All File Changes
v276_preview2 to v276_base (2012-11-13 to 2012-11-20) v276
- python/lib/ucscGb/encode/cv.py
- lines changed 14, context: html, text, full: html, text
added support for new cv terms (cell and antibody) as well as some bugfixes for library
- python/lib/ucscGb/encode/encodeUtils.py
- lines changed 49, context: html, text, full: html, text
added support for new cv terms (cell and antibody) as well as some bugfixes for library
- python/lib/ucscGb/encode/mdb.py
- lines changed 1, context: html, text, full: html, text
added support for new cv terms (cell and antibody) as well as some bugfixes for library
- python/lib/ucscGb/encode/track.py
- lines changed 23, context: html, text, full: html, text
added support for new cv terms (cell and antibody) as well as some bugfixes for library
- python/lib/ucscGb/externalData/geo/soft.py
- lines changed 671, context: html, text, full: html, text
added support for new cv terms (cell and antibody) as well as some bugfixes for library
- python/lib/ucscGb/externalData/geo/submission.py
- lines changed 2, context: html, text, full: html, text
added support for new cv terms (cell and antibody) as well as some bugfixes for library
- src/hg/hgHubConnect/hgHubConnect.c
- lines changed 31, context: html, text, full: html, text
fix bug in keeping track of error message introduced last cycle (#9609). Also fix bug in unlisted hubs where assembly was listed incorrectly.
- src/hg/hgTables/identifiers.c
- lines changed 12, context: html, text, full: html, text
temporary tables will now be created in a special database hgTemp
- src/hg/hgTracks/vcfTrack.c
- lines changed 36, context: html, text, full: html, text
VCF with mixed haploid status, for example on chrX where females are diploid andmales are haploid, was having gtHapIx assigned in two different ways, not good.
Same formula for gtHapIx now applies to both diploid and haploid genotypes.
We no longer have the invariant that the number of clustered haplotypes is the
same as the max gtHapIx number, but it all works, trust me. :)
- src/hg/hgc/hgc.c
- lines changed 2, context: html, text, full: html, text
Track #9401 (DGV update): loaded Nov. '12 data.
- src/hg/hgc/numtsClick.c
- lines changed 11, context: html, text, full: html, text
Code Review #9591: combined duplicated blocks of code in numtsClick.c
- src/hg/htdocs/ENCODE/dataStandards.html
- src/hg/htdocs/ENCODE/dataSummary.html
- lines changed 14, context: html, text, full: html, text
Add warning about versioned data. Redmine #9563
- src/hg/htdocs/ENCODE/dataSummaryMouse.html
- lines changed 15, context: html, text, full: html, text
Add warning about versioned data. Redmine #9563
- src/hg/htdocs/ENCODE/index.html
- lines changed 6, context: html, text, full: html, text
Update Education & Outreach page and restore link on main page
- src/hg/htdocs/ENCODE/usageResources.html
- lines changed 8, context: html, text, full: html, text
Update Education & Outreach page and restore link on main page
- src/hg/htdocs/goldenPath/credits.html
- lines changed 15, context: html, text, full: html, text
Made changes to ensure agreement between links to downloads/credits pages and names of sections in downloads/credits pages
- src/hg/htdocs/goldenPath/newsarch.html
- lines changed 37, context: html, text, full: html, text
added announcement about OpenHelix encode tutorials
- src/hg/htdocs/goldenPath/pubs.html
- lines changed 10, context: html, text, full: html, text
adding the advance access location of the NAR paper for 2013. I will change the citation to the more usual style when the paper version gets printed. Yes, the rule is to only list the first 10 authors, but I think that we usually list all of the authors for our NAR papers!
- lines changed 2, context: html, text, full: html, text
a little more polish: italics, open in new tab/window.
- lines changed 1, context: html, text, full: html, text
a little more polish: looks like we have been announcing E-pubs.
- src/hg/htdocs/indexNews.html
- lines changed 68, context: html, text, full: html, text
added announcement about OpenHelix encode tutorials
- src/hg/lib/dgv.as
- lines changed 2, context: html, text, full: html, text
Track #9401 (DGV update): loaded Nov. '12 data.
- src/hg/lib/dgv.sql
- lines changed 3, context: html, text, full: html, text
Track #9401 (DGV update): loaded Nov. '12 data.
