All File Changes

v272_preview to v272_preview2 (2012-08-14 to 2012-08-21) v272

• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 1, context: html, text, full: html, text
    removed need for dataBrowser
• src/hg/hgSuggest/hgSuggest.c
  • lines changed 2, context: html, text, full: html, text
    add missing clause in like to fix problem with exact queries in non-knowGene assemblies (see #8807)
  • lines changed 13, context: html, text, full: html, text
    use correct name for refGene internal_id name; break up long lines per angie's code review
• src/hg/hgTables/bigBed.c
  • lines changed 58, context: html, text, full: html, text
    fixed #8834 by querying only part of the chrom to get ten items for schema
• src/hg/hgTracks/gencodeTracks.c
  • lines changed 21, context: html, text, full: html, text
    fixed crash accessing 2way consensus pseudogenes because they don't have the extended genePred field
  • lines changed 1, context: html, text, full: html, text
    removed extra call to genePredAssignConfiguredName that did nothing
• src/hg/hgTracks/menu.c
  • lines changed 1, context: html, text, full: html, text
    Added text, (Convert), after 'in other Genomes' since this was previously labelled convert. Also changed casing or words to standard grammar since whether to capitalize all words or not is in the css. Leaves more flexibility to the css.
• src/hg/hgc/bigBedClick.c
  • lines changed 31, context: html, text, full: html, text
    display multiples for bigBed when more than one record share exactly the same chrom, start, end, and name
• src/hg/hgc/encodeClick.c
  • lines changed 11, context: html, text, full: html, text
    fix hgc/encodeClick doEncodePeak to support items and use them to match unique display - even though multiples are now incredibly rare with new item=name matching, the code improves the display of the multiples by separating them with a vertical space
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    fix hgc/encodeClick doEncodePeak to support items and use them to match unique display - even though multiples are now incredibly rare with new item=name matching, the code improves the display of the multiples by separating them with a vertical space
  • lines changed 2, context: html, text, full: html, text
    display multiples for bigBed when more than one record share exactly the same chrom, start, end, and name
• src/hg/hgc/hgc.h
  • lines changed 1, context: html, text, full: html, text
    fix hgc/encodeClick doEncodePeak to support items and use them to match unique display - even though multiples are now incredibly rare with new item=name matching, the code improves the display of the multiples by separating them with a vertical space
  • lines changed 1, context: html, text, full: html, text
    display multiples for bigBed when more than one record share exactly the same chrom, start, end, and name
• src/hg/htdocs/ENCODE/downloadsMouse.html
  • lines changed 2, context: html, text, full: html, text
    Correcting labels for link added to ENCODE mouse download page for PSU RNA-seq (Release 1) RM#107
  • lines changed 4, context: html, text, full: html, text
    Adding link for ENCODE mouse downloads for PSU DNase (Release 1) RM#109
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 1, context: html, text, full: html, text
    Added new geoFor1 entry.
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 45, context: html, text, full: html, text
    Added Medium ground finch to credits. It still needs a link to use restrictions.
  • lines changed 22, context: html, text, full: html, text
    Updated use restrictions for Medium ground finch.
  • lines changed 2, context: html, text, full: html, text
    Opps, copy and pasted some text from opossum and didn't change the references for Medium ground finch. Done.
• src/hg/htdocs/goldenPath/help/mysql.html
  • lines changed 1, context: html, text, full: html, text
    Changed link per code review feedback.
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 61, context: html, text, full: html, text
    Added news item on Medium ground finch and archived some items.
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 1, context: html, text, full: html, text
    Removed Help link to Mirrors, as we added a whole pulldown for Mirrors info, so it seemed redundant.
  • lines changed 3, context: html, text, full: html, text
    changed references to .cse. to .soe.
• src/hg/htdocs/inc/topbar.html
  • lines changed 0, context: html, text, full: html, text
    Changed url reference from .cse. to .soe.; redmine #8831.
