
Finishing up Old UCSC Genes track for mm9.
- lines changed 7, context: html, text, full: html, text
Updated new OMIM tracks entries.
- lines changed 23, context: html, text, full: html, text
retro track changes to add ucscRetroOrtho table and hgc, hgTrackUI changes.
- lines changed 1, context: html, text, full: html, text
removing 'dupeOk' from all.joiner for Roberts ucscRetroOrtho statement to get all.joiner working again
- lines changed 5, context: html, text, full: html, text
Ignore 4 laminaB1 tables of mm9
- lines changed 6, context: html, text, full: html, text
add version to ucscRetro tables and fix dupeOk
- src/hg/makeDb/trackDb/chimp/trackDb.chainNet.ra
- lines changed 1, context: html, text, full: html, text
override matrix for rheMac2
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 84, context: html, text, full: html, text
Modified antibody tags. Rules: sortable. meaningful. ideally same as target. uppercase. multiple antibodies with same target have lowercase suffixes to distinguish.
- lines changed 265, context: html, text, full: html, text
Recovered 8 cell lines accidently deleted.
- lines changed 18, context: html, text, full: html, text
Commented out the SK-N-SH_RA 'cell type', since this term is now obsolete. SK-N-SH_RA didn't represent a separate cell type so much as a separate treatment performed on SK-N-SH cells. Instances of SK-N-SH_RA have been replaced with SK-N-SH in trackDb and metaDb, and SK-N-SH_RA is now commented out and should be deleted soon
- lines changed 172, context: html, text, full: html, text
Adding lineage data and removing capitolization
- lines changed 134, context: html, text, full: html, text
Numerous small changes to address validation errors. Collectively, these have reduced the number of validation errors from 597 to 220
- lines changed 5, context: html, text, full: html, text
Fixed a couple more easy validation errors
- lines changed 1, context: html, text, full: html, text
changed an orderUrl tag from ordrUrl. All human cell types are now validating - yay
- lines changed 18, context: html, text, full: html, text
Reinstated SK-N-SH_RA, which had been removed prematurely
- lines changed 51, context: html, text, full: html, text
Cleaned up view tags and turned on cvDefined for views.
- src/hg/makeDb/trackDb/dog/canFam2/description.html
- lines changed 3, context: html, text, full: html, text
putting the dog back in the right corner
- src/hg/makeDb/trackDb/human/hg18/evoCpg.html
- lines changed 25, context: html, text, full: html, text
Added reference section and link to Amos Tanay's lab.
- src/hg/makeDb/trackDb/human/hg18/metaDb/beta/wgEncodeYaleChIPseq.ra
- lines changed 4378, context: html, text, full: html, text
staging Yale TFBS on beta, redmine# 1319
- src/hg/makeDb/trackDb/human/hg18/trackDb.ra
- lines changed 53, context: html, text, full: html, text
trackDb and sql changes for retrotracks
- lines changed 1, context: html, text, full: html, text
fix version in retro search
- src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
- lines changed 2, context: html, text, full: html, text
staging Yale TFBS on beta, redmine# 1319
- src/hg/makeDb/trackDb/human/hg18/ucscRetroAli1.html
- lines changed 68, context: html, text, full: html, text
track descriptions and trackDb.ra for retro tracks
- src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseq.new.html
- lines changed 3, context: html, text, full: html, text
fixed out dated link and added release date for Yale TFBS, redmine# 1319
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
- lines changed 2, context: html, text, full: html, text
Changing YaleRnaSeq to SydhRnaSeq
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
- lines changed 737, context: html, text, full: html, text
Inventory Check. Made mdb and trackDb consistant.