- src/hg/lib/hdb.c
- lines changed 7, context: html, text, full: html, text
Tweak to 10-year-old code: in hGetCtBedRange, when we need a placeholderfor a column in the sql query, use "0" instead of the startField. It's a
tiny bit more efficient and hopefully less eye-catching for Jorge. :)
Speaking of efficiency, the CGIs could use a position-only (bed3) version.
- src/hg/lib/hubConnect.c
- lines changed 1, context: html, text, full: html, text
fix bug in keeping track of error message introduced last cycle (#9609). Also fix bug in unlisted hubs where assembly was listed incorrectly.
- src/hg/lib/jksql.c
- lines changed 10, context: html, text, full: html, text
temporary tables will now be created in a special database hgTemp
- src/hg/liftUp/liftUp.c
- lines changed 216, context: html, text, full: html, text
adding the lift of .align files from Robert Hubley
- src/hg/makeDb/doc/bosTau6.txt
- lines changed 26, context: html, text, full: html, text
Redmine Track #8533 NumtS tracks: initial work for bosTau6 and susScr2.
- src/hg/makeDb/doc/hg17.txt
- lines changed 90, context: html, text, full: html, text
Track #9401 (DGV update): loaded Nov. '12 data.
- src/hg/makeDb/doc/hg18.txt
- lines changed 92, context: html, text, full: html, text
Track #9401 (DGV update): loaded Nov. '12 data.
- src/hg/makeDb/doc/hg19.txt
- lines changed 77, context: html, text, full: html, text
Track #9401 (DGV update): loaded Nov. '12 data.
- src/hg/makeDb/doc/nomLeu1.txt
- lines changed 20, context: html, text, full: html, text
construct liftOver to nomLeu2
- src/hg/makeDb/doc/susScr2.txt
- lines changed 25, context: html, text, full: html, text
Redmine Track #8533 NumtS tracks: initial work for bosTau6 and susScr2.
- src/hg/makeDb/genbank/etc/euronode-copy
- lines changed 0, context: html, text, full: html, text
make euronode-copy executable
- src/hg/makeDb/genbank/etc/rr.dbs
- lines changed 9, context: html, text, full: html, text
Added nomLeu2, papHam1, proCap1, pteVam1, sorAra1, susScr3, tarSyr1, tupBel and vicPac1
- src/hg/makeDb/genbank/src/ccds/createKeys.sql
- lines changed 1, context: html, text, full: html, text
the schema changes yet again
- src/hg/makeDb/genbank/src/ccds/createTables.sql
- lines changed 2, context: html, text, full: html, text
the schema changes yet again
- src/hg/makeDb/genbank/src/ccds/ncbiSql/createKeys.sql
- lines changed 10, context: html, text, full: html, text
the schema changes yet again
- src/hg/makeDb/genbank/src/ccds/ncbiSql/createTables.sql
- lines changed 2, context: html, text, full: html, text
the schema changes yet again
- src/hg/makeDb/trackDb/alpaca/vicPac1/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/armadillo/dasNov3/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/baboon/papAnu2/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/baboon/papHam1/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/birds/geoFor1/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- lines changed 2, context: html, text, full: html, text
Made changes to ensure agreement between links to downloads/credits pages and names of sections in downloads/credits pages
- src/hg/makeDb/trackDb/birds/melUnd1/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/bushbaby/otoGar3/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/cat/felCat5/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/chicken/galGal4/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/chimp/panTro4/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/chinchilla/chiLan1/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/cow/bosTau6/trackDb.ra
- lines changed 24, context: html, text, full: html, text
Redmine Track #8533 NumtS tracks: initial work for bosTau6 and susScr2.
- src/hg/makeDb/trackDb/cow/bosTau7/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 1, context: html, text, full: html, text
Fixing url from Nr4a1 to NR4A1
- lines changed 3, context: html, text, full: html, text
Trying to further clarify the POL3 versus POL2
- lines changed 1, context: html, text, full: html, text
That human file for hardison was bogus, it was a pointer to the mouse file
- lines changed 9, context: html, text, full: html, text
Adding some periods and caplitalizing some E's before copying alpha cv.ra to beta cv.ra
- src/hg/makeDb/trackDb/dog/canFam3/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/dolphin/turTru2/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/gadMor/gadMor1/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/gator/allMis1/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/gibbon/nomLeu2/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/guineaPig/cavPor3/description.html
- lines changed 2, context: html, text, full: html, text
Made changes to ensure agreement between links to downloads/credits pages and names of sections in downloads/credits pages
- src/hg/makeDb/trackDb/hedgehog/eriEur1/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
- lines changed 11, context: html, text, full: html, text
Correcting the md5sums for these files
- src/hg/makeDb/trackDb/human/hg19Patch9/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 9, context: html, text, full: html, text
Noticed that termRegex was misspelled, and regexes were in shell globformat instead of regex format. Also, semiShortCircuit is appropriate
for very specific patterns that wouldn't appear in any other track.