• src/hg/htdocs/index.html
  • lines changed 3, context: html, text, full: html, text
    Changed .cse. to .soe. in url, fixed a couple html bugs.
• src/hg/htdocs/indexNews.html
  • lines changed 24, context: html, text, full: html, text
    Added story about new browser look and feel
  • lines changed 2, context: html, text, full: html, text
    fixed link to go to genome.ucsc
  • lines changed 106, context: html, text, full: html, text
    Added news item on Medium ground finch and archived some items.
• src/hg/htdocs/makefile
  • lines changed 6, context: html, text, full: html, text
    allow overriding CGI_BIN user directory and htdocs in environment
• src/hg/lib/hdb.c
  • lines changed 5, context: html, text, full: html, text
    fix #8796. Hub tracks don't have a tdb in the track hash, so we shouldn't expect to find one there.
  • lines changed 39, context: html, text, full: html, text
    more changes to support UCSC genes (#7045). Added script to build new proteome database, fixed some utilities used in the building of that database, removed dependency on gdbPdb table in hgcentral (now it just uses the most recent proteome database rather than having a proteins database per assembly)
• src/hg/makeDb/doc/encodeDccHg19/gencodeV12.txt
  • lines changed 1, context: html, text, full: html, text
    imported GENCODE V13
• src/hg/makeDb/doc/encodeDccHg19/gencodeV13.txt
  • lines changed 63, context: html, text, full: html, text
    imported GENCODE V13
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibTfbs.release3.notes
  • lines changed 37, context: html, text, full: html, text
    updated notes even more
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhTfbs.release3.notes
  • lines changed 4734, context: html, text, full: html, text
    added in notes for sydh tfbs
  • lines changed 59, context: html, text, full: html, text
    added in supplemental files in notes
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeCshlLongRnaSeq.release3.notes
  • lines changed 1569, context: html, text, full: html, text
    First draft of notes file, I think the replace did not work
  • lines changed 91, context: html, text, full: html, text
    Added in supplemental and the renames for some of the V2s
  • lines changed 11, context: html, text, full: html, text
    Adding readme and files.txt
• src/hg/makeDb/doc/encodeDccMm9/wgEncodePsuDnase.release1.notes
  • lines changed 73, context: html, text, full: html, text
    Added release notes for release 1 of dataset. Redmine #109.
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeSydhHist.release2.notes
  • lines changed 37, context: html, text, full: html, text
    updated notes
• src/hg/makeDb/doc/encodeDccMm9/wgEncodeSydhTfbs.release4.notes
  • lines changed 1035, context: html, text, full: html, text
    added in sydh tfbs mm9 notes first draft
• src/hg/makeDb/doc/geoFor1.txt
  • lines changed 1, context: html, text, full: html, text
    add a time result from exonNuc.fa.gz construction
• src/hg/makeDb/doc/mm10.txt
  • lines changed 3, context: html, text, full: html, text
    fixup assembly ID
  • lines changed 74, context: html, text, full: html, text
    rerun the 4D phyloFit with the new groupings
• src/hg/makeDb/doc/proteins/120806.txt
  • lines changed 693, context: html, text, full: html, text
    more changes to support UCSC genes (#7045). Added script to build new proteome database, fixed some utilities used in the building of that database, removed dependency on gdbPdb table in hgcentral (now it just uses the most recent proteome database rather than having a proteins database per assembly)
• src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes13.csh
  • lines changed 4, context: html, text, full: html, text
    more changes to support UCSC genes (#7045). Added script to build new proteome database, fixed some utilities used in the building of that database, removed dependency on gdbPdb table in hgcentral (now it just uses the most recent proteome database rather than having a proteins database per assembly)
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 1, context: html, text, full: html, text
    add CCDS track to mm10
  • lines changed 2, context: html, text, full: html, text
    use ensembl genes instead of refGene for the upstream files because there's no UTR defined for the refGene models
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 14, context: html, text, full: html, text
    Added 14 almost-archived assemblies back to the list. See http://redmine.soe.ucsc.edu/issues/698#note-35.