- lines changed 1537, context: html, text, full: html, text
Final packaging for QA, moved the Contigs to only be in release3, some short and long label edits, some clean up of inconsitant metadata
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
- lines changed 487, context: html, text, full: html, text
Doing inventory to make trackDb consistent with mdb
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
- lines changed 3, context: html, text, full: html, text
Removed 2 GEO accession numbers that were remnants of previous errors
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
- lines changed 3047, context: html, text, full: html, text
added dcc's and expid's to HaibTfbs
- lines changed 547, context: html, text, full: html, text
added in sub id 4156 4159 4104 to haib tfbs
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
- lines changed 148, context: html, text, full: html, text
added subid# 4161, 4155, 4154 into the Open Chrom tracks
- lines changed 15, context: html, text, full: html, text
added expId's and dccAccession to OpenChrom Faire and Chip
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
- lines changed 11, context: html, text, full: html, text
removed attic tags from OpenChromDnase
- lines changed 14, context: html, text, full: html, text
replaced attic values after a misunderstanding
- lines changed 125, context: html, text, full: html, text
added subid# 4161, 4155, 4154 into the Open Chrom tracks
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
- lines changed 127, context: html, text, full: html, text
added subid# 4161, 4155, 4154 into the Open Chrom tracks
- lines changed 15, context: html, text, full: html, text
added expId's and dccAccession to OpenChrom Faire and Chip
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
- lines changed 44, context: html, text, full: html, text
Inventory check. Updated entries so that mdb matched with trackDb
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
- lines changed 2, context: html, text, full: html, text
Fixed typo in file name for wgEncodeSydhHistoneNt2d1H3k27me3BUcdAlnRep2.bam with capitol B should be wgEncodeSydhHistoneNt2d1H3k27me3bUcdAlnRep2.bam
- lines changed 385, context: html, text, full: html, text
started the next release for sydh histone
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhNsome.ra
- lines changed 721, context: html, text, full: html, text
added in subIDs 4152 and 4153 to sydh nsome
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhRnaSeq.ra
- lines changed 234, context: html, text, full: html, text
Changing YaleRnaSeq to SydhRnaSeq
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
- lines changed 2, context: html, text, full: html, text
staging UChicago TFBS on beta, redmine#1665
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSydhHistone.ra
- lines changed 163, context: html, text, full: html, text
updating metaDb for SydhHistone on beta
- lines changed 2, context: html, text, full: html, text
adding fix for metaDb error, Redmine#68, note #27
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUchicagoTfbs.ra
- lines changed 1570, context: html, text, full: html, text
staging UChicago TFBS on beta, redmine#1665
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
- lines changed 1, context: html, text, full: html, text
preparing for BU Orchid to be released, redmine# 1440
- lines changed 1, context: html, text, full: html, text
preparing ENCODE Regulation super-track for release, redmine 3454
- lines changed 1, context: html, text, full: html, text
releasing SYDH Histone, redmine #68
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeBuOrchid.ra
- lines changed 46, context: html, text, full: html, text
preparing for BU Orchid to be released, redmine# 1440
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeReg.ra
- lines changed 233, context: html, text, full: html, text
preparing ENCODE Regulation super-track for release, redmine 3454
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeSydhHistone.ra
- lines changed 1924, context: html, text, full: html, text
releasing SYDH Histone, redmine #68
- src/hg/makeDb/trackDb/human/hg19/omimAvSnp.html
- lines changed 1, context: html, text, full: html, text
Added Brooke into Credits section of OMIM tracks.
- src/hg/makeDb/trackDb/human/hg19/omimGene2.html
- lines changed 9, context: html, text, full: html, text
Updated description page info on omimGene2.
- lines changed 12, context: html, text, full: html, text
Updated class descriptions.
- lines changed 5, context: html, text, full: html, text
Updated omimGene2 color scheme.
- src/hg/makeDb/trackDb/human/hg19/omimLocation.html
- lines changed 2, context: html, text, full: html, text
Added Brooke into Credits section of OMIM tracks.
- lines changed 12, context: html, text, full: html, text
Updated class discriptions of omimLocation.
- lines changed 6, context: html, text, full: html, text
Updated color scheme of omimLocation track.
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 2, context: html, text, full: html, text
retro track changes to add ucscRetroOrtho table and hgc, hgTrackUI changes.