- lines changed 13, context: html, text, full: html, text
Track #9401 (DGV update): loaded Nov. '12 data.
- src/hg/makeDb/trackDb/kangarooRat/dipOrd1/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/lamprey/petMar2/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/lancelet/braFlo2/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/latCha/latCha1/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/manatee/triMan1/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/megabat/pteVam1/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/moleRat/hetGla1/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- lines changed 1, context: html, text, full: html, text
Added underscore to link to downloads page
- lines changed 15, context: html, text, full: html, text
update to correct information
- src/hg/makeDb/trackDb/moleRat/hetGla2/description.html
- lines changed 118, context: html, text, full: html, text
updating to new style home page
- lines changed 3, context: html, text, full: html, text
Replaced 'HTML' with 'HTTP'; corrected links
- src/hg/makeDb/trackDb/mouse/mm10Patch1/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/mouse/mm10Strains1/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
- lines changed 4, context: html, text, full: html, text
reverted change to LicrTfbs since files are still there
- src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
- lines changed 6, context: html, text, full: html, text
Noticed that termRegex was misspelled, and regexes were in shell globformat instead of regex format. Also, semiShortCircuit is appropriate
for very specific patterns that wouldn't appear in any other track.
- src/hg/makeDb/trackDb/mouseLemur/micMur1/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/oreNil/oreNil2/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/other/centromers1/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/pig/susScr2/trackDb.ra
- lines changed 24, context: html, text, full: html, text
Redmine Track #8533 NumtS tracks: initial work for bosTau6 and susScr2.
- src/hg/makeDb/trackDb/pig/susScr3/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/pika/ochPri2/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/rat/rn5/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/rhesus/rheMac2/description.html
- src/hg/makeDb/trackDb/rhesus/rheMac3/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/rhino/cerSim1/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/rockHyrax/proCap1/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/saiBol/saiBol1/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/shrew/sorAra1/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/sloth/choHof1/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/squirrel/speTri2/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/tarsier/tarSyr1/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/tasmanianDevil/sarHar1/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/tenrec/echTel1/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/trackDb.ra
- lines changed 67, context: html, text, full: html, text
Redmine Track #8533 NumtS tracks: initial work for bosTau6 and susScr2.
- src/hg/makeDb/trackDb/treeShrew/tupBel1/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/turtle/chrPic1/description.html
- lines changed 1, context: html, text, full: html, text
Edited link to downloads page - changed 'HTML' to 'HTTP'
- src/hg/makeDb/trackDb/xenTro/xenTro1/description.html
- lines changed 2, context: html, text, full: html, text
Made changes to ensure agreement between links to downloads/credits pages and names of sections in downloads/credits pages
- src/hg/makeDb/trackDb/xenTro/xenTro2/description.html
- lines changed 2, context: html, text, full: html, text
Made changes to ensure agreement between links to downloads/credits pages and names of sections in downloads/credits pages
- src/hg/makeDb/trackDb/xenTro/xenTro3/description.html
- lines changed 10, context: html, text, full: html, text
Made changes to ensure agreement between links to downloads/credits pages and names of sections in downloads/credits pages
- src/hg/makeDb/trackDb/zebraFinch/taeGut1/description.html
- lines changed 1, context: html, text, full: html, text
Made changes to ensure agreement between links to downloads/credits pages and names of sections in downloads/credits pages
- lines changed 1, context: html, text, full: html, text
Made changes to ensure agreement between links to downloads/credits pages and names of sections in downloads/credits pages
- src/hg/utils/automation/configFiles/hetGla1.config.ra
- lines changed 23, context: html, text, full: html, text
update hetGla1 to be correct
- src/makefile
- lines changed 2, context: html, text, full: html, text
Code Review #9591 Put back BLAT_APPLIST = blat gfClient gfServe which was accidentally removed.
- src/product/README.building.source
- lines changed 3, context: html, text, full: html, text
Feature #6336 (samtabix): The official git repository is now on genome-source.cse.ucsc.eduinstead of github.com.
- src/product/README.mysql.setup
- lines changed 13, context: html, text, full: html, text
temporary tables will now be created in a special database hgTemp
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed: 2068
- files changed: 120