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 1, context: html, text, full: html, text
    Added geoFor1 assembly to list. Releasing in a couple of days.
  • lines changed 14, context: html, text, full: html, text
    Added 14 almost-archived assemblies back to the list. See http://redmine.soe.ucsc.edu/issues/698#note-35.
• src/hg/makeDb/genbank/makefile
  • lines changed 1, context: html, text, full: html, text
    fix up makefile to build libraries before executables with target install-rr
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • lines changed 10, context: html, text, full: html, text
    Renamed dsprint to dyOut. Hopefully this proves to be a more popular name.
• src/hg/makeDb/trackDb/alpaca/vicPac1/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    update gold track frag search rule
• src/hg/makeDb/trackDb/armadillo/dasNov3/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    update gold track frag search rule
• src/hg/makeDb/trackDb/baboon/papAnu2/description.html
  • lines changed 1, context: html, text, full: html, text
    Fix the wrong picture problem.
• src/hg/makeDb/trackDb/baboon/papHam1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    update gold track frag search rule
• src/hg/makeDb/trackDb/birds/geoFor1/cons7way.html
  • lines changed 1, context: html, text, full: html, text
    update vertebrate.mod hgdownload reference
• src/hg/makeDb/trackDb/bushbaby/otoGar3/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    update gold track frag search rule
• src/hg/makeDb/trackDb/cat/felCat5/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    update gold track frag search rule
• src/hg/makeDb/trackDb/chimp/panTro4/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    update gold track frag search rule
  • lines changed 1, context: html, text, full: html, text
    better regex specification to catch all frag names
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 973, context: html, text, full: html, text
    Alphabetizing a set of antibodies in CV
  • lines changed 6, context: html, text, full: html, text
    Adding to labels in CV
  • lines changed 1, context: html, text, full: html, text
    Fixing typo in alpha cv
  • lines changed 30, context: html, text, full: html, text
    Adding some fixes to CV
  • lines changed 1, context: html, text, full: html, text
    Fixed some strain designations.
  • lines changed 16, context: html, text, full: html, text
    Fixing up some labels in the CV
  • lines changed 4, context: html, text, full: html, text
    Testing label change in CV and wiki
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 2, context: html, text, full: html, text
    Fixing target for REST antibody
  • lines changed 1347, context: html, text, full: html, text
    Copying alpha cv to beta
  • lines changed 1, context: html, text, full: html, text
    Fixing typo in cv
  • lines changed 30, context: html, text, full: html, text
    Pushing some fixes from alpha cv to beta
• src/hg/makeDb/trackDb/dolphin/turTru2/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    update gold track frag search rule
• src/hg/makeDb/trackDb/gadMor/gadMor1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    update gold track frag search rule
• src/hg/makeDb/trackDb/gibbon/nomLeu2/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    update gold track frag search rule
• src/hg/makeDb/trackDb/hedgehog/eriEur1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    update gold track frag search rule
• src/hg/makeDb/trackDb/human/hg19/altSeqComposite9.ra
  • lines changed 1, context: html, text, full: html, text
    Undid changes I made previously; Hiram's changes went out with today's CGI release, so the altSeqLiftOverPsl table can have the 'P9' added back and it will no longer interfere with the Patch 5 track (redmine #7195)
• src/hg/makeDb/trackDb/human/hg19/description.html
  • lines changed 1, context: html, text, full: html, text
    Updated link as per MLQ #8799.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylWgbs.ra
  • lines changed 6, context: html, text, full: html, text
    Adding expID
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 553, context: html, text, full: html, text
    added in new open chrom tracks
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 41, context: html, text, full: html, text
    renaming antibody to proper name
  • lines changed 203, context: html, text, full: html, text
    removed duplicate experiement, added md5sums
  • lines changed 524, context: html, text, full: html, text
    added in EpxIDs and missing controls
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSydhTfbs.ra
  • lines changed 7306, context: html, text, full: html, text
    Staging on beta Stanford Yale TFBS (Release 3) RM#7827
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeGisRnaPet.ra
  • lines changed 4558, context: html, text, full: html, text
    Staging on public, GIS RNA PET (Release 2) RM#5942
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeSydhTfbs.ra
  • lines changed 7306, context: html, text, full: html, text
    Staging on public Stanford Yale TFBS (Release 3) RM#7827