- lines changed 21, context: html, text, full: html, text
trackDb and sql changes for retrotracks
- lines changed 1, context: html, text, full: html, text
fix version in retro search
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- lines changed 1, context: html, text, full: html, text
preparing for BU Orchid to be released, redmine# 1440
- lines changed 4, context: html, text, full: html, text
Changing YaleRnaSeq to SydhRnaSeq
- lines changed 1, context: html, text, full: html, text
removing release tags for release of ENCODE Regulation, redmine 3454
- lines changed 1, context: html, text, full: html, text
staging UChicago TFBS on beta, redmine#1665
- lines changed 1, context: html, text, full: html, text
Recovering Riken, one of the Clusters was missing rep
- lines changed 2, context: html, text, full: html, text
started the next release for sydh histone
- src/hg/makeDb/trackDb/human/hg19/ucscRetroAli1.html
- lines changed 68, context: html, text, full: html, text
track descriptions and trackDb.ra for retro tracks
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.ra
- lines changed 162, context: html, text, full: html, text
Short labels, and some adjusting of the defaults
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.new.html
- lines changed 29, context: html, text, full: html, text
Final packaging for QA, moved the Contigs to only be in release3, some short and long label edits, some clean up of inconsitant metadata
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.new.r3.ra
- lines changed 2323, context: html, text, full: html, text
Final packaging for QA, moved the Contigs to only be in release3, some short and long label edits, some clean up of inconsitant metadata
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.new.ra
- lines changed 54, context: html, text, full: html, text
Inventory Check. Made mdb and trackDb consistant.
- lines changed 378, context: html, text, full: html, text
Final packaging for QA, moved the Contigs to only be in release3, some short and long label edits, some clean up of inconsitant metadata
- src/hg/makeDb/trackDb/human/hg19/wgEncodeExonArraySuper.html
- lines changed 1, context: html, text, full: html, text
Samples are hybridized not data
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.ra
- lines changed 256, context: html, text, full: html, text
Doing inventory to make trackDb consistent with mdb
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
- lines changed 1466, context: html, text, full: html, text
Shortened all the shortlabels to be less than 17 chars
- lines changed 528, context: html, text, full: html, text
added filesort order to haib tfbs and prioritized the cell lines according to tiers
- lines changed 121, context: html, text, full: html, text
added in sub id 4156 4159 4104 to haib tfbs
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.html
- lines changed 3, context: html, text, full: html, text
added a link to the download in the description for the validation files
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.html
- lines changed 5, context: html, text, full: html, text
added a link to the download in the description for the validation files
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.new.ra
- lines changed 31, context: html, text, full: html, text
added in the trackdb snippet from subid #4155, corrected errors in snippet
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.html
- lines changed 3, context: html, text, full: html, text
added a link to the download in the description for the validation files
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.new.ra
- lines changed 109, context: html, text, full: html, text
Inventory check. Updated entries so that mdb matched with trackDb
- lines changed 1, context: html, text, full: html, text
Recovering Riken, one of the Clusters was missing rep
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.new.ra
- lines changed 354, context: html, text, full: html, text
started the next release for sydh histone
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhNsome.ra
- lines changed 2, context: html, text, full: html, text
changed longLabel names in SYDH Nucleosome
- lines changed 5, context: html, text, full: html, text
recorrected Sydh Nsome long labels
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhRnaSeq.ra
- lines changed 136, context: html, text, full: html, text
Changing YaleRnaSeq to SydhRnaSeq
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
- lines changed 26, context: html, text, full: html, text
added GATA1 data to SYDH TFBS trackDB, and added in FetalPBDE as a celltype in cellType
- lines changed 404, context: html, text, full: html, text
reformed the long labels on SYDH TFBS to be the norm, and shortened when needed
- lines changed 16, context: html, text, full: html, text
Jumped the gun the the previous commit, missed an error.
- lines changed 1, context: html, text, full: html, text
added in cell type PBMC to sydh tfbs
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.html
- lines changed 50, context: html, text, full: html, text
fixed html formatting issues,fixed citation format for UChicago TFBS, redmine# 1665
- lines changed 9, context: html, text, full: html, text
added data release policy secion, redmine# 1665
- lines changed 1, context: html, text, full: html, text
fixed a typo, redmine# 1665
- lines changed 3, context: html, text, full: html, text
Had Jeff edit this sentence to make more sense, redmine# 1665, note# 24
- src/hg/makeDb/trackDb/human/hg19/wgEncodeYaleRnaSeq.ra
- lines changed 2, context: html, text, full: html, text
Changing YaleRnaSeq to SydhRnaSeq
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 40, context: html, text, full: html, text
trackDb and sql changes for retrotracks
- lines changed 6, context: html, text, full: html, text
Changed colors for new OMIM Gene tracks.