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Undid changes I made previously; Hiram's changes went out with today's CGI release, so the altSeqLiftOverPsl table can have the 'P9' added back and it will no longer interfere with the Patch 5 track (redmine #7195)
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    Staging on public, GIS RNA PET (Release 2) RM#5942
  • lines changed 8, context: html, text, full: html, text
    Updated release tags to make new highlighting feature available on the RR (redmine #8634)
  • lines changed 8, context: html, text, full: html, text
    A bug was discovered in conjunction with the GENCODE highlighting feature; putting it back on beta for the moment (redmine #8634)
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    imported GENCODE V13
  • lines changed 8, context: html, text, full: html, text
    Re-enabling the GENCODE highlighting feature... again... (redmine #8634)
  • lines changed 2, context: html, text, full: html, text
    Staging on beta Stanford Yale TFBS (Release 3) RM#7827
  • lines changed 2, context: html, text, full: html, text
    Staging on public Stanford Yale TFBS (Release 3) RM#7827
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV13.html
  • lines changed 352, context: html, text, full: html, text
    imported GENCODE V13
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV13.ra
  • lines changed 227, context: html, text, full: html, text
    added fogotten V13.ra file
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.release2.html
  • lines changed 19, context: html, text, full: html, text
    Adding notes about the porr scores and disabling score usage
  • lines changed 1, context: html, text, full: html, text
    Typo fix
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisRnaPet.release2.ra
  • lines changed 1, context: html, text, full: html, text
    Adding notes about the porr scores and disabling score usage
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylWgbs.html
  • lines changed 16, context: html, text, full: html, text
    changed the html page for HAIB WGBS to fix errors Steve found during QA
  • lines changed 4, context: html, text, full: html, text
    fixed the release notes and added link to bowtie for HAIB WGBS
  • lines changed 5, context: html, text, full: html, text
    made some additional changes that Steve noticed for this track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylWgbs.ra
  • lines changed 9, context: html, text, full: html, text
    Small changes in labels and defaults for ticket #6770
  • lines changed 2, context: html, text, full: html, text
    adding the darn dashes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.release3.ra
  • lines changed 107, context: html, text, full: html, text
    adding in trackDb tracks for openchnrom Dnase
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release3.html
  • lines changed 6, context: html, text, full: html, text
    added in qa corrections
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.release3.ra
  • lines changed 8, context: html, text, full: html, text
    renaming antibody to proper name
  • lines changed 16, context: html, text, full: html, text
    removing duplicate experiment
  • lines changed 8, context: html, text, full: html, text
    added in EpxIDs and missing controls
  • lines changed 102, context: html, text, full: html, text
    first pass at new short labels
  • lines changed 38, context: html, text, full: html, text
    more short labels
  • lines changed 1, context: html, text, full: html, text
    removing default on configuration box
  • lines changed 825, context: html, text, full: html, text
    qa fixes including alphabetization, and labels
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    UCDavis -> UC Davis
  • lines changed 1, context: html, text, full: html, text
    one more UCDavis -> UC Davis
  • lines changed 7, context: html, text, full: html, text
    fixed labels
  • lines changed 1, context: html, text, full: html, text
    moved znf 263 to correct place
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProtGenc.release1.ra
  • lines changed 2, context: html, text, full: html, text
    fix order in matrix in responding to Brian's note 67, #8419
  • lines changed 7, context: html, text, full: html, text
    fix orders
  • lines changed 12, context: html, text, full: html, text
    clean up long labels
• src/hg/makeDb/trackDb/kangarooRat/dipOrd1/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    update gold track frag search rule
• src/hg/makeDb/trackDb/latCha/latCha1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    update gold track frag search rule
• src/hg/makeDb/trackDb/manatee/triMan1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    update gold track frag search rule
• src/hg/makeDb/trackDb/megabat/pteVam1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    update gold track frag search rule
• src/hg/makeDb/trackDb/moleRat/hetGla2/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    update gold track frag search rule
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.60way.ra
  • lines changed 3, context: html, text, full: html, text
    Reordered organisms to match the order in the phylo tree image. Tree shrew is currently part of the glire group for phastcons and phyloP; waiting to see if we are going to change that before moving it here.
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.vertebrateChainNet.ra
  • lines changed 1, context: html, text, full: html, text
    add special note about geoFor1
• src/hg/makeDb/trackDb/mouse/mm10/vertebrateChainNet.html
  • lines changed 191, context: html, text, full: html, text
    add special note about geoFor1
  • lines changed 19, context: html, text, full: html, text
    Cleaned up some html and made the table and list look nicer.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 53, context: html, text, full: html, text
    Giving accession numbers for the spikeins
  • lines changed 33, context: html, text, full: html, text
    Revoking older objects
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    part of the double compression fix, this fix was for mm9 cshl
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHist.ra
  • lines changed 145, context: html, text, full: html, text
    added in expIds
  • lines changed 28, context: html, text, full: html, text
    filled in missing controls
  • lines changed 220, context: html, text, full: html, text
    added in missing controls
  • lines changed 10, context: html, text, full: html, text
    added in md5sums
  • lines changed 28, context: html, text, full: html, text
    adding in expIds and accessions
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 133, context: html, text, full: html, text
    filled in missing controls
  • lines changed 265, context: html, text, full: html, text
    added in expIds
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 237, context: html, text, full: html, text
    update with new dataset
  • lines changed 71, context: html, text, full: html, text
    Updated md5sum's. Redmine #4468.
  • lines changed 661, context: html, text, full: html, text
    adding in accessions
  • lines changed 46, context: html, text, full: html, text
    Changed rename to renamed and shortened message to not have special chars. This was confusing metacheck
  • lines changed 22, context: html, text, full: html, text
    Added strain to expVars so that 3 experiments on Liver E18.5 cells could be differentiated. Redmine #4468.
  • lines changed 222, context: html, text, full: html, text
    Fixed naming of V2 of objects for ZhBTc4 that were resubmitted but had the wrong sex. Added objStatus to old submissions. Redmine #4468.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    Staging beta mm9 PSU Dnase (Release 1/Final) RM#109
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeCshlLongRnaSeq.ra
  • lines changed 9916, context: html, text, full: html, text
    part of the double compression fix, this fix was for mm9 cshl
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodePsuDnase.ra
  • lines changed 398, context: html, text, full: html, text
    Staging beta mm9 PSU Dnase (Release 1/Final) RM#109
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeSydhHist.ra
  • lines changed 2236, context: html, text, full: html, text
    Staging SYDH Histone (Release 2) on beta (redmine #5404)
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/beta/wgEncodeSydhTfbs.ra
  • lines changed 3316, context: html, text, full: html, text
    Staging on beta, Stanford Yale TFBS (Release 4) RM#7981
  • lines changed 265, context: html, text, full: html, text
    Restaging on beta Stanford Yale TFBS (Release 4) RM#7981 to update metadata
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/makefile
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    Staging on public PSU DNase (Release 1/Final) RM#109
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodePsuDnase.ra
  • lines changed 398, context: html, text, full: html, text
    Staging on public PSU DNase (Release 1/Final) RM#109
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeSydhHist.ra
  • lines changed 2236, context: html, text, full: html, text
    Releasing SYDH Histone (Release 2) to the RR (redmine #5404)
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/public/wgEncodeSydhTfbs.ra
  • lines changed 3580, context: html, text, full: html, text
    Staging public for Standford Yale TFBS (Release 4) RM# 7981
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    replaced trackDb with release 4 for sydh tfbs
  • lines changed 2, context: html, text, full: html, text
    Staging on beta, Stanford Yale TFBS (Release 4) RM#7981
  • lines changed 2, context: html, text, full: html, text
    Staging public for Standford Yale TFBS (Release 4) RM# 7981
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    Staging SYDH Histone (Release 2) on beta (redmine #5404)
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    Added track Description. Redmine #109.