- lines changed 6, context: html, text, full: html, text
Updated default color of OMIM tracks.
- src/hg/makeDb/trackDb/initTableList
- lines changed 4, context: html, text, full: html, text
skip information_schema database in a cleaner way
- src/hg/makeDb/trackDb/lizard/anoCar2/cons7way.html
- lines changed 395, context: html, text, full: html, text
description page ready to go for 7-way
- src/hg/makeDb/trackDb/lizard/anoCar2/description.html
- lines changed 5, context: html, text, full: html, text
add notes about future names of several chrLG chroms
- src/hg/makeDb/trackDb/lizard/anoCar2/trackDb.ra
- lines changed 104, context: html, text, full: html, text
adding 7-way conservation definitions
- src/hg/makeDb/trackDb/makefile
- lines changed 1, context: html, text, full: html, text
adding ce10 to the browser
- lines changed 1, context: html, text, full: html, text
adding caeRem4 to the build
- lines changed 1, context: html, text, full: html, text
adding caeJap4 to the build
- lines changed 1, context: html, text, full: html, text
adding caeSp71 to the build
- lines changed 2, context: html, text, full: html, text
adding caeSp91 and caeSp111
- src/hg/makeDb/trackDb/mouse/mm9/knownGeneOld4.html
- lines changed 10, context: html, text, full: html, text
Finishing up Old UCSC Genes track for mm9.
- src/hg/makeDb/trackDb/mouse/mm9/laminB1Mm9.html
- lines changed 17, context: html, text, full: html, text
Fixed several minor grammar/puctuation errors. Corrected some html formatting. Turned listed url into an ectual link for better readability.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhRnaSeq.ra
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
- lines changed 29, context: html, text, full: html, text
Updated alignments for 2 experiments with Version 2 of files. Version 1 files submitted were the wrong files.
- src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
- lines changed 19, context: html, text, full: html, text
Finishing up Old UCSC Genes track for mm9.
- lines changed 24, context: html, text, full: html, text
Refreshing from Angie's tree.
- lines changed 53, context: html, text, full: html, text
trackDb and sql changes for retrotracks
- lines changed 1, context: html, text, full: html, text
fix version in retro search
- lines changed 1, context: html, text, full: html, text
Darken the green color for laminB1_MEF track for mm9
- lines changed 2, context: html, text, full: html, text
Change MEF track colore to 0,100,0 (darker green)
- src/hg/makeDb/trackDb/mouse/mm9/ucscRetroAli1.html
- lines changed 68, context: html, text, full: html, text
track descriptions and trackDb.ra for retro tracks
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.ra
- lines changed 41, context: html, text, full: html, text
Added submission 4044 to Histone Track that was missing. Added view subtrack configurable option and viewLimits set for each Signal subtrack, which were provided by the lab.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.ra
- lines changed 26, context: html, text, full: html, text
Added submission 4044 to Histone Track that was missing. Added view subtrack configurable option and viewLimits set for each Signal subtrack, which were provided by the lab.
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhRnaSeq.ra
- src/hg/makeDb/trackDb/rhesus/trackDb.chainNet.ra
- lines changed 1, context: html, text, full: html, text
added an override for the matrix table showing in the panTro3 chainNet track description
- src/hg/makeDb/trackDb/tagTypes.tab
- lines changed 1, context: html, text, full: html, text
retro track changes to add ucscRetroOrtho table and hgc, hgTrackUI changes.