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    Changes for Redmine #109
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    Q3. Updated sentence to use rather and not but
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    This reverts commit 591237cefaf980b1b84ff87b2ceb9ae0a517f67a.
    
    •
    • modified: src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.release2.ra
    this file is an old release, need to revert the update which was meaned for the new release#
    Untracked files:
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    new dataset was accidently added to this old release
    
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    new dataset was updated in this old release, it should have been done in the new release
    
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    Reverts commits: b912549a8ffa41615f1c72d646ae32f88b56c8d8 and c6168a81d1fb9bee0512eb6ef38f35cd406543ac, where wrangler copied over file from release1 that trampled changes that were unique to release2. Redmine #4468.
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    Fixed naming of V2 of objects for ZhBTc4 that were resubmitted but had the wrong sex. Added objStatus to old submissions. Redmine #4468.
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• src/hg/utils/automation/ensGene/tetNig2.ensGene.ra
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• src/hg/utils/automation/ensGene/tupBel1.ensGene.ra
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• src/hg/utils/automation/ensGene/turTru1.ensGene.ra
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• src/hg/utils/automation/ensGene/vicPac1.ensGene.ra
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• src/hg/utils/automation/ensGene/xenTro2.ensGene.ra
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• src/hg/utils/automation/ensGene/xenTro3.ensGene.ra
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• src/hg/utils/automation/grcIncidentDb.pl
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    eliminate the difficulty with the changing structure of issue.sql by using database load and select
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    need full path to hgsql
• src/hg/utils/gff3ToGenePred/gff3ToGenePred.c
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    handled turning GFF3 transcript records into non-coding genes
• src/hg/utils/gff3ToGenePred/tests/expected/geneTranscriptTest.gp
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    handled turning GFF3 transcript records into non-coding genes
• src/hg/utils/gff3ToGenePred/tests/input/geneTranscript.gff3
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    handled turning GFF3 transcript records into non-coding genes
• src/hg/utils/gff3ToGenePred/tests/makefile
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    handled turning GFF3 transcript records into non-coding genes
• src/inc/cgi_build_rules.mk
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    allow overriding CGI_BIN user directory and htdocs in environment
• src/inc/dsPrint.h
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    Renamed dsprint to dyOut. Hopefully this proves to be a more popular name.
• src/inc/dyOut.h
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    Renamed dsprint to dyOut. Hopefully this proves to be a more popular name.
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    Renamed dsPrint/dsp module to dyOut. Hopefully this will satisfy Angie's request to remove 'print' from the names because it is a verb and Mark's request to make a more standard/consistent module name. It should also serve my desire for brevity and everyone's desire for catchy names. Also added comments and changed a casting of pointer to size_t at Mark's urging.
• src/inc/gff3.h
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    handled turning GFF3 transcript records into non-coding genes
• src/lib/dsPrint.c
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    Renamed dsprint to dyOut. Hopefully this proves to be a more popular name.
• src/lib/dyOut.c
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    Renamed dsPrint/dsp module to dyOut. Hopefully this will satisfy Angie's request to remove 'print' from the names because it is a verb and Mark's request to make a more standard/consistent module name. It should also serve my desire for brevity and everyone's desire for catchy names. Also added comments and changed a casting of pointer to size_t at Mark's urging.
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    Converted a couple of macros to INLINEs at Mark's request.
• src/lib/gff3.c
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    handled turning GFF3 transcript records into non-coding genes
• src/lib/makefile
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    Renamed dsPrint/dsp module to dyOut. Hopefully this will satisfy Angie's request to remove 'print' from the names because it is a verb and Mark's request to make a more standard/consistent module name. It should also serve my desire for brevity and everyone's desire for catchy names. Also added comments and changed a casting of pointer to size_t at Mark's urging.
• src/product/README.mysql.setup
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    the readonly user needs INSERT privs
• src/utils/bedPileUps/bedPileUps.c
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    bedPileUps is a new utility for finding where how many pileups there are in input including the locations and the sizes, with a summary maximum and its location, plus average pileup size. Matching is on chrom/start/end with name as an additional option for uniqueness.
• src/utils/bedPileUps/checkBedTablePileUps.csh
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    bedPileUps is a new utility for finding where how many pileups there are in input including the locations and the sizes, with a summary maximum and its location, plus average pileup size. Matching is on chrom/start/end with name as an additional option for uniqueness.
• src/utils/bedPileUps/makefile
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    bedPileUps is a new utility for finding where how many pileups there are in input including the locations and the sizes, with a summary maximum and its location, plus average pileup size. Matching is on chrom/start/end with name as an additional option for uniqueness.
• src/utils/bedPileUps/tests/expected/foo.bed.txt
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    bedPileUps is a new utility for finding where how many pileups there are in input including the locations and the sizes, with a summary maximum and its location, plus average pileup size. Matching is on chrom/start/end with name as an additional option for uniqueness.
• src/utils/bedPileUps/tests/expected/foo2.bed.txt
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    bedPileUps is a new utility for finding where how many pileups there are in input including the locations and the sizes, with a summary maximum and its location, plus average pileup size. Matching is on chrom/start/end with name as an additional option for uniqueness.
• src/utils/bedPileUps/tests/expected/foo3.bed.txt
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    bedPileUps is a new utility for finding where how many pileups there are in input including the locations and the sizes, with a summary maximum and its location, plus average pileup size. Matching is on chrom/start/end with name as an additional option for uniqueness.
• src/utils/bedPileUps/tests/expected/foo4.bed.txt
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    bedPileUps is a new utility for finding where how many pileups there are in input including the locations and the sizes, with a summary maximum and its location, plus average pileup size. Matching is on chrom/start/end with name as an additional option for uniqueness.
• src/utils/bedPileUps/tests/input/foo.bed
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    bedPileUps is a new utility for finding where how many pileups there are in input including the locations and the sizes, with a summary maximum and its location, plus average pileup size. Matching is on chrom/start/end with name as an additional option for uniqueness.
• src/utils/bedPileUps/tests/input/foo2.bed
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    bedPileUps is a new utility for finding where how many pileups there are in input including the locations and the sizes, with a summary maximum and its location, plus average pileup size. Matching is on chrom/start/end with name as an additional option for uniqueness.
• src/utils/bedPileUps/tests/input/foo3.bed
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    bedPileUps is a new utility for finding where how many pileups there are in input including the locations and the sizes, with a summary maximum and its location, plus average pileup size. Matching is on chrom/start/end with name as an additional option for uniqueness.
• src/utils/bedPileUps/tests/input/foo4.bed
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    bedPileUps is a new utility for finding where how many pileups there are in input including the locations and the sizes, with a summary maximum and its location, plus average pileup size. Matching is on chrom/start/end with name as an additional option for uniqueness.
• src/utils/makefile
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    bedPileUps is a new utility for finding where how many pileups there are in input including the locations and the sizes, with a summary maximum and its location, plus average pileup size. Matching is on chrom/start/end with name as an additional option for uniqueness.
• src/utils/qa/weeklybld/buildEnv.csh
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