- src/hg/makeDb/trackDb/trackDb.chainNet.ra
- lines changed 50, context: html, text, full: html, text
Lastz Chain/Net bosTau6 vs mm9 and hg19
- src/hg/makeDb/trackDb/trackDb.ra
- lines changed 1, context: html, text, full: html, text
track descriptions and trackDb.ra for retro tracks
- lines changed 53, context: html, text, full: html, text
trackDb and sql changes for retrotracks
- src/hg/makeDb/trackDb/worm/caeJap4/description.html
- lines changed 129, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- lines changed 71, context: html, text, full: html, text
adding caeJap4 to the build
- src/hg/makeDb/trackDb/worm/caeJap4/gap.html
- lines changed 64, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- lines changed 62, context: html, text, full: html, text
adding caeJap4 to the build
- src/hg/makeDb/trackDb/worm/caeJap4/gold.html
- lines changed 23, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- lines changed 28, context: html, text, full: html, text
adding caeJap4 to the build
- src/hg/makeDb/trackDb/worm/caeJap4/trackDb.ra
- lines changed 40, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/worm/caePb3/description.html
- lines changed 129, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/worm/caePb3/gap.html
- lines changed 64, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/worm/caePb3/gold.html
- lines changed 23, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/worm/caePb3/trackDb.ra
- lines changed 40, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/worm/caeRem4/description.html
- lines changed 129, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- lines changed 65, context: html, text, full: html, text
Updated descriptions to match this release
- src/hg/makeDb/trackDb/worm/caeRem4/gap.html
- lines changed 64, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- lines changed 56, context: html, text, full: html, text
Updated descriptions to match this release
- src/hg/makeDb/trackDb/worm/caeRem4/gold.html
- lines changed 23, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- lines changed 40, context: html, text, full: html, text
Updated descriptions to match this release
- src/hg/makeDb/trackDb/worm/caeRem4/trackDb.ra
- lines changed 40, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/worm/caeSp111/description.html
- lines changed 129, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/worm/caeSp111/gap.html
- lines changed 64, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/worm/caeSp111/gold.html
- lines changed 23, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/worm/caeSp111/trackDb.ra
- lines changed 40, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/worm/caeSp71/description.html
- lines changed 129, context: html, text, full: html, text
initial source from makeGenomeDb.pl
- src/hg/makeDb/trackDb/worm/caeSp71/gap.html
- lines changed 64, context: html, text, full: html, text
initial source from makeGenomeDb.pl
- src/hg/makeDb/trackDb/worm/caeSp71/gold.html
- lines changed 23, context: html, text, full: html, text
initial source from makeGenomeDb.pl
- src/hg/makeDb/trackDb/worm/caeSp71/trackDb.ra
- lines changed 40, context: html, text, full: html, text
initial source from makeGenomeDb.pl
- src/hg/makeDb/trackDb/worm/caeSp91/description.html
- lines changed 129, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/worm/caeSp91/gap.html
- lines changed 64, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/worm/caeSp91/gold.html
- lines changed 23, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/worm/caeSp91/trackDb.ra
- lines changed 40, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/worm/cb4/description.html
- lines changed 129, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/worm/cb4/gap.html
- lines changed 64, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/worm/cb4/gold.html
- lines changed 23, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- src/hg/makeDb/trackDb/worm/cb4/trackDb.ra
- lines changed 8, context: html, text, full: html, text
initial files from makeGenomeDb.pl
- lines changed 2, context: html, text, full: html, text
default vis for gold and gap
- src/hg/makeDb/trackDb/worm/ce10/description.html
- lines changed 129, context: html, text, full: html, text
initial contents from makeGenomeDb
- lines changed 106, context: html, text, full: html, text
update doc to represent actual assembly
- src/hg/makeDb/trackDb/worm/ce10/gap.html
- lines changed 64, context: html, text, full: html, text
initial contents from makeGenomeDb
- src/hg/makeDb/trackDb/worm/ce10/gold.html
- lines changed 23, context: html, text, full: html, text
initial contents from makeGenomeDb
- src/hg/makeDb/trackDb/worm/ce10/trackDb.ra
- lines changed 8, context: html, text, full: html, text
initial contents from makeGenomeDb
- src/hg/makeDb/trackDb/zebrafish/trackDb.ra
- lines changed 1, context: html, text, full: html, text
trackDb and sql changes for retrotracks
- src/hg/oneShot/doOmimDisorders/doOmimDisorders.c
- lines changed 109, context: html, text, full: html, text
Created doOmimDisorders.c.
- src/hg/oneShot/doOmimDisorders/makefile
- src/hg/txCds/txCdsRepick/txCdsRepick.c
- lines changed 1, context: html, text, full: html, text
Fixing the build by adding a missing argument to cdsEvidenceSetBedThick (arg was added to hg/lib/cdsEvidence.c's cdsEvidenceSetBedThick in d1b4008e).
- lines changed 1, context: html, text, full: html, text
Added the missing third argument to to cdsEvidenceSetBedThick
- src/hg/txCds/txCdsToGene/txCdsToGene.c
- lines changed 8, context: html, text, full: html, text
I previously modified txCdsToGene so that it would issue a warning and not errAbort when it came across a CDS with a premature stop codon. That change was at the urging of Markd, who pointed out that the CDS transcripts in question had not been provisionally accepted or rejected yet, and that it's now accepted that we don't understand NMD as well as we'd thought. But when I changed the premature stop codon condition from an errAbort to warning condition, I'd neglected to do the second part: addressing what sort of thick start and end to have in the output bed. I decided that if a PTC is detected when trying to generate a protein sequence (which yields no protein sequence), then the thickStart and thickEnd should be the same
- src/hg/utils/hubPublicCheck/hubPublicCheck.c
- lines changed 85, context: html, text, full: html, text
the beginnings of a program to validate hubPublic against the labels that are in the hub's themselves.
- lines changed 64, context: html, text, full: html, text
adding hubCheck and hubPublicCheck to the build. hubPublicCheck is called from my crontab now to check that the hubPublic table is consistent with what's in the hubPublic table
- src/hg/utils/hubPublicCheck/makefile
- lines changed 19, context: html, text, full: html, text
the beginnings of a program to validate hubPublic against the labels that are in the hub's themselves.
- src/hg/utils/makefile
- lines changed 1, context: html, text, full: html, text
adding hubCheck and hubPublicCheck to the build. hubPublicCheck is called from my crontab now to check that the hubPublic table is consistent with what's in the hubPublic table
- src/inc/cheapcgi.h
- lines changed 5, context: html, text, full: html, text
changing uses of cgiServerName to better cgiServerNamePort
- src/inc/net.h
- lines changed 3, context: html, text, full: html, text
Adding support for preserving user:password in urls during redirection
- src/inc/obscure.h
- lines changed 2, context: html, text, full: html, text
add a routine to find a name in a comma separate list (Jim wrote this but I'm moving it)
- src/lib/cheapcgi.c
- lines changed 20, context: html, text, full: html, text
changing uses of cgiServerName to better cgiServerNamePort
- src/lib/errabort.c
- lines changed 2, context: html, text, full: html, text
removing misleading newlines
- src/lib/net.c
- lines changed 133, context: html, text, full: html, text
Check the Content-Range for 206 response to confirm that it matches the byteRange requested - this can detect certain kinds of caching errors by servers; also removed unneeded newlines in warn and errAbort calls.
- lines changed 58, context: html, text, full: html, text
adding support for redirects to byterange urls
- lines changed 17, context: html, text, full: html, text
Adding support for preserving user:password in urls during redirection
- lines changed 6, context: html, text, full: html, text
fixing cgiEncoding of user and password in redirected urls
- src/lib/obscure.c
- lines changed 25, context: html, text, full: html, text
add a routine to find a name in a comma separate list (Jim wrote this but I'm moving it)
- src/lib/udc.c
- lines changed 1, context: html, text, full: html, text
adding support for redirects to byterange urls
- src/makefile
- lines changed 1, context: html, text, full: html, text
add bigWigAverageOverBed to userApps
- src/product/ex.hg.conf
- lines changed 11, context: html, text, full: html, text
add notes about how the wiki cookie names are constructed
- src/utils/git-reports/git-reports.c
- lines changed 44, context: html, text, full: html, text
adding ability for git-reports to show merge-commits with common combined diffs
- lines changed 25, context: html, text, full: html, text
It seems that only the diff for merge commits can supply the filenames used in it.
- src/utils/git-reports/makefile
- lines changed 1, context: html, text, full: html, text
adding ability for git-reports to show merge-commits with common combined diffs
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed: 38158
- files changed: